Publications – Bhattacharya Lab

2023

Lee J, Yang JH, Weber APM, Bhattacharya D, Kim W-Y, Yoon HS. Accepted. Circadian gene expression in the red seaweed Gracilariopsis chorda is characterized by unique regulatory networks of carbon metabolism. Mol Biol Evol.

Gates C, Ananyev G, Foflonker F, Bhattacharya D, Dismukes GC. Accepted. Exceptional quantum efficiency powers biomass production in halotolerant algae Picochlorum sp. Photosynth Res.

Dougan KE, Deng ZL, Wöhlbrand L, Reuse C, Bunk B, Chen Y, Hartlich J, Hiller K, John U, Kalvelage J, Mansky J, Neumann-Schaal M, Overmann J, Petersen J, Sanchez-Garcia S, Schmidt-Hohagen K, Shah S, Spröer C, Sztajer H, Wang H, Bhattacharya D, Rabus R, Jahn D, Chan CX, Wagner-Döbler I. Multi-omics analysis reveals the molecular response to heat stress in a “red tide” dinoflagellate. Genome Biol. 2023 Nov 23;24(1):265. doi: 10.1186/s13059-023-03107-4

Bhattacharya D, Stephens TG, Chille EE, Benites LF, Chan CX. Facultative lifestyle drives diversity of coral algal symbionts. Trends Ecol Evol. 2023 Nov 10:S0169-5347(23)00270-7. doi: 10.1016/j.tree.2023.10.005.

Shah S, Dougan KE, Chen Y, Bhattacharya D, Chan CX. Gene duplication is the primary driver of intraspecific genomic divergence in coral algal symbionts. Open Biol. 2023 Sep;13(9):230182. doi: 10.1098/rsob.230182.

Ishida H, John U, Murray SA, Bhattacharya D, Chan CX. Developing model systems for dinoflagellates in the post-genomic era. J Phycol. 2023 Oct;59(5):799-808. doi: 10.1111/jpy.13386.

Stephens TG, Strand EL, Putnam HM, Bhattacharya D. Ploidy variation and its implications for reproduction and population dynamics in two sympatric Hawaiian coral species. Genome Biol Evol. 2023 Aug 1;15(8):evad149. doi: 10.1093/gbe/evad149.

Van Etten J, Stephens TG, Bhattacharya D. A k-mer-based approach for phylogenetic classification of taxa in environmental genomic data. Syst Biol. 2023 Nov 1;72(5):1101-1118. doi: 10.1093/sysbio/syad037

Lee Y, Cho CH, Noh C, Yang JH, Park SI, Lee YM, West JA, Bhattacharya D, Jo K, Yoon HS. Origin of minicircular mitochondrial genomes in red algae. Nat Commun. 2023 Jun 8;14(1):3363. doi: 10.1038/s41467-023-39084-2.

Davies SW, Gamache MH, Howe-Kerr LI, Kriefall NG, Baker AC, Banaszak AT, Bay LK, Bellantuono AJ, Bhattacharya D, Chan CX, Claar DC, Coffroth MA, Cunning R, Davy SK, Del Campo J, Díaz-Almeyda EM, Frommlet JC, Fuess LE, González-Pech RA, Goulet TL, Hoadley KD, Howells EJ, Hume BCC, Kemp DW, Kenkel CD, Kitchen SA, LaJeunesse TC, Lin S, McIlroy SE, McMinds R, Nitschke MR, Oakley CA, Peixoto RS, Prada C, Putnam HM, Quigley K, Reich HG, Reimer JD, Rodriguez-Lanetty M, Rosales SM, Saad OS, Sampayo EM, Santos SR, Shoguchi E, Smith EG, Stat M, Stephens TG, Strader ME, Suggett DJ, Swain TD, Tran C, Traylor-Knowles N, Voolstra CR, Warner ME, Weis VM, Wright RM, Xiang T, Yamashita H, Ziegler M, Correa AMS, Parkinson JE. Building consensus around the assessment and interpretation of Symbiodiniaceae diversity. PeerJ. 2023 May 2;11:e15023. doi: 10.7717/peerj.15023.

Van Etten J, Benites LF, Stephens TG, Yoon HS, Bhattacharya D. Algae obscura: The potential of rare species as model systems. J Phycol. 2023 Apr;59(2):293-300. doi: 10.1111/jpy.13321.

Cho CH, Park SI, Huang TY, Lee Y, Ciniglia C, Yadavalli HC, Yang SW, Bhattacharya D, Yoon HS. Genome-wide signatures of adaptation to extreme environments in red algae. Nat Commun. 2023 Jan 4;14(1):10. doi: 10.1038/s41467-022-35566-x.

Bhattacharya D, Etten JV, Benites LF, Stephens TG. Endosymbiotic ratchet accelerates divergence after organelle origin: The Paulinella model for plastid evolution. Bioessays. 2023 Jan;45(1):e2200165. doi: 10.1002/bies.202200165.

Van Etten J, Cho CH, Yoon HS, Bhattacharya D. Extremophilic red algae as models for understanding adaptation to hostile environments and the evolution of eukaryotic life on the early earth. Semin Cell Dev Biol. 2023 Jan 30;134:4-13. doi: 10.1016/j.semcdb.2022.03.007.

Williams A, Stephens TG, Shumaker A, Bhattacharya D. Peeling back the layers of coral holobiont multi-omics data. iScience. 2023 Aug 14;26(9):107623. doi: 10.1016/j.isci.2023.107623

2022

Cho CH, Park SI, Huang T-Y, Lee Y, Ciniglia C, Yadavalli HC, Yang SW, Bhattacharya D, Yoon HS. Genome-wide signatures of adaptation to extreme environments. Nat Commun. 2022 [in press]. doi: 10.1038/s41467-022-35566-x (link will work soon).

L Felipe Benites, Timothy G Stephens, Debashish Bhattacharya.
Multiple waves of viral invasions in Symbiodiniaceae algal genomes. Virus Evolution. doi: 10.1093/ve/veac101

Deeksha Misri, Erin E. ChilleTimothy G. Stephens, Debashish Bhattacharya (Faculty Advisor).
Differential Gene Expression Analysis and Gene Ontology in Triploid and Diploid Pocillopora Acuta. doi: 10.14713/arestyrurj.v1i4.208

Timothy G Stephens, JunMo Lee, YuJin Jeong, Hwan Su Yoon, Hollie M Putnam, Eva Majerová, Debashish Bhattacharya.
High-quality genome assembles from key Hawaiian coral species. GigaScience, Volume 11, 2022, giac098, doi: 10.1093/gigascience/giac098

D Bhattacharya, JV Etten, LF Benites, TG Stephens.
Endosymbiotic ratchet accelerates divergence after organelle origin: The Paulinella model for plastid evolution. BioEssays, 2200165. doi: 10.1002/bies.202200165

Gabr, TG Stephens, D Bhattacharya.
Loss of key endosymbiont genes may facilitate early host control of the chromatophore in Paulinella. Iscience 25 (9), 104974. doi: 10.1016/j.isci.2022.104974

D Bhattacharya, TG Stephens, AI Tinoco, RH Richmond, PA Cleves.
Life on the edge: Hawaiian model for coral evolution. Limnology and Oceanography 67 (9), 1976-1985. doi: 10.1002/lno.12181

Zhuolun Meng, Amanda Williams, Pinky Liau, Timothy G Stephens, Crawford Drury, Eric N Chiles, Xiaoyang Su, Mehdi Javanmard, Debashish Bhattacharya.
Development of a portable toolkit to diagnose coral thermal stress. Nature Publishing Group. doi: 10.1038/s41598-022-18653-3

Yibi Chen, Sarah Shah, Katherine E Dougan, Madeleine JH van Oppen, Debashish Bhattacharya, Cheong Xin Chan.
Improved Cladocopium goreaui Genome Assembly Reveals Features of a Facultative Coral Symbiont and the Complex Evolutionary History of Dinoflagellate Genes. Microorganisms 10 (8), 1662. doi: 10.3390/microorganisms10081662

Yibi Chen, Sarah Shah, Katherine E Dougan, Madeleine van Oppen, Debashish Bhattacharya, Cheong Xin Chan.
Improved assembled genome of Cladocopium goreaui SCF055. The University of Queensland. Data Collection. doi: 10.48610/fba3259

Calatrava V, Stephens TG, Gabr A, Bhaya D, Bhattacharya D, Grossman AR. Retrotransposition Facilitated the Establishment of a Primary Plastid in the Thecate Amoeba Paulinella. Proc Acad Natl Sci USA. doi:
10.1073/pnas.2121241119.

Lo R, Dougan KE, Chen Y, Shah S, Bhattacharya D, Chan CX.
Alignment-free analysis of Symbiodiniaceae whole-genome sequences reveals differential phylogenetic signals in distinct regions. Front Plant Sci. doi: 10.3389/fpls.2022.815714.

Shah S, Dougan KE, Bhattacharya D, Chan CX. Coral conservation from the genomic perspective on Symbiodiniaceae diversity and function in the holobiont. In: Coral Reef Conservation and Restoration in the ‘Omics’ Age” [eds. van Oppen M, Aranda M], Springer. doi: 10.1007/978-3-031-07055-6_6.

Van Etten J, Cho CH, Yoon HS, Bhattacharya D.
Extremophilic red algae as models for understanding adaptation to hostile environments and the evolution of eukaryotic life on the early earth. Semin Cell Dev Biol. 2022 Mar 23:S1084-9521(22)00074-X. doi: 10.1016/j.semcdb.2022.03.007. Epub ahead of print. PMID: 35339358.

Gabr A, Stephens TG, Bhattacharya D. Hypothesis: Trans-splicing Generates Evolutionary Novelty in the Photosynthetic Amoeba Paulinella. J Phycol. 2022 Mar 7. doi: 10.1111/jpy.13247. Epub ahead of print. PMID: 35255163.

Dougan KE, González-Pech RA, Stephens TG, Shah S, Chen Y, Ragan MA, Bhattacharya D, Chan CX. Genome-powered classification of microbial eukaryotes: focus on coral algal symbionts. Trends Microbiol. 2022 Feb 25:S0966-842X(22)00035-X. doi: 10.1016/j.tim.2022.02.001. Epub ahead of print. PMID: 35227551.

Gabr A, Zournas A, Stephens TG, Dismukes GC, Bhattacharya D. Evidence for a robust photosystem II in the photosynthetic amoeba Paulinella. New Phytol. 2022 May;234(3):934-945. doi: 10.1111/nph.18052. Epub 2022 Mar 8. PMID: 35211975.

Kim D, Lee J, Cho CH, Kim EJ, Bhattacharya D, Yoon HS. Group II intron and repeat-rich red algal mitochondrial genomes demonstrate the dynamic recent history of autocatalytic RNAs. BMC Biol. 2022 Jan 7;20(1):2. doi: 10.1186/s12915-021-01200-3. PMID: 34996446; PMCID: PMC8742464.

Trigg SA, Venkataraman YR, Gavery MR, Roberts SB, Bhattacharya D, Downey-Wall A, Eirin-Lopez JM, Johnson KM, Lotterhos KE, Puritz JB, Putnam HM. Invertebrate methylomes provide insight into mechanisms of environmental tolerance and reveal methodological biases. Mol Ecol Resour. 2022 May;22(4):1247-1261. doi: 10.1111/1755-0998.13542. Epub 2021 Nov 15. PMID: 34709728.

Uthanumallian K, Iha C, Repetti SI, Chan CX, Bhattacharya D, Duchene S, Verbruggen H. Tightly Constrained Genome Reduction and Relaxation of Purifying Selection during Secondary Plastid Endosymbiosis. Mol Biol Evol. 2022 Jan 7;39(1):msab295. doi: 10.1093/molbev/msab295. PMID: 34613411; PMCID: PMC8763093.

Sarah Davies, Matthew H Gamache, Lauren I Howe-Kerr, Nicola G Kriefall, Andrew C Baker, Anastazia T Banaszak, Line K Bay, Anthony J Bellantuono, Debashish Bhattacharya, Cheong Xin Chan, Danielle C Claar, Mary Alice Coffroth, Ross Cunning, Simon K Davy, Javier Del Campo, Erika M Diaz-Almeyda, Jorg C Frommlet, Lauren E Fuess, Raul A Gonzalez-Pech, Tamar L Goulet, Kenneth D Hoadley, Emily J Howells, Benjamin CC Hume, Dustin W Kemp, Carly Kenkel, Sheila A Kitchen, Todd C LaJeunesse, Senjie Lin, Shelby McIlroy, Ryan McMinds, Matthew R Nitschke, Clinton A Oakley, Raquel S Peixoto, Carlos Prada, Hollie M Putnam, Kate Quigley, Hannah G Reich, James Davis Reimer, Mauricio Rodriguez-Lanetty, Stephanie Rosalas, Osama S Saad, Eugenia M Sampayo, Scott Santos, Eiichi Shoguchi, Edward G Smith, Michael Stat, Timothy G Stephens, Marie E Strader, David J Suggett, Timothy D Swain, Cawa Tran, Nikki Traylor-Knowles, Christian R Voolstra, Mark E Warner, Virginia M Weis, Rachel Wright, Tingting Xiang, Hiroshi Yamashita, Maren Ziegler, Adrienne Correa, John Everett Parkinson.
Building consensus around the assessment and interpretation of Symbiodiniaceae diversity. MDPI AG. doi: 10.20944/preprints202206.0284.v1

Katherine Elisabeth Dougan, Zhi-Luo Deng, Lars Woehlbrand, Carsten Reuse, Boyke Bunk, Yibi Chen, Juliane Hartlich, Karsten Hiller, Uwe John, Jana Kalvelage, Johannes Mansky, Meina Neumann-Schaal, Joerg Overmann, Joern Petersen, Selene Sanchez-Garcia, Kerstin Schmidt-Hohagen, Sarah Shah, Cathrin Sproer, Helena Sztajer, Hui Wang, Debashish Bhattacharya, Ralf Rabus, Dieter Jahn, Cheong Xin Chan, Irene Wagner-Doebler.
Evolution of resilience against heat stress in a red-tide dinoflagellate.

2021

Stephens TG, Gabr A, Calatrava V, Grossman AR, Bhattacharya D. Why is primary endosymbiosis so rare? New Phytol. 2021 Sep;231(5):1693-1699. doi: 10.1111/nph.17478. Epub 2021 Jun 21.

Park H, Park JH, Lee Y, Woo DU, Jeon HH, Sung YW, Shim S, Kim SH, Lee KO, Kim JY, Kim CK, Bhattacharya D, Yoon HS, Kang YJ. Genome of the world’s smallest flowering plant, Wolffia australiana, helps explain its specialized physiology and unique morphology. Commun Biol. 2021 Jul 22;4(1):900. doi: 10.1038/s42003-021-02422-5.

González-Pech RA, Stephens TG, Chen Y, Mohamed AR, Cheng Y, Shah S, Dougan KE, Fortuin MDA, Lagorce R, Burt DW, Bhattacharya D, Ragan MA, Chan CX. Comparison of 15 dinoflagellate genomes reveals extensive sequence and structural divergence in family Symbiodiniaceae and genus Symbiodinium. BMC Biol. 2021 Apr 13;19(1):73. doi: 10.1186/s12915-021-00994-6.

Lhee D, Bhattacharya D, Yoon HS. Independent evolution of the thioredoxin system in photosynthetic Paulinella species. Curr Biol. 2021 Apr 12;31(7):R328-R329. doi: 10.1016/j.cub.2021.02.029.

Williams A, Chiles EN, Conetta D, Pathmanathan JS, Cleves PA, Putnam HM, Su X, Bhattacharya D. Metabolomic shifts associated with heat stress in coral holobionts. Sci Adv. 2021 Jan 1;7(1):eabd4210. doi: 10.1126/sciadv.abd4210. Print 2021 Jan.

Graf L, Shin Y, Yang JH, Choi JW, Hwang IK, Nelson W, Bhattacharya D, Viard F, Yoon HS. A genome-wide investigation of the effect of farming and human-mediated introduction on the ubiquitous seaweed Undaria pinnatifida. Nat Ecol Evol. 2021 Mar;5(3):360-368. doi: 10.1038/s41559-020-01378-9. Epub 2021 Jan 25.

A Williams*, EN Chiles*, D Conetta, JS Pathmanathan, PA Cleves, HM Putnam, X Su and D Bhattacharya. 2021. Metabolomic shifts associated with heat stress in coral holobionts. Science Advances Vol. 7, no. 1, eabd4210. doi: 10.1126/sciadv.abd4210
*Equal contribution.

2020

Van Etten J, Bhattacharya D. 2020. Horizontal gene transfer in eukaryotes: not if, but how much? Trends Genet. doi: 10.1016/j.tig.2020.08.006.

Cho CH, Park SI, Ciniglia C, Yang EC, Graf L, Bhattacharya D, Yoon HS. 2020. Potential causes and consequences of rapid mitochondrial genome evolution in thermoacidophilic Galdieria (Rhodophyta). BMC Evol Biol. Sep 7;20(1):112. doi: 10.1186/s12862-020-01677-6.

Van Etten J, Shumaker A, Mass T, Putnam HM, Bhattacharya D. 2020. Transcriptome analysis provides a blueprint of coral egg and sperm functions. PeerJ. Aug 18;8:e9739. doi: 10.7717/peerj.9739.

Lhee D, Lee J, Ettahi K, Cho CH, Ha JS, Chan YF, Zelzion U, Stephens TG, Price DC, Gabr A, Nowack ECM, Bhattacharya D, Yoon HS. 2020. Amoeba genome reveals dominant host contribution to plastid endosymbiosis. Mol Biol Evol. Aug 13:msaa206. doi: 10.1093/molbev/msaa206.

Wang D, Yu X, Xu K, Bi G, Cao M, Zelzion E, Fu C, Sun P, Liu Y, Kong F, Du G, Tang X, Yang R, Wang J, Tang L, Wang L, Zhao Y, Ge Y, Zhuang Y, Mo Z, Chen Y, Gao T, Guan X, Chen R, Qu W, Sun B, Bhattacharya D, Mao Y. 2020. Pyropia yezoensis genome reveals diverse mechanisms of carbon acquisition in the intertidal environment. Nat Commun. Aug 12;11(1):4028. doi: 10.1038/s41467-020-17689-1.

Fan X, Qiu H, Han W, Wang Y, Xu D, Zhang X, Bhattacharya D, Ye N. 2020. Phytoplankton pangenome reveals extensive prokaryotic horizontal gene transfer of diverse functions. Science Advances 6(18):eaba0111. doi: 10.1126/sciadv.aba0111.

Shah S, Chen Y, Bhattacharya D, Chan CX. 2020. Sex in Symbiodiniaceae dinoflagellates: genomic evidence for independent loss of the canonical synaptonemal complex. Sci Rep. doi: 10.1038/s41598-020-66429-4.

Zhang Z, Qu C, Zhang K, He Y, Zhao X, Yang L, Zheng Z, Ma X, Wang X, Wang W, Wang K, Li D, Zhang L, Zhang X, Su D, Chang X, Zhou M, Gao D, Jiang W, Leliaert F, Bhattacharya D, De Clerck O, Zhong B, Miao J. 2020. Adaptation to extreme Antarctic environments revealed by the genome of a sea ice green alga. Curr Biol. doi: 10.1016/j.cub.2020.06.029.

Sui J, Foflonker F, Bhattacharya D, Javanmard M. 2020. Electrical impedance as an indicator of microalgal cell health. Sci Rep. 10(1):1251. doi: 10.1038/s41598-020-57541-6

Cleves PA, Shumaker A, Lee J, Putnam HM, Bhattacharya D. 2020. Unknown to known: advancing knowledge of coral gene function. Trends Genet. 36(2):93-104. doi: 10.1016/j.tig.2019.11.001

Stephens TG, González-Pech RA, Cheng Y, Mohamed AR, Burt DW, Bhattacharya D, Ragan MA, Chan CX. 2020. Genomes of the dinoflagellate Polarella glacialis encode tandemly repeated single-exon genes with adaptive functions. BMC Biol. 18(1):56. doi: 10.1186/s12915-020-00782-8

Teulière J, Bhattacharya D, Bapteste E. 2020. Ancestral germen/soma distinction in microbes: Expanding the disposable soma theory of aging to all unicellular lineages. Ageing Res. Rev. 60:101064. doi: 10.1016/j.arr.2020.101064

Gabr A, Grossman AR, Bhattacharya D. 2020. Paulinella, a model for understanding plastid primary endosymbiosis. J Phycol. Apr 14. doi: 10.1111/jpy.13003

Shoguchi E, Yoshioka Y, Shinzato C, Arimoto A, Bhattacharya D, Satoh N. 2020. Correlation between organelle genetic variation and RNA editing in finoflagellates associated with the coral Acropora digitifera. Genome Biol Evol. 12(3):203-209. doi: 10.1093/gbe/evaa042

Chen Y, González-Pech RA, Stephens TG, Bhattacharya D, Chan CX. 2020. Evidence that inconsistent gene prediction can mislead analysis of dinoflagellate genomes. J Phycol. 2020 Feb;56(1):6-10. doi: 10.1111/jpy.12947

Bhattacharya D, Price DC. 2020. The algal tree of life from a genomics perspective. In: Photosynthesis in Algae: Biochemical and Physiological Mechanisms. Eds: Larkum AWD, Grossmann AR, Raven JA. Springer International Publishing. doi: 10.1007/978-3-030-33397-3_2.

2019

Lee J, Kim D, Bhattacharya D, Yoon HS. 2019. Expansion of phycobilisome linker gene families in mesophilic red algae. Nature Communications. doi: 10.1038/s41467-019-12779-1.

Lord E, Pathmanathan JS, Corel E, Makarenkov V, Lopez P, Bouchard F, Bhattacharya D, Antoine PO, Guyader HL, Lapointe FJ, Bapteste E. 2019. Introducing trait networks to elucidate the fluidity of organismal evolution using palaeontological data. Genome Biology and Evolution Sep. 5. DOI

Price DC, Goodenough UW, Roth R, Lee J-H, Kariyawasam T, Mutwil M, Ferrari C, Facchinelli F, Ball SG, Cenci U, Chan CX, Wagner NE, Yoon HS, Weber APM, Bhattacharya D. 2019. Analysis of an improved Cyanophora paradoxagenome assembly. DNA Research. doi: 10.1093/dnares/dsz009

González-Pech RA, Bhattacharya D, Ragan MA, Chan CX. 2019. Genome evolution of coral reef symbionts as intracellular residents. Trends in Ecology and Evolution . DOI.

Ferrari C, Proost S, Janowski M, Becker J, Nikoloski Z, Bhattacharya D, Price D, Tohge T, Bar-Even A, Fernie A, Stitt M, Mutwil M. 2019. Kingdom-wide comparison reveals the evolution of diurnal gene expression in Archaeplastida. Nature Communications 10:737. DOI

Nissimov JI, Talmy D, Haramaty L, Fredricks H, Zelzion U, Eren M, Vandzura R, Laber C, Schieler B, Johns C, More KD, Coolen MJL, Follows MJ, Bhattacharya D, Van Mooy BAS, Bidle KD. 2019. Biochemical diversity of glycosphingolipid biosynthesis as a driver of Coccolithovirus competitive ecology. Environmental Microbiology. doi: 10.1111/1462-2920.14633.

Bhattacharya D, Price DC. 2019. The algal tree of life from a genomics perspective. In: Photosynthesis in Algae: Photobiology and Molecular Systems, (eds.) Larkum A, Grossmann A, Raven J, Springer [in the press].

Shumaker A, Putnam HM, Qiu H, Price DC, Zelzion E, Harel A, Wagner NE, Gates R, Yoon HS, Bhattacharya D. 2019. Genome analysis of the rice coral Montipora capitata. Scientific Reports. doi; 10.1038/s41598-019-39274-3

Lhee D, Ha J-S, Kim S, Park MG, Bhattacharya D, Yoon HS. 2019. Evolutionary dynamics of the chromatophore genome in three photosynthetic Paulinella species. Scientific Reports. doi: 10.1038/s41598-019-38621-8

2018

Wei G, Jia Q, Chen X, Köllner T, Bhattacharya D, Wong G, Gershenzon J, Chen F. 2018. Terpene biosynthesis in red algae is catalyzed by microbial type but not typical plant terpene synthases. Plant Physiology [accepted].

Stephens TG, Ragan MA, Bhattacharya D, Chan CX. 2018. Core genes in diverse dinoflagellate lineages include a wealth of conserved dark genes with unknown functions. Scientific Reports [accepted].

Lee J, Song HJ, Park SI, Lee YM, Jeong SY, Cho TO, Kim JH, Cho H-G, Choi CG, Nelson WA, Fredericq S, Bhattacharya D, Yoon HS. 2018. Mitochondrial and plastid genomes from coralline red algae provide insights into the incongruent evolutionary histories of organelles. Genome Biology and Evolution [in press].

Cenci U*, Qiu H*, Pillonel T, Cardol P, Remacle C, Colleoni C, Kadouche D, Chabi M, Greub G, Bhattacharya D*, Ball, SG*. 2018. Host-pathogen biotic interactions shaped vitamin K metabolism in Archaeplastida. Scientific Reports [accepted].
*Equal contribution.

Foflonker F, Mollegard D, Ong M, Yoon HS, Bhattacharya. 2018. Genomic analysis of Picochlorum species reveals how microalgae may adapt to variable environments. Molecular Biology and Evolution. msy167-01 0737-4038. September 2018.
doi

Bhattacharya D, Qiu H, Lee J, Yoon HS, Weber APM, Price DC. 2018. When less is more: red algae as models for studying gene loss and genome evolution in eukaryotes. Crit Rev Plant Sci. 37(1):1-19.
doi

Lee J, Yang EC, Graf L, Yang JH, Qi H, Zelzion U, Chan CX, Stephens TG, Weber APM, Boo GH, Boo SM, Kim KM, Shin Y, Jung M, Lee SJ, Yim HS, Lee JY, Bhattacharya D*, Yoon HS*. 2018. Analysis of the draft genome of the red seaweed Gracilariopsis chorda provides insights into genome size evolution in Rhodophyta. Molecular Biology and Evolution 35(8):1869-1886.
*co-senior authors.
doi

Chan, C. X., Vaysberg, P., Price, D. C., Pelletreau, K. P., Rumpho, M. E., and Bhattacharya, D. 2018. Active host response to algal symbionts in the sea slug Elysia chlorotica. Mol. Biol. Evol. 35(7):1706-1711.
doi

Qiu, H., Rossoni, A., Weber, A. P. M., Yoon, H. S., and Bhattacharya, 2018. Unexpected conservation of the RNA splicing apparatus in the highly streamlined genome of Galdieria sulphuraria. BMC Evol. Biol. 18(1):41.
doi

Zhang, N., Cai, G., Price, D. C., Crouch, J. A., Gladieux, P., Hillman, B., Khang, C. H., LeBrun, M-. H., Lee, Y.- H., Luo, J., Qiu, H., Veltri, D., Wisecaver, J. H., Zhu, J., and Bhattacharya, D. 2018. Genome wide analysis of the transition to pathogenic lifestyles in Magnaporthales fungi. Sci. Rep. 8(1):5862.
doi

Méheust, R., Bhattacharya, D., Pathmanathan, J. S., McInerney, J. O., Lopez, P., and Bapteste, E. 2018. Formation of chimeric genes with essential functions at the origin of eukaryotes. BMC Biol. 16(1):30.
doi

De Clerck O, Kao S-M, Bogaert K, Blomme J, Foflonker F, Kwantes M, Vancaester E, Vanderstraeten L, Aydogdu E, Boesger J, Califano J, Charrier B6, Clewes R, Coates J, Del Cortona A, Fernandez-Pozo N, Gachon C, Hanikenne M, Lattermann L, Leliaert F, Liu X, Maggs C, Popper ZA, Raven J, Sterck L, Van Bel M, Wilhelmsson PKI, Bhattacharya D, Rensing SA, Van Der Straeten D, Vardi1 A, Vandepoele K, Van de Peer Y, Wichard T, Bothwell J. 2018. Insights into the evolution of multicellularity from the sea lettuce genome. Curr Biol. Volume 28, Issue 18, Pages 2921-2933.e5.
doi

2017

Brodie J, Ball SG, Bouget F-Y, Chan CX, De Clerck O, Cock M, Gachon C, Grossman AR, Mock T, Raven J, Saha M, Smith AG, Vardi A, Yoon HS, Bhattacharya D. 2017. Biotic interactions as drivers of algal origin and evolution. New Phytol. (Invited Tansley Review) doi:10.1111/nph.14760.
doi

Brawley SH, Blouin NA, Ficko-Blean E, Wheeler GL, Lohr M, Goodson HV, Jenkins JW, Blaby-Haas CE, Helliwell KE, Xin Chan Cl, Marriage TK, Bhattacharya D, Klein AS, Badis Y, Brodie , Cao Y, Collén J, Dittam SM, Gachon CMM, Green BR, Karpowicz SJ, Kim JW, Kudahl UJ, Lin S, Michel G, Mittag M, Olson BJSC, Pangilinan JL, Peng Y, Qiu H, Shuh S, Singer JT, Smith AG, Sprecher BN, Wagner V, Wang W, Wang Z-Y, Yan J, Yarish C, Zäuner-Rieka S, Zhuang Y, Zou Y, Lindquist EA, Grimwood J, Barry KW, Rokhsar DH, Schmutz J, Stiller JW, Grossman AR, Prochnik SE. 2017. Insights into the red algae and eukaryotic evolution from the genome of Porphyra umbilicalis (Bangiophyceae, Rhodophyta). Proc Natl Acad Sci USA. 114:E6361-E6370.
doi

Kim JI, Moore CE, Archibald JM, Bhattacharya D, Yi G, Yoon HS, Shin W. 2017. Evolutionary dynamics of cryptophyte plastid genomes. Genome Biol and Evol. 9:1859-1872.
doi

Qiu H, Zelzion E, Putnam HM, Gates RD, Wagner NE, Adams DK, Bhattacharya D. 2017. Discovery of SCORs: Anciently derived, highly conserved gene-associated repeats in stony corals. Genomics. Jun 17. doi:10.1016/j.ygeno.2017.06.003. [Epub ahead of print]
doi

Brodie J, Chan CX, De Clerck O, Cock JM, Coelho SM, Gachon C, Grossman AR, Mock T, Raven JA, Smith AG, Yoon HS, Bhattacharya D. 2017. The algal revolution. Trends Plant Sci. 22:726-738.
doi

Tripp EA, Zhang N, Schneider H, Huang Y, Mueller GM, Hu Z, Häggblom M, Bhattacharya D. 2017. Reshaping Darwin’s tree: impact of the symbiome. Trends Ecol Evol. 32:552-555.
doi

Putnam HM, Adams DK, Zelzion E, Wagner NE, Qiu H, Mass T, Falkowski PG, Gates RD, Bhattacharya D. 2017. Divergent evolutionary histories of DNA markers in a Hawaiian population of the coral Montipora capitata. PeerJ. 5:e3319.
doi

Price DC, Bhattacharya D. 2017. Robust Dinoflagellata phylogeny inferred from public transcriptome databases. J Phycol. 53:725-729.
doi

Zhang R, Nowack EC, Price DC, Bhattacharya D, Grossman AR. 2017. Impact of light intensity and quality on chromatophore and nuclear gene expression in Paulinella chromatophora, an amoeba with nascent photosynthetic organelles. Plant J. 90:221-234.
doi

Qiu H, Lee JM, Yoon HS, Bhattacharya D. 2017. Hypothesis: gene-rich plastid genomes in red algae may be an outcome of nuclear genome reduction. J Phycol. 53:715-719.
doi

Cenci U, Bhattacharya D, Weber AP, Colleoni C, Subtil A, Ball SG. 2017. Biotic host-pathogen interactions as major drivers of plastid endosymbiosis. Trends Plant Sci. 22:316-328.
doi

Pandey RS, Saxena G, Bhattacharya D, Qiu H, Azad RK. 2017. Using complementary approaches to identify trans-domain nuclear gene transfers in the extremophile Galdieria sulphuraria (Rhodophyta). J Phycol. 53:7-11.
doi

Honig JA, Zelzion E, Wagner NE, Kubik C, Averello V, Vaiciunas J, Bhattacharya D, Bonos SA, Meyer WA. 2017. Microsatellite identification in perennial ryegrass using next-generation sequencing. Crop Sci. 57:1-10.
doi

2016

ECM Nowack, DC Price, D Bhattacharya, A Singer, M Melkonian, and AR Grossman. 2016. Gene transfers from diverse bacteria compensate for reductive genome evolution in the chromatophore of Paulinella chromatophora, PNAS 2016: 1608016113v1-201608016
doi

Bhattacharya D, Agrawal S, Aranda M, Baumgarten S, Belcaid M, Drake JL, Erwin D, Foret S, Gates RD, Gruber DF, et al. 2016. Comparative genomics explains the evolutionary success of reef-forming corals. eLife. 5:e13288.
doi

Ball SG, Bhattacharya D, Weber AP. 2016. EVOLUTION. Pathogen to powerhouse. Science. 351:659-660.
doi

Ball SG, Bhattacharya D, Weber APM. 2016. Response to SB Gould, Infection and first eukaryotes. Science 27 May 2016. Vol. 352, Issue 6289, pp. 1065-1066.
doi

Méheust R, Zelzion E, Bhattacharya D, Lopez P, Bapteste E. 2016. Protein networks identify novel symbiogenetic genes resulting from plastid endosymbiosis. Proc. Natl. Acad. Sci. USA. 113:3579-3584.
doi

Mass T, Putnam HM, Drake JL, Zelzion E, Gates RD, Bhattacharya D, Falkowski PG. 2016. Temporal and spatial expression patterns of biomineralization proteins during early development in the stony coral Pocillopora damicornis. Proc. Biol. Sci. 283:20160322.
doi

Stephens TG, Bhattacharya D, Ragan MA, Chan CX. 2016. PhySortR: a fast, flexible tool for sorting phylogenetic trees in R. PeerJ. 4:e2038.
doi

Qiu H, Cai G, Luo J, Bhattacharya D, Zhang N. 2016. Extensive horizontal gene transfers between plant pathogenic fungi. BMC Biol. 14:41.
doi

Leliaert F, Tronholm A, Lemieux C, Turmel M, DePriest MS, Bhattacharya D, Karol KG, Fredericq S, Zechman FW, Lopez-Bautista JM. 2016. Chloroplast phylogenomic analyses reveal the deepest-branching lineage of the Chlorophyta, Palmophyllophyceae class. nov. Sci. Rep. 6:25367.
doi

Ball SG, Bhattacharya D, Qiu H, Weber AP. 2016. Commentary: Plastid establishment did not require a chlamydial partner. Front. Cell Infect Microbiol. 6:43.
doi

Foflonker F, Ananyev G, Qiu H, Morrison A, Palenik B, Dismukes GC, Bhattacharya D. 2016. The unexpected extremophile: Tolerance to fluctuating salinity in the green alga Picochlorum. Algal Res. 16:465-472.
doi

Lee J, Kim KM, Yang EC, Miller KA, Boo SM, Bhattacharya D, Yoon HS. 2016. Reconstructing the complex evolutionary history of mobile plasmids in red algal genomes. Sci. Rep. 6:23744.
doi

Yang EC, Boo SM, Bhattacharya D, Saunders GW, Knoll AH, Fredericq S, Graf L, Yoon HS. 2016. Divergence time estimates and the evolution of major lineages in the florideophyte red algae. Sci. Rep. 6:21361.
doi

2015

Karkar S, Facchinelli F, Price DC, Weber APM, and Bhattacharya D. 2015. Metabolic connectivity as a driver of host and endosymbiont integration. Proc Natl Acad Sci USA. 112:10208-10215.
doi

J. Luo, H. Qiu, G. Cai, N. E. Wagner, D. Bhattacharya & N. Zhang. 2015. Phylogenomic analysis uncovers the evolutionary history of nutrition and infection mode in rice blast fungus and other Magnaporthales. Sci. Rep. 5:9448.
doi

MM Perrineau, DC Price, G Mohr, D Bhattacharya. 2015. Recent mobility of plastid encoded group II introns and twintrons in five strains of the unicellular red alga Porphyridium. 2015. PeerJ. 3:e1017.
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Foflonker F, Price DC, Qiu H, Palenik B, Wang S, Bhattacharya D. 2015. Genome of the halotolerant green alga Picochlorum SENEW3 reveals strategies for thriving under fluctuating environmental conditions. Environ. Microbiol. 17:412-426.
doi

Harel A, Karkar S, Cheng S, Falkowski PG, and Bhattacharya D. 2015. Deciphering primordial cyanobacterial genome functions from protein network analysis. Curr. Biol. 25:628-634.
doi

Bhattacharya D, Qiu H, Price DC, Yoon HS. 2015. Why we need more algal genomes. J. Phycol. 51:1-5
doi

Levitan O, Dinamarca J, Zelzion E, Lun DS, Guerra LT, Kim MK, Kim J, Van Mooy BA, Bhattacharya D, Falkowski PG. 2015. Remodeling of intermediate metabolism in the diatom Phaeodactylum tricornutum under nitrogen stress. Proc Natl Acad Sci USA 112(2):412-417.
doi

H Qiu, DC Price, EC Yang, HS Yoon, D Bhattacharya. 2015. Evidence of ancient genome reduction in red algae (Rhodophyta). J. Phycol. 51:624-636.
doi

Yang EC, Kim KM, Kim SY, Lee J, Boo GH, Lee JH, Nelson WA, Yi G, Schmidt WE, Fredericq S, Boo SM, Bhattacharya D, Yoon HS. 2015. Highly conserved mitochondrial genomes among multicellular red algae of the Florideophyceae. Genome Biol. Evol. 7:2394-2406.
doi

2014

Rockwell NC, Lagarias JC, and Bhattacharya D. 2014. Primary endosymbiosis and the evolution of light and oxygen sensing in photosynthetic eukaryotes. Front Ecol Evol 2:66.
doi

Roy R, Bhattacharya D, Schliep A. 2014. Turtle: Identifying frequent k-mers with cache-efficient algorithms. Bioinformatics 30(14):1950-1957. 2014 Apr 2.
software download

Roy RS, Price DC, Schliep A, Cai G, Korobeynikov A, Yoon HS, Yang EC, Bhattacharya D. 2014. Single cell genome analysis of an uncultured heterotrophic stramenopile. 2014. Sci Rep. 2014 Apr 24;4:4780.
doi | pdf

Harel A, Bromberg Y, Falkowski PG, Bhattacharya D. 2014. The evolutionary history of redox metal-binding domains across the tree of life. Proc Natl Acad Sci USA 111:7042-7047.
doi

Debashish Bhattacharya, Rajat S. Roy, Dana C. Price and Alexander Schliep. 2014. Single-cell genomics of marine plankton. Biochemist Magazine – Journal of the Biochemical Society, 36:1 February 16–22.
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Rockwell NC, Duanmu D, Martin SS, Bachy C, Price DC, Bhattacharya D, Worden AZ, Lagarias JC. 2014. Eukaryotic algal phytochromes span the visible spectrum. Proc Natl Acad Sci USA. Mar 11;111(10):3871-6.
doi

Foflonker F, Price DC, Qiu H, Palenik B, Wang S, and Bhattacharya D. 2014. Genome of the halotolerant green alga Picochlorum SENEW3 reveals strategies for thriving under fluctuating environmental conditions. Environ Microbiology in press.
doi

Cheng S, Price DC, Karkar S, Bhattacharya D. 2014. Exploring biotic interactions within protist cell populations using network methods. J Eukaryot Microbiol 61(4):399-403.
doi

Kim KM, Park J-H, Bhattacharya D, Yoon HS. 2014. Applications of next-generation sequencing to unravelling the evolutionary history of algae. International Journal of Systematic and Evolutionary Microbiology 64(2):333-345.
doi

Bhattacharya D, Roy RS, Price DC, Schliep A. 2014. Single-cell genomics of marine plankton. Biochemist Magazine – Journal of the Biochemical Society, February 16-22.
pdf

MM Perrineau, E Zelzion, J Gross, DC Price, J Boyd, D Bhattacharya. Evolution of salt tolerance in a laboratory reared population of Chlamydomonas reinhardtii. 2014. Environmental Microbiology 16:1755-1766.
doi

Perrineau MM, Gross J, Zelzion E, Price DC, Levitan O, Boyd J, Bhattacharya D. 2014. Using natural selection to explore the adaptive potential of Chlamydomonas reinhardtii. PLoS One: 9:e92533. March 21, 2014.
doi| pdf

Polashock J, Zelzion E, Fajardo D, Zalapa J, Georgi L, Bhattacharya D, Vorsa N. 2014. The American cranberry: first insights into the whole genome of a species adapted to bog habitat. BMC Plant Biol 14:165.
doi

Cheng S, Karkar S, Bapteste E, Yee N, Falkowski P, Bhattacharya D. 2014. Sequence similarity network reveals the imprints of major diversification events in the evolution of microbial life. Frontiers in Ecology and Evolution 2:72.
doi

Chan CX, Bhattacharya D. 2014. Analysis of horizontal genetic transfer in red algae in the post-genomics age. Mobile Genetic Elements 3(6): e27669 .
doi

DePriest MS, Bhattacharya D, López-Bautista JM. 2014. The mitochondrial genome of Grateloupia taiwanensis (Halymeniaceae, Rhodophyta) and comparative mitochondrial genomics of red algae. Biol Bull 227(2):191-200.

2013

S Nyati, D Bhattacharya, S Werth, R Honegger. Phylogenetic analysis of LSU and SSU rDNA group I introns of lichen photobionts associated with the genera Xanthoria and Xanthomendoza (Teloschistaceae, lichenized Ascomycetes). Journal of Phycology 49 (6), 1154-1166, 11 Nov 2013.
doi

D Bhattacharya, KN Pelletreau, DC Price, KE Sarver, ME Rumpho. Genome analysis of Elysia chlorotica egg DNA provides no evidence for horizontal gene transfer into the germ line of this kleptoplastic mollusc. Molecular biology and Evolution 30(8), 1843-1852. 11 July 2013.
doi

C. X. Chan, F. L. Baglivi, C. E. Jenkins, and D. Bhattacharya. Foreign gene recruitment to the fatty acid biosynthesis pathway in diatoms. Mobile Genetic Elements 3, e27313; September/October 2013.
doi

Huan Qiu, Dana C. Price, Andreas P.M. Weber, Fabio Facchinelli, Hwan Su Yoon, and Debashish Bhattacharya. Assessing the bacterial contribution to the plastid proteome. Trends in Plant Science. 2013 Oct 16. S1360-1385(13)00198-2.
doi

Huan Qiu, Dana C. Price, Andreas P.M. Weber, Valérie Reeb, Eun Chan Yang, Jun Mo Lee, Su Yeon Kim, Hwan Su Yoon, and Debashish Bhattacharya, Adaptation through horizontal gene transfer in the cryptoendolithic red alga Galdieria phlegrea. Current Biology. Oct 7;23(19):R865-6.
doi

Ugo Cenci, Malika Chabi, Mathieu Ducatez, Catherine Tirtiaux, Jennifer Nirmal-Raj, Yoshinori Utsumi, Daiki Kobayashi, Satoshi Sasaki, Eiji Suzuki, Yasunori Nakamura, Jean-Luc Putaux, Xavier Roussel, Amandine Durand-Terrasson, Debashish Bhattacharya, Anne-Sophie Vercoutter-Edouart, Emmanuel Maes, Maria Cecilia Arias, Monica Palcic, Lyann Sim, Steven G. Ball and Christophe Colleoni. 2013. Convergent Evolution of Polysaccharide Debranching Defines a Common Mechanism for Starch Accumulation in Cyanobacteria and Plants. The Plant Cell October 2013 tpc.113.118174.
doi

Huan Qiu, Hwan Su Yoon, and Debashish Bhattacharya. 2013. Algal endosymbionts as vectors of horizontal gene transfer in photosynthetic eukaryotes. Frontiers in Plant Science, 19 September 2013.
doi

Depriest MS, Bhattacharya D, López-Bautista JM. 2013. The Plastid Genome of the Red Macroalga Grateloupia taiwanensis (Halymeniaceae). PLoS One. 2013 Jul 19;8(7):e68246.
doi

Skorupa DJ, Reeb V, Castenholz RW, Bhattacharya D, McDermott TR. 2013. Cyanidiales diversity in Yellowstone National Park Lett Appl Microbiol. 2013 Jul 19. [Epub ahead of print]
doi

Drake JL, Massa T, Haramaty L, Zelzion E, Bhattacharya D, Falkowski PG.
Reply to Ramos-Silva et al.: Regarding coral skeletal proteome. Proc Natl Acad Sci U S A. 2013 Jun 11;110(24):E2147-8.

Shoguchi E, Shinzato C, Kawashima T, Gyoja F, Mungpakdee S, Koyanagi R, Takeuchi T, Hisata K, Tanaka M, Fujiwara M, Hamada M, Seidi A, Fujie M, Usami T, Goto H, Yamasaki S, Arakaki N, Suzuki Y, Sugano S, Toyoda A, Kuroki Y, Fujiyama A, Medina M, Coffroth MA, Bhattacharya D, Satoh N. 2013. Draft Assembly of the Symbiodinium minutum Nuclear Genome Reveals Dinoflagellate Gene Structure. Curr Biol. 2013 Jul 9.
doi

Bhattacharya D, Price DC, Chan CX, Qiu H, Rose N, Ball S, Weber AP, Cecilia Arias M, Henrissat B, Coutinho PM, Krishnan A, Zäuner S, Morath S, Hilliou F, Egizi A, Perrineau MM, Yoon HS. 2013. Genome of the red alga Porphyridium purpureum. Nat Commun. 2013 Jun 17;4:1941.
doi

Jeferson Gross, Sana Wajid, Dana C. Price, Ehud Zelzion, Junyi Li, Cheong Xin Chan, Debashish Bhattacharya. 2013. Evidence for Widespread Exonic Small RNAs in the Glaucophyte Alga Cyanophora paradoxa. PLoS ONE 8(7): e67669.
doi| pdf

Tali Mass, Jeana L. Drake, Liti Haramaty, J. Dongun Kim, Ehud Zelzion, Debashish Bhattacharya, and Paul G. Falkowski. Cloning and Characterization of Four Novel Coral Acid-Rich Proteins that Precipitate Carbonates In Vitro. Current Biology, Volume 23, Issue 12, 17 June 2013, Pages 1126-1131.
doi | RU news release

Bhattacharya, D., D.C. Price, C. Bicep, E. Bapteste, M. Sarwade, V.D. Rajah, and H. S. Yoon. 2013. Identification of a marine cyanophage in a protist single cell metagenome assembly. Journal of Phycology Volume 49, Issue 1, pages 207-212, February.
doi

Drake J.L., Mass T., Haramaty L., Zelzion E., Bhattacharya D., Falkowski P.G. 2013. Proteomic analysis of skeletal organic matrix from the stony coral Stylophora pistillata. Proc Natl Acad Sci U S A. 2013 Feb 19.
doi| pdf

Ball, S.G., A. Subtil, D. Bhattacharya, A. Moustafa, A.P.M. Weber, L. Gehre, C. Colleoni, M.-C. Arias, U. Cenci, and D. Dauvillée. 2013. Metabolic effectors secreted by bacterial pathogens: essential facilitators of plastid endosymbiosis? The Plant Cell January 2013 tpc.112.101329.
doi|free full text online

Facchinelli, F., M. Pribil, U. Oster, N. Ebert, D. Bhattacharya, D. Leister, and A. Weber. 2013. Proteomic analysis of the Cyanophora paradoxa muroplast provides clues on early events in plastid endosymbiosis. Planta: 2013 Feb;237(2):637-51, epub ahead of print
doi

2012

Steiner, J.M., D. Bhattacharya, and W. Löffelhardt. 2012. Conservative sorting in the muroplasts of Cyanophora paradoxa: a reevaluation based on the completed genome sequence. Symbiosis 57: epub ahead of print
doi

Georgi, L., J. Johnson-Cicalese, J. Honig, S. Parankush Das, V.D. Rajah, D. Bhattacharya, N. Bassil, L.J. Rowland, J. Polashock, and N. Vorsa. 2012. The first genetic map of the American cranberry: exploration of synteny conservation and quantitative trait loci. Theoretical and Applied Genetics: 2012 Dec 8. epub ahead of print
doi

Gross, J., and D. Bhattacharya. 2012. Evolution: Eukaryotes. Encyclopedia fo Genetics, 2nd Edition, Elsevier.

Price D.C., Chan C.X., Yoon HS, Yang E.C., Qiu H., Weber A.P., Schwacke R., Gross J., Blouin N.A., Lane C., Reyes-Prieto A., Durnford D.G., Neilson J.A., Lang F.B., Gertraud Burger G., Steiner J.M., Löffelhardt W., Meuser J.E., Posewitz M.C., Ball S., Arias M.C., Henrissat B., Coutinho P.M., Rensing S.A., Symeonidi A., Doddapaneni H., Green B.R., Rajah V.D., Boore J., and Bhattacharya D. 2012. Cyanophora paradoxa genome elucidates origin of photosynthesis in algae and plants. Science 17 February 2012: Vol. 335 no. 6070 pp. 843-847
doi|Nature news|ScientificAmerican.com|biotechnologie.de [German]|RU news|Cyanophora BLAST and data download|
See commentary by Spiegel FW. 2012. Contemplating the first Plantae. Science 17 February 2012: Vol. 335 no. 6070 pp. 809-810 |doi

Chan CX, Soares MB, Bonaldo MF, Wisecaver JH, Hackett JD, Anderson DM, Erdner DL, Bhattacharya D. 2012. Analysis of Alexandrium tamarense (Dinophyceae) genes reveals the complex evolutionary history of a microbial eukaryote. Journal of Phycology 48:1130-1142.
doi

Chan CX, Bhattacharya D and Reyes-Prieto A. 2012. Endosymbiotic and horizontal gene transfer in microbial eukaryotes: impacts on cell evolution and the tree of life. Mobile Genetic Elements, 2(2)
doi

Chan, C.X., S. Zaeuner, G. Wheeler, A.R. Grossman, S.E. Prochnik, N.A. Blouin, Y. Zhuang, C. Benning, G.M. Berg, C.Yarish, R.L. Eriksen, A.S. Klein, S. Lin, I. Levine, S.H. Brawley, and D. Bhattacharya. 2012. Analysis of Porphyra membrane transporters demonstrates gene transfer among photosynthetic eukaryotes and numerous sodium-coupled transport systems. Plant Physiology. February 2012 pp.112.193896.
doi|pdf

Salcedo T, Upadhyay RJ, Nagasaki K, and Bhattacharya D. 2012. Dozens of toxin-related genes are expressed in a non-toxic strain of the dinoflagellate Heterocapsa circularisquama. Mol Biol Evol (2012) 29(6): 1503-1506.
doi

Hackett JD, Wisecaver JH, Brosnahan ML, Kulis DM, Anderson DM, Bhattacharya D, Plumley FG, and Erdner DL. 2012. Evolution of saxitoxin synthesis in cyanobacteria and dinoflagellates. Mol Biol Evol first published online May 23, 2012.
doi

Qiu H, Yang EC, Bhattacharya D, Yoon HS. 2012. Ancient gene paralogy may mislead inference of plastid phylogeny.
Mol Biol Evol. 2012 Nov;29(11):3333-43. Epub 2012 May 21.
doi

Bhattacharya D, Price DC, Yoon HS, Yang EC, Poulton NJ, Andersen RA, Das SP. 2012. Single cell genome analysis supports a link between phagotrophy and primary plastid endosymbiosis. Sci Rep. 2012;2:356. Epub 2012 Apr 10.
doi

2011

Chan CX, Reyes-Prieto A, Bhattacharya D. 2011. Red and Green Algal Origin of Diatom Membrane Transporters: Insights into Environmental Adaptation and Cell Evolution. PLoS ONE 6(12): e29138.
doi |pdf

Chan CX and Bhattacharya D. 2011. Plastid origin and evolution. In: Encyclopedia of Life Sciences (eLS). Wiley & Sons.
doi

Bhattacharya D. 2011. As an evolutionary biologist. Debashish Bhattacharya., Curr Biol. Sep 27;21(18):R676-7.
doi

Yoon, H.S., D.C. Price, R. Stepanauskas, V.D. Rajah, M.E. Sieracki, W.H. Wilson, E.C. Yang, S. Duffy, and D. Bhattacharya. 2011. Single cell genomics reveals trophic interactions and evolutionary history of uncultured protists. Science 6 May 2011: Vol. 332 no. 6030 pp. 714-717.
doi|RU news article|Science Daily

Chan, CX and Bhattacharya, D (2011). Non-random sharing of Plantae genes. Communicative and Integrative Biology 4(3): 361 – 363.
doi|pdf

Cheong Xin Chan, Jeferson Gross, Hwan Su Yoon, and Debashish Bhattacharya. 2011. Plastid Origin and Evolution: New Models Provide Insights into Old Problems. Plant Physiology 155(4):1552-1560.
Download this publication (PDF file)| doi | pubmed

Jeferson Gross, Debashish Bhattacharya. 2011. Endosymbiont or host: who drove mitochondrial and plastid evolution? Biology Direct, 6:12. Published on 19 February 2011.
Download this publication (PDF file)|doi|pubmed

Karen N. Pelletreau, Debashish Bhattacharya, Dana C. Price, Jared M. Worful, Ahmed Moustafa, and Mary E. Rumpho. 2011. Update on Sea Slug Kleptoplasty and Plastid Maintenance in a Metazoan. Plant Physiology 155(4):1561-1565.
Download this publication (PDF file)|doi|pubmed|supplement

Chan CX, Yang EC, Banerjee T, Yoon HS, Martone PT, Estevez JM and Bhattacharya D (2011). Red-and-green algal monophyly and extensive gene sharing found in a rich repertoire of red algal genes. Current Biology 21(4):328-333.
Download this publication (PDF file)|doi|pubmed|supplemental|RU news article|Futurity.org article

2010

Valérie Reeb, Avraham Kolel, Timothy R. McDermott and Debashish Bhattacharya. Good to the bone: microbial community thrives within bone cavities of a bison carcass at Yellowstone National Park Environmental Microbiology (2010).
doi|pubmed

Vis ML, Yoon HS, Bhattacharya D, Lopez-Bautista JM. RedTol – The Red Algal Tree of Life. In: Why Study the Tree of Life? – Scientists Speak, (Edited by Mikkelsen P). American Paleontologist 18(3) Fall 2010 13.
Download this publication (PDF file)

Sung Min Boo, Han Soon Kim, Woongghi Shin, Ga Hun Boo, Sung Min Cho, Bok Yeon Jo, Jee-Hwan Kim, Jin Hee Kim, Eun Chan Yang, Peter A. Siver, Alexander P. Wolfe, Debashish Bhattacharya, Robert A. Andersen and Hwan Su Yoon. 2010. Complex phylogeographic patterns in the freshwater alga Synura provide new insights into ubiquity vs. endemism in microbial eukaryotes. Molecular Ecology 19: 4328-4338.
doi

Chan, C. X. & Bhattacharya, D. (2010) The Origin of Plastids. Nature Education 3(9):84.
Download this publication (PDF file)|scitable

Gross J, Bhattacharya D. 2010. Uniting sex and eukaryote origins in an emerging oxygenic world.
Biol Direct. 2010 Aug 23;5:53.
Download this publication (PDF file)|doi|pubmed

Rumpho, M. E., K. N. Pelletreau, A. Moustafa, and D. Bhattacharya. 2011. The making of a photosynthetic animal.
J Exp Biol:2011 Jan 15;214(Pt 2):303-11.
doi|pubmed

Kerry Knudsen, Valérie Reeb, Martin Westberg, Rithu Srikantha and Debashish Bhattacharya. 2010. Acarospora rosulata in Europe, North America and Asia. The Lichenologist 42)3): 291-296.
doi

Moustafa, A., A.N. Evans, D.M. Kulis, J.D. Hackett, D.L. Erdner, D.M. Anderson, and D. Bhattacharya. Transcriptome profiling of a toxic dinoflagellate reveals a highly gene-rich protist and a major impact on gene expression due to bacterial presence. PLoS ONE.
Download this publication (PDF file)|doi|pubmed

Reyes-Prieto, A.R., H.S. Yoon, A. Moustafa, E.C. Yang, R.A. Andersen, S.M. Boo, T. Nakayama, K.-i. Ishida, and D. Bhattacharya. 2010. Differential gene retention in plastids of common recent origin.
Mol Biol Evol. 27(7):1530-1537. 2010 Feb 1.
doi|pubmed

2009

Borchert, G.M., B.L. Gilmore, R.M. Spengler, Y. Xing, W. Lanier, D. Bhattacharya, and B.L. Davidson. 2009. Adenosine deamination in human transcripts generates novel microRNA binding sites. Hum. Mol. Genet. 18:4801-4807.
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Rumpho, M.E., S. Pochareddy, J.M. Worful, E.J. Summer, D. Bhattacharya, K.N. Pelletreau, M.S. Tyler, J. Lee, J.R. Manhart, and K.M. Soule. 2009. Molecular characterization of the Calvin cycle enzyme phosphoribulokinase in the stramenopile alga Vaucheria litorea and the plastid hosting mollusc Elysia chlorotica. Mol. Plant 2:1384-1396.
doi|pubmed

Soares, M.B., M. de Fatima Bonaldo, J.D. Hackett, and D. Bhattacharya. 2009. Expressed sequence tags: normalization and subtraction of cDNA libraries expressed sequence tags\ normalization and subtraction of cDNA libraries. Methods Mol. Biol. 533:109-122.
doi|pubmed

Moustafa, A., B. Beszteri, U.G. Maier, C. Bowler, K. Valentin, and D. Bhattacharya. 2009. Genomic footprints of a cryptic plastid endosymbiosis in diatoms.Science 324: 1724-1726.
doi| pubmed

Gross, J., and D. Bhattacharya. 2009. Mitochondrial and plastid evolution in eukaryotes: an outsider’s perspective. Nature Rev. Genet. 10:495-505.
doi|pubmed

Reeb, V.C., M.T. Peglar, H.S. Yoon, J.R. Bai, M. Wu, P. Shiu, J.L. Grafenberg, A. Reyes-Prieto, S.E. R&#uuml;mmele, J. Gross, and D. Bhattacharya. 2009. Interrelationships of chromalveolates within a broadly sampled tree of photosynthetic protists. Mol Phylogenet. Evol. 53:202-211.
doi|pubmed

Worden, A.Z., J-H. Lee, T. Mock, P. Rouzé, M.P. Simmons, A.L. Aerts, A.E. Allen, M.L. Cuvelier, E. Derelle, M.V. Everett, E. Foulon, J. Grimwood, H. Gundlach, B. Henrissat, C. Napoli, S.M. McDonald, M. Schnitzler Parker, S. Rombauts, A. Salamov, P. Von Dassow, J.H. Badger, P.M. Coutinho, E. Demir, I. Dubchak, C. Gentemann, W. Eikrem, J.E. Gready, U. John, W. Lanier, E.A. Lindquist, S. Lucas, K.F.X. Mayer, H. Moreau, F. Not, R. Otillar, O. Panaud, J. Pangilinan, I. Paulsen, B. Piegu, A. Poliakov, S. Robbens, J. Schmutz, E. Toulza, T. Wyss, A. Zelensky, K. Zhou, E.V. Armbrust, D. Bhattacharya, U.W. Goodenough, Y. Van de Peer, and I.V. Grigoriev. 2009. Green evolution and dynamic adaptations revealed by genomes of the marine picoeukaryotes Micromonas. Science 324:268-272.
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Wu, M., J. Comeron, H.S. Yoon, and D. Bhattacharya. 2009. Unexpected dynamic gene family evolution in algal actins. Mol. Biol. Evol. 26:249-253.
doi|pubmed

Yoon, H.S, T. Nakayama, A. Reyes-Prieto, R.A. Andersen, S.M. Boo, K-i Ishida, and D. Bhattacharya. 2009. A single origin of the photosynthetic organelle in different Paulinella lineages. BMC Evol. Biol. 9:98.
doi|pubmed

Moustafa, A., J.E. Loram, J.D. Hackett, D.M. Anderson, F.G. Plumley, and D. Bhattacharya. 2009. Origin of saxitoxin biosynthetic genes in cyanobacteria. PLoS One 4:e5758.
doi|pubmed

Gross, J., and D. Bhattacharya. 2009. Revaluating the evolution of the Toc/Tic protein translocons. Trends Plant Sci. 14:13-20.
doi|pubmed

2008

Frommolt, R., S. Werner, H. Paulsen, R. Goss, C. Wilhelm, S. Zauner, U.G. Maier, A.R. Grossman, D. Bhattacharya, and M. Lohr. 2008. Ancient recruitment by chromists of green algal genes encoding enzymes for carotenoid biosynthesis. Mol. Biol. Evol. 25:2653-2667.
doi|pubmed

Rumpho, M.E., J.M. Worful, J. Lee, K. Kannan, M.S. Tyler, D. Bhattacharya, A. Moustafa, and J.R. Manhart. 2008 . Horizontal gene transfer of the algal nuclear gene psbO to the photosynthetic sea slug Elysia chlorotica. Proc. Natl. Acad. Sci. USA 105:17867-17871.
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Gross, J., J. Meurer, and D. Bhattacharya. 2008. Evidence of a chimeric genome in the cyanobacterial ancestor of plastids. BMC Evol. Biol. 8:117.
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Grosskurth, S.E., D. Bhattacharya, Q. Wang, and J.J. Lin. 2008. Emergence of Xin demarcates a key innovation in heart evolution. PLoS ONE. 2008 Aug 6;3(8):e2857.
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Lanier, W., A. Moustafa, D. Bhattacharya, and J.M. Comeron. 2008. Analysis of Ostreococcus lucimarinus EST data shows more introns in highly expressed genes. PLoS ONE:e2171.
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Moustafa, A., and D. Bhattacharya. 2008. PhyloSort: a user-friendly phylogenetic sorting tool and its application to estimating the cyanobacterial contribution to the nuclear genome of Chlamydomonas. BMC Evol. Biol. 8:6.
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Moustafa, A., A. Reyes-Prieto, and D. Bhattacharya. 2008. Chlamydiae has contributed at least 55 genes to Plantae with predominantly plastid functions. PLoS One. 2008 May 21;3(5):e2205.
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Nosenko, T., and D. Bhattacharya. 2008. Endosymbiotic and horizontal gene transfer in chromalveolates. J. Phycol. 44:7-10.
Journal cover|doi

Phillips, N., S. Calhoun, A. Moustafa, D. Bhattacharya, and E.L. Braun. 2008. Genomic insights into evolutionary relationships among heterokont lineages emphasizing the Phaeophyceae. J. Phycol. 44:15-18.
doi

Reyes-Prieto, A., A. Moustafa, and D. Bhattacharya. 2008. Multiple genes of apparent algal origin suggest ciliates may once have been photosynthetic. Curr Biol. 2008 Jul 8;18(13):956-62. (with accompanying commentary)
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Yoon, H.S., J. Grant, Y.I. Tekle, M. Wu, B.C. Chaon, J.C. Cole, J.M. Logsdon, D.J. Patterson, D. Bhattacharya, and L.A. Katz. 2008. Broadly sampled multigene trees of eukaryotes. BMC Evol Biol. 2008 Jan 18;8:14
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Zhang, H., D. Bhattacharya, L. Maranda, and S. Lin. 2008. Mitochondrial cob and cox1 and their mRNA editing in Dinophysis acuminata from Narragansett Bay, with special reference to the phylogenetic position of Dinophysis. Appl. Environ. Microbiol. 74:1546-1554.
doi |pubmed

2007

Bhattacharya, D., J.M. Archibald, A.P.M. Weber, and A. Reyes-Prieto. 2007. How do endosymbionts become organelles? Understanding early events in plastid evolution. BioEssays 2007 Dec;29(12):1239-46.
doi|pubmed

Reyes-Prieto, A., and D. Bhattacharya. 2007. Phylogeny of nuclear encoded plastid targeted proteins suggests an early divergence of glaucophytes within Plantae. Mol Biol Evol. 2007 Sep 6.
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Tyra, H.M., Linka, M., Weber, A.P.M., and D. Bhattacharya. 2007. Host origin of plastid solute transporters in the first photosynthetic eukaryotes. Genome Biol. 8:R212.
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Nosenko, T., and D. Bhattacharya. 2007. Horizontal gene transfer in chromalveolates. BMC Evol. Bio. 2007 Sep 25;7(1):173
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Reyes-Prieto, A., A. Weber, and D. Bhattacharya. 2007. The origin and establishment of the plastid in algae and plants. Annu. Rev. Genet. 41:147-168.
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Hackett, J.D., H.S. Yoon, S. Li, A. Reyes-Prieto, S.E. Ruemmele, and D. Bhattacharya. 2007. Phylogenomic analysis supports the monophyly of cryptophytes and haptophytes and the association of ‘Rhizaria’ with chromalveolates. Mol. Biol. Evol. 24: 1702-1713.
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J.D. Hackett, H.S. Yoon, N.J. Butterfield, M.J. Sanderson, and D. Bhattacharya. 2007. Plastid endosymbiosis: sources and timing of the major events. In: Evolution of Primary Producers in the Sea, (Eds.) P. Falkowski and A. Knoll. Elsevier Academic Press. 109-133.Nosenko, T., B. Boese, and D. Bhattacharya. 2007. Pulsed field gel electrophoresis analysis of genome size and structure in Pavlova gyrans and Diacronema sp. (Haptophyta). J. Phycol. 43:763-767.
Download this publication (PDF file)| doi This is an electronic version of an article published in Journal of Phycology ©2007,
The Phycological Society of America.

Reyes-Prieto, A., and D. Bhattacharya. 2007. Phylogeny of Calvin cycle enzymes supports Plantae monophyly. Mol. Phylogenet. Evol. 45:384-391.
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Haugen, P., D. Bhattacharya, J.D. Palmer, S. Turner, L.A. Lewis, and K.M. Pryer. 2007. Cyanobacterial ribosomal RNA genes with multiple, endonuclease-encoding group I introns. BMC Evol. Biol. 7:159.
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Reeb, V., P. Haugen, D. Bhattacharya, and F. Lutzoni. 2007. Evolution of Pleopsidium (Lichenized Ascomycota) S943 Group I Introns and the Phylogeography of an Intron-Encoded Putative Homing Endonuclease. J. Mol. Evol. 64:285-298.
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Zhang, H., S. Lin, and D. Bhattacharya. 2007. A three-gene dinoflagellate phylogeny suggests monophyly of prorocentrales and a basal position for amphidinium and heterocapsa. J. Mol. Evol. 65:463-474.
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Book Chapters

2014

Yoon HS, Yang EC, Qiu H, Bhattacharya D. 2014. Photosynthetic Paulinella -recapitulation of primary plastid establishment. In. Endosymbiosis (ed. W. Löffelhardt) 2014, pp 151-166, Springer, Wien.

Bhattacharya D, Price DC, Chan CX, Gross J, Steiner JM, Löffelhardt W. 2014. Analysis of the genome of Cyanophora paradoxa: an algal model for understanding primary endosymbiosis. In. Endosymbiosis (ed. W. Löffelhardt) 2014, pp 135-148, Springer, Wien.

2010

Gantt, E., G.M. Berg, D. Bhattacharya, N.A. Blouin, J.A. Brodie, C.X. Chan, J. Collén, F.X. Cunningham Jr., J. Gross, A.R. Grossman, S. Karpowicz, Y. Kitade, A.S. Klein, I.A. Levine, S. Lin, S. Lu, M. Lynch, S.C. Minocha, K. M&#uuml;ller, C.D. Neefus, M.C. De Oliveira, L. Rymarquis, A. Smith, J.W. Stiller, W.-K. Wu, C. Yarish, Y.Y. Zhuang, And S.H. Brawley. 2010. Porphyra: complex life histories in a harsh environment: P. umbilicalis, an intertidal red alga for genomic analysis. In: Red algae in the Genomic Age, (Eds.) J. Seckbach and D. Chapman. Cellular Origin, Life in Extreme Habitats and Astrobiology 13, 129 – 148, Springer 2010.
doi|read online

Reeb, V., and D. Bhattacharya. 2010. The thermo-acidophilic Cyanidiophyceae (Cyanidiales). In: Red Algae in the Genomic Age, (Eds.) J. Seckbach and D. Chapman. Cellular Origin, Life in Extreme Habitats and Astrobiology 13, 409–426. Springer 2010.
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Reyes-Prieto, A., H.S. Yoon, and D. Bhattacharya. 2010. Marine protist (algal) genomics and evolution. Encyclopedia of Ocean Sciences, Wiley, in press.

Yoon, H.S., G.C. Zuccarello, and D. Bhattacharya. 2010. Evolutionary history and taxonomy of red algae. In: Red algae in the genomic age, (Eds.) J. Seckbach and D. Chapman, Springer, in press.

2009

Bhattacharya, D., H.S. Yoon, S.B. Hedges, and J.D. Hackett. 2009. Eukaryotes (Eukaryota). Timetree of Life, In: Timetree of life, (Eds.) S.B. Hedges and S. Kumar, Oxford University Press, pp. 116-120.

Yoon, H.S., R.A. Andersen, S.M. Boo, and D. Bhattacharya. 2009. Evolutionary history and diversity of Stramenopiles. Encyclopedia of Microbiology, Elsevier, pp. 721-731.

2008

Moustafa, A., C.X. Chan, M. Danforth, D. Zear, H. Ahmed, N. Jadhav, T. Savage, and D. Bhattacharya. 2008. A phylogenomic approach for studying plastid endosymbiosis. Genome Inform. 21:165-176.

2007

Hackett, J.D., H.S. Yoon, N.J. Butterfield, M.J. Sanderson, and D. Bhattacharya. 2007. Plastid endosymbiosis: origins and timing of events. In: Evolution of Aquatic Photoautotrophs, Eds. Falkowski, P., and A. Knoll, Elsevier, p. 109-131.

Edited Volumes

Katz, L.A., and D. Bhattacharya. 2006. Genome evolution in eukaryotic microbes. Oxford
University Press.
Book cover

Bhattacharya, D. 1997. Origins of algae and their plastids. (Editor) Springer-Verlag, Wien. Three reviews from different journals are included in the appendix to the dossier.

Electronic Publications (Invited) “Virtual” Book Bhattacharya, D. 2007. Origin and molecular evolution of the plastid. In: Understanding chloroplasts, Organizer J.K. Hoober. Henry Stewart Talks.

Invited Lectures after 2007

Plastid origin and its consequences for the eukaryote tree of life. Darwin Science Talk (Cruikshank Lecture), University of Rhode Island, Nov. 16, 2009, Kingston, RI.

Genomic approaches to understanding red tide. Darwin Public Talk (Cruikshank Lecture), University of Rhode Island, Nov. 16, 2009, Kingston, RI.

Genome based insights into the origin of the plastid in algae and plants. National Institute of Natural Resources Symposium in Honor of Darwin, Oct. 9, 2009, Seoul, South Korea.

The evolution of photosynthesis on the tree of life. PSA/ASPB, July 19, 2009, Honolulu, Hawaii. On the evolutionary origin(s) of photosynthesis, November 20, 2008, Brown & Williamson Distinguished Speaker Series, University of Louisville, Kentucky.

The genomics of extremophiles and red tides, November 21, 2008, Brown & Williamson Distinguished Speaker Series, University of Louisville, Kentucky.

Genomic methods in algal biology, June 4-7, 2008, Marine genomics exploratory workshop, Alfred Wegener Institute for Polar and Marine Research, Plenary Speaker, Bremerhaven, Germany.

Algal genomics and phylogenomics: windows into endosymbiosis and eukaryotic evolution. April 16, 2007. European Marine Genomics Exploratory Workshop, Keynote Speaker, Roscoff, France.

Unraveling the evolutionary history of eukaryotic photosynthesis through genomic and phylogenomic analyses of algae. European Phycological Congress (EPC-4), Keynote Speaker. July 26, 2007, Oviedo, Spain.

Using comparative genomics to unravel the tangled evolutionary history of photosynthesis in microbial eukaryotes. Plenary Speaker, 15th Annual International Meeting on Microbial Genomics, September 16-20, 2007, University of Maryland, College Park, MD.

Other Invited Lectures

Greening of the eukaryotic tree of life. Biological Sciences, University of Wisconsin-Milwaukee, Dec. 11, 2009, Milwaukee, WI.

Greening of the tree of life. Geosciences, Princeton University, Nov. 19, 2009, Princeton, NJ.

Hidden endosymbioses and rampant gene transfer: the impact of genomics on clarifying algal evolution. IPMB 2009, Oct. 26, 2009, St. Louis, MO.

Genomics and evolution of dinoflagellates: towards understanding the origin and spread of red tides. Bowling Green State University, Feb. 9, 2009, Bowling Green, OH.

Ancient (and a more recent) origin of photosynthesis in eukaryotes. IGERT Annual Symposium, University of Arizona, May 6, 2009, Tucson, AZ.

Endosymbiotic origin of algal plastids, July 18-22, 2009, American Society of Plant Biologists, Honolulu, Hawaii. Ancient and more recent origins of photosynthesis in eukaryotes. NSF IGERT “Deep Genomics” Symposium, May 6, 2009, University of Arizona, Tucson.

Genomics and evolution of dinoflagellates: towards understanding the origin and spread of red tides. February 9, 2009, Bowling Green State University, Bowling Green, Ohio.

Matryoshka plastids: primary, secondary, and tertiary, endosymbioses, October 20-23, 2008, Ecole Thématique, Station Biologique de Roscoff, France, CNRS Environnement et Développement Durable.

Piecing together the composition and origin of the plastid proteome in the first photosynthetic eukaryotes, June 2, 2008, American Society of Microbiology, Division X Symposium, Boston, MA.

Origin and molecular evolution of phytoplankton, June 10-19, 2008, EU Marine Genomics Summer Course in Plankton Bloom Dynamics, Alfred Wegener Institute for Polar and Marine Research, Bremerhaven, Germany.

The origin and spread of photosynthesis in the eukaryotic tree of life. Department of Ecology, Evolution, and Natural Resources, Rutgers University, February 13, 2008.

Cyanidiophyceae and Red Tides: Phylogenetic and Genomic Approaches to Understanding the Biology of Two Remarkable Groups of Algae. Institute of Marine and Coastal Sciences, Rutgers University, February 12, 2008.

(Re)Tracing the spread of photosynthesis in the eukaryotic tree of life. Scripps Institute of Oceanography-UCSD Marine Biology Seminar Series, January 11, 2008.

The complete genome sequence of the glaucophyte alga Cyanophora paradoxa. National Science Foundation, MGSP Meeting, January 12, 2008, San Diego, CA.

Algal genomics and phylogenomics: windows into endosymbiosis and eukaryotic evolution. Febraury 12, 2007. Dept. of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA.

Evolution of photosynthetic eukaryotes: life at both extremes. Montana State University, June 1, 2007, Bozeman, Montana.

Taxon breadth or phylogenetic marker breadth: two attempts at reconstructing the eukaryotic tree of life. Invited Lecture. Society for Molecular Biology and Evolution/Canadian Institute of Advanced Research, June 24-28, 2007, Halifax, Canada.

Endosymbiotic gene transfer and plastid origin in chromalveolate protists. Speaker and co-organizer, NSF Funded Mini-Symposium on chromalveolate evolution, Botanical Society of America Meeting, July 7-11, 2007, Chicago, IL.

From genomes to the environment: a coordinated effort to improve our understanding of Alexandrium and the formation of red tides. Biology Department, Woods Hole Oceanographic Institution, August 9, 2007, Woods Hole, MA.

Using Comparative genomic approaches to unravel the complex evolutionary history of chromalveolates. German Botanical Society Annual Meeting, Invited Lecture, September 3-7, 2007, Hamburg, Germany.

The need for a microbial genome database to spur evolutionary and applied research. US-EC Workshop on Cyberinfrastructure Resources for Genome-Enabled Research on Microbial Life and the Marine Environment. Washington, DC, September 9-11, 2007.

Understanding red tides using genomic methods. University of Iowa Biology Department Annual Retreat, November 10, 2007, Dubuque, IA.

Debashish Bhattacharya – Publications before 2007

Reyes-Prieto, A., J.D. Hackett, M.F. Bonaldo, M.B. Soares, and D. Bhattacharya. 2006. Cyanobacterial contribution to algal nuclear genomes is primarily limited to plastid functions. Curr. Biol. 16:2320-2325. (with accompanying commentary)
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Bhattacharya, D., and J.M. Archibald. 2006. Response to Theissen and Martin, “The difference between organelles and endosymbionts”. Curr. Biol. 16:R1017-1018. doiHwan Su Yoon, Jeremiah D. Hackett and Debashish Bhattacharya 2006. A genomic and phylogenetic perspective on endosymbiosis and algal origin.Journal of Applied Phycology (2006) 18: 475-481.
Download this publication (PDF file)|doi This is an electronic version of an article published in Journal of Phycology ©2006,
The Phycological Society of America.

Parfrey, L.W., E. Barbero, E. Lasser, M.S. Dunthorn, D. Bhattacharya, D.J. Patterson, and L.A. Katz. 2006. Evaluating support for the current classification of eukaryotic diversity. PLoS Genet. 2:e220.
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Yoon, H.S., C. Ciniglia, M. Wu , J. Comeron, G. Pinto, A. Pollio, and D. Bhattacharya. 2006. Establishment of endolithic populations of extremophilic Cyanidiales (Rhodophyta). BMC Evol. Biol. 6:78.
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Yoon, H.S., A. Reyes-Prieto, M. Melkonian, and D. Bhattacharya. 2006. Minimal plastid genome evolution in the Paulinella endosymbiont. Curr. Biol. 16:R670-R672.
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With accompanying commentary: Scientific American.com|TerraDaily.com|ScienceDaily.com|FAZ.net, Germany

Nosenko, T., K.L. Lidie, F.M. Van Dolah, E. Lindquist, J.-F. Cheng, US Department of Energy-Joint Genome Institute, and D. Bhattacharya. 2006. Chimeric plastid proteome in the Florida “Red Tide” dinoflagellate Karenia brevis.Mol. Biol. Evol. 23:2026-2038.
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Lin, S., H. Zhang, Y. Hou, and D. Bhattacharya. 2006. Development of a dinoflagellate-oriented PCR primer set leads to the detection of picoplanktonic dinoflagellates from Long Island Sound. Appl. Environ. Microbiol. 72:5626-5630.
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Reyes-Prieto, A., H.S. Yoon and D. Bhattacharya. 2006. Phylogenomics and its growing impact on algal phylogeny and evolution. Algae 21:1-10.
Download this publication (PDF file)|doiYoon, H.S., K.M. Müller, R.G. Sheath, F.D. Ott, and D. Bhattacharya. 2006. Defining the major lineages of red algae (Rhodophyta).J. Phycol. 42:482-492.
Download this publication (PDF file)|doi This is an electronic version of an article published in Journal of Phycology ©2006,
The Phycological Society of America.

Weber, A., M. Linka, and D. Bhattacharya. 2006. Single, ancient origin of a plastid metabolite translocator family in Plantae from an endomembrane-derived ancestor. Eukaryot. Cell. 5:609-612. pubmed

Li, S., T. Nosenko, J.D. Hackett, and D. Bhattacharya. 2006. Phylogenomic analysis provides evidence for the endosymbiotic transfer of red algal genes in chromalveolates. Mol. Biol. Evol. 23:663-674.
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Bhattacharya, D., and L. Katz. 2005. Workshop report – Frontiers in genomics: insights into protist evolutionary biology. J. Eukaryot. Microbiol. 52:170-172.
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Hackett, J.D., T.E. Scheetz, H.S. Yoon, M.B. Soares, M.F. Bonaldo, T.L. Casavant, and D. Bhattacharya. 2005. Insights into a dinoflagellate genome through expressed sequence tag analysis. BMC Genomics 6:80.
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Yoon, H.S., J.D. Hackett, F.M. Van Dolah, T. Nosenko, K.L. Lidie, and D. Bhattacharya. 2005. Tertiary endosymbiosis driven genome evolution in dinoflagellate algae. Mol. Biol. Evol. 22:1299-1308.
Download this publication (PDF file)|pubmedZhang, H., D. Bhattacharya, and S. Lin. 2005. Phylogeny of dinoflagellates based on mitochondrial cytochrome b and nuclear small subunit rDNA sequence comparisons.J. Phycol. 41:411-420.
Download this publication (PDF file)|doi This is an electronic version of an article published in Journal of Phycology ©2005,
The Phycological Society of America.

Bhattacharya, D., H.S. Yoon, and J.D. Hackett. 2004. Photosynthetic eukaryotes unite: endosymbiosis connects the dots. BioEssays 26:50-60.
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Ciniglia, C., H.S. Yoon, A. Pollio, G. Pinto, and D. Bhattacharya. 2004.Hidden biodiversity of the extremophilic Cyanidiales red algae. Mol. Ecol. 13:1827-1838.
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Hackett, J.D., D.M. Anderson, D. Erdner, and D. Bhattacharya. 2004. Dinoflagellates: a remarkable evolutionary experiment. Am. J. Bot. 91:1523-1534.
Download this publication (PDF file)|abstract

Hackett, J.D., H.S. Yoon, M.B. Soares, M.F. Bonaldo, T.L. Casavant, T.E. Scheetz, T. Nosenko, and D. Bhattacharya. 2004. Migration of the plastid genome to the nucleus in a peridinin dinoflagellate. Curr. Biol. 14: 213-218.
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Hagopian, J.C., M. Reis, J.P. Kitajima, D. Bhattacharya, and M.C. de Oliveira. 2004. Comparative analysis of the complete plastid genome sequence of the red alga Gracilaria tenuistipitata var. liui provides insights on the evolution of rhodoplasts and their relationship to other plastids. J. Mol. Evol. 59:464-477.
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Yoon, H.S., J.D. Hackett, C. Ciniglia, G. Pinto, and D. Bhattacharya, D. 2004. A molecular timeline for the origin of photosynthetic eukaryotes. Mol. Biol. Evol. 21:809-818.
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Bhattacharya D., Medlin LK. 2004. Dating algal origin using molecular clock methods. Protist. 2004 Mar;155(1):9-10. doi| pubmed

Hackett, J.D., L. Maranda, H.S. Yoon, and D. Bhattacharya. 2003. Phylogenetic evidence for the cryptophyte origin of the plastid of Dinophysis (Dinophysiales, Dinophyceae). J. Phycol. 39:440-448. doi

Pinto, G., Albertano, P., Ciniglia, C., Cozzolino, S., Pollio, A., Yoon, H.S., and D. Bhattacharya. 2003. Comparative approaches to the taxonomy of the genus Galdieria Merola (Cyanidiales, Rhodophyta). Crypt. Algol. 24(1):13-32.

Yoon, H.S., J. Hackett, and D. Bhattacharya. 2002.A single origin of the peridinin-, and fucoxanthin-containing plastids in dinoflagellates through tertiary endosymbiosis. Proc. Nat. Acad. Sci. USA 99:11724-11729. doi|pubmed

Yoon, H.S., J. Hackett, G. Pinto, and D. Bhattacharya. 2002.The single, ancient origin of chromist plastids. Proc. Nat. Acad. Sci. USA 99:15507-15512.
doi|pubmed|cover photo

Müller, K.M., M.C. Oliveira, R. Sheath, and D. Bhattacharya. 2001. Ribosomal DNA phylogeny of the Bangiophycidae (Rhodophyta) and the origin of secondary plastids. Am J. Bot. 88:1390-1400. abstract

Yoon, H.S, J.Y. Lee, S.M. Boo, and D. Bhattacharya. 2001. Phylogeny of Alariaceae, Laminariaceae, and Lessoniaceae (Phaeophyta) based on plastid-encoded RuBisCo spacer and nuclear-encoded ITS sequence comparisons. Mol. Phylogenet. Evol. 21:231-243. doi|pubmed

Stibitz, T., P. Keeling, and D. Bhattacharya. 2000. Symbiotic origin of a novel actin gene in the cryptophyte Pyrenomonas helgolandii. Mol. Biol. Evol. 17:1731-1738. read online|pubmed

Bhattacharya, D. 2000. A molecular phylogenetic perspective on the primary and secondary endosymbiotic origins of algal plastids. Algae 15:1-5.
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Oliveira, M., and D. Bhattacharya. 2000. Phylogeny of the Bangiophycidae (Rhodophyta) and the secondary endosymbiotic origin of algal plastids. Am. J. Bot. 87:482-492. abstract|pubmed

Bhattacharya, D., and L. Medlin. 1998. Algal phylogeny and the origin of land plants. Plant Physiol. 116: 9-15. doi

Bhattacharya, D., and L. Medlin. 1995. The phylogeny of plastids: A review based on comparisons of small subunit ribosomal RNA coding regions. J. Phycol. 31:489-498. doi

Bhattacharya, D., Helmchen, T., and M. Melkonian. 1995. Molecular evolutionary analyses of nuclear-encoded small subunit ribosomal RNA identify an independent rhizopod lineage containing the Euglyphidae and the Chlorarachniophyta. J. Euk. Microbiol. 42:65-69. doi|pubmed

Helmchen, T., D. Bhattacharya, and M. Melkonian. 1995. Analyses of ribosomal RNA sequences from glaucocystophyte cyanelles provide new insights into the evolutionary relationships of plastids. J. Mol. Evol. 41:203-210. doi|pubmed

Bhattacharya, D., T. Helmchen, C. Bibeau, and M. Melkonian. 1995. Comparisons of small subunit ribosomal RNAs reveal the evolutionary position of the Glaucocystophyta. Mol. Biol. Evol. 12:415-420. abstract|pubmed|read online

Surek, B., U. Beemelmenns, M. Melkonian, and D. Bhattacharya. 1994. Ribosomal RNA sequence comparisons demonstrate an evolutionary relationship between Zygnematales and charophytes. Pl. Syst. Evol. 191:171-181. doi

Steinkötter, J., D. Bhattacharya, I. Semmelroth, C. Bibeau, and M. Melkonian. 1994. Prasinophytes form independent lineages within the Chlorophyta: Evidence from ribosomal RNA sequence comparisons. J. Phycol. 30:340-345. doi

Bhattacharya, D., L. Medlin, P.O. Wainright, E.V. Ariztia, C. Bibeau, S.K. Stickel, and M.L. Sogin. 1992. Algae containing chlorophylls a+c are polyphyletic: Molecular evolutionary analysis of the Chromophyta. Evolution 46:1801-1817. read online

Bhattacharya, D., C. Mayes, and L.D. Druehl. 1991. Restriction endonuclease analysis of ribosomal DNA sequence variation in Laminaria (Phaeophyta). J. Phycol. 27:624-628. doi

Bhattacharya, D., H.J. Elwood, L.J. Goff, and M.L. Sogin. 1990. The phylogeny of Gracilaria lemaneiformis (Rhodophyta) based on the sequence analysis of its small subunit ribosomal RNA coding region. J. Phycol. 26:181-186. doi

Bhattacharya, D., D.L. Baillie, and L.D. Druehl. 1990. Population analysis of the kelp Costaria costata (Phaeophyta) using a polymorphic ribosomal DNA probe. Pl. Syst. Evol. 170:177-191. doi

Bhattacharya, D., and L.D. Druehl. 1989. Morphological and DNA sequence variation in the kelp Costaria costata (Phaeophyta). Mar. Biol. 102:15-23. doi|read online

Bhattacharya, D., and L.D. Druehl. 1988. Phylogenetic comparison of the small-subunit ribosomal DNA sequence of Costaria costata (Phaeophyta) with those of other algae, vascular plants and oomycetes. J. Phycol. 24:539-543. doi

Bhattacharya, D. 1985. The demography of fronds of Chondrus crispus. J. Exp. Mar. Biol. Ecol. 91:217-231. doi

Intron Evolution

Bhattacharya, D., V. Reeb, D. Simon, F. Lutzoni,. 2005.Phylogenetic analyses suggest reverse splicing spread of group I introns in fungal ribosomal DNA. BMC Evol Biol. 5:68. (Highly Accessed Article)
doi| pubmed

Haugen, P., D. Simon, and D. Bhattacharya. 2005. The natural history of group I introns. Trends in Genetics. 21:111-119.
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Simon, D., J. Moline, G. Helms, T. Friedl, and D. Bhattacharya. 2005. Divergent histories of lichen rDNA group I introns. J. Mol. Evol. 60:434-446.
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Simon, D., C. Hummel, S. Sheeley and D. Bhattacharya. 2005. Heterogeneity of intron presence or absence in rDNA genes of the lichen species Physcia aipolia and P. stellaris. Curr. Genet. 47:389-399.
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Haugen, P., and D. Bhattacharya. 2004. The spread of LAGLIDADG homing endonuclease genes in rDNA. Nucleic Acids Res. 32:2049-2057.
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Haugen, P., H.J. Runge, and D. Bhattacharya. 2004. Long-term evolution of the S788 fungal nuclear small subunit rRNA group I introns. RNA 10:1084-1096.
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Haugen, P., V. Reeb, F. Lutzoni, and D. Bhattacharya. 2004. The evolution of homing endonuclease genes and group I introns in nuclear rDNA. Mol. Biol. Evol. 21:129-140.
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Bhattacharya, D., D. Simon, J. Huang, J.J. Cannone, and R.R. Gutell. 2003. The exon context and distribution of rRNA introns. BMC Evol. Biol. 3:7.
doi|pubmed

Simon, D., D. Fewer, T. Friedl, and D. Bhattacharya. 2003. Phylogeny and self-splicing ability of the tRNA-Leu group I intron. J. Mol. Evol. 57:710-720. doi|pubmed

Bhattacharya, D., T. Friedl, and G. Helms. 2002. Vertical evolution and intragenic spread of lichen-fungal group I introns. J. Mol. Evol. 55:74-84. doi|pubmed

Bhattacharya, D., J.J. Cannone, and R.R. Gutell. 2001. Group I intron lateral transfer between red and brown algal ribosomal RNA. Curr. Genet. 40:82-90. doi|pubmed

Bhattacharya, D., and M. Oliveira. 2000. The SSU rDNA coding region of a filose amoeba contains a group I intron lacking the universally conserved G at the 3′-terminus. J. Euk. Microbiol. 47:585-589. doi|pubmed

Bhattacharya, D., F. Lutzoni, V. Reeb, D. Simon, F. Fernandez. 2000. Widespread occurrence of spliceosomal introns in the rDNA genes of ascomycetes. Mol. Biol. Evol. 17:1971-1984.
read online|pubmed

Friedl, T., A. Besendahl, P. Pfeiffer, and D. Bhattacharya. 2000. The distribution of group I introns in lichen algae suggests that lichenization facilitates intron lateral transfer. Mol. Phylogenet. Evol. 14:342-352. doi|pubmed

Besendahl, A., Y.-L. Qiu, J. Lee, J.D. Palmer, and D. Bhattacharya. 2000. The cyanobacterial origin and vertical transmission of the plastid tRNALeu group-I intron. Curr. Genet. 37:12-23. doi|pubmed

Besendahl A., and D. Bhattacharya. 1999. Evolutionary analyses of small subunit rDNA coding regions and the 1506 group I introns of the Zygnematales (Charophyceae, Streptophyta). J. Phycol. 35:560-569. doi

Bhattacharya, D. 1998. The origin and evolution of protist group I introns. Protist 149: 113-122. doi

Bhattacharya, D., T. Friedl, and S. Damberger. 1996. Nuclear-encoded rDNA group I introns: Origin and evolutionary relationships of insertion site lineages in the green algae/charophytes. Mol. Biol. Evol. 13:978-989.
pubmed|abstract|read online

Bhattacharya, D., S. Damberger, B. Surek, and M. Melkonian. 1996. Primary and secondary structure analyses of the rDNA group I introns of the Zygnematales (Charophyta). Curr. Genet. 29:282-286. doi|pubmed

Bhattacharya, D., B. Surek, M. Ruesing, and M. Melkonian. 1994. Group I introns are inherited through common ancestry in the nuclear-encoded rRNA of Zygnematales (Charophyceae). Proc. Natl. Acad. Sci. USA 91:9916-9920. abstract|pubmed

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Book Chapters

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Debashish Bhattacharya – Publications before 2007

Intron Evolution

Other Topics in Molecular Evolution