Debashish Bhattacharya - Publications before 2007

Publications 2007 to present | Publications by D. Bhattacharya listed in PubMed after 2000 | Downloadable publications

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.doi

Hwan 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.
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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.
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Yoon, 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.
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Zhang, 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.
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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.
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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

Other Topics in Molecular Evolution

Williford, A., B. Stay, and D. Bhattacharya. 2004. Evolution of a novel function: nutritive milk in the viviparous cockroach Diploptera punctata. Evol. Dev. 6:67-77.
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Hartmann, S., J.D. Nason, and D. Bhattacharya. 2002. Phylogenetic origins of Lophocereus (Cactaceae) and the senita cactus – senita moth pollination mutualism. Am. J. Bot. 89:1085-1092.abstract|read online

Hartmann, S., J. Nason, and D. Bhattacharya. 2001.Extensive genic variation in rDNA paralogs in the columnar cactus Lophocereus. J. Mol. Evol. 53:124-134. pubmed

Bhattacharya, D., J. Aubry, E. Twait, S. Jurk. 2000. Actin gene duplication and the evolution of morphological complexity in land plants. J. Phycol. 36:813-820.doi

Karabinos, A, and D. Bhattacharya. 2000. Molecular evolution of calmodulin and calmodulin-like genes in the cephalochordate Branchiostoma. J. Mol. Evol. 51:141-148.pubmed

Albert, S., D. Bhattacharya, J. Klaudiny, J. Schmitzova, and J. Simuth. 1999. The Family of Major Royal Jelly Proteins and Its Evolution. J. Mol. Evol. 49:290-297.doi|pubmed

An, S.S, B. Möpps, K. Weber, and D. Bhattacharya. 1999.The origin and evolution of green algal and plant actins. Mol. Biol. Evol. 16:275-285.abstract|pubmed

Karabinos, A., D. Bhattacharya, H.D. Kratzin, and N. Hilschmann. 1998. Origin of the NEFA and Nuc signal sequences. J. Mol. Evol. 46: 327-333.doi|pubmed

Bhattacharya, D., S.S. An, K. Weber, and W. Berning-Koch. 1998. Actin phylogeny identifies Mesostigma viride as a flagellate ancestor of the land plants. J. Mol. Evol. 47:544-550.doi|pubmed

Bhattacharya, D., and K. Weber. 1997. The actin gene of the glaucocystophyte Cyanophora paradoxa: analysis of the coding region and introns and an actin phylogeny of eukaryotes. Curr. Genet. 31:439-446.pubmed

Bhattacharya, D. 1996. Analysis of the distribution of bootstrap tree lengths using the maximum parsimony method. Mol. Phylogenet. Evol. 6:339-350.doi|pubmed

Karabinos, A., D. Bhattacharya, H.D. Kratzin, S. Barnikol-Watanabe, and N. Hilschmann. 1996. The divergent domains of the NEFA and nucleobindin proteins are derived from an EF-Hand ancestor. Mol. Biol. Evol. 13:990-998.abstract|pubmed

Bhattacharya, D., and J. Ehlting. 1995. Actin coding regions: Gene family evolution and use as a phylogenetic marker. Archiv Protistenkunde. 145:155-164.

Bhattacharya, D., and S.K. Stickel. 1994. Sequence analysis of duplicated actin genes in Lagenidium giganteum and Pythium irregulare (Oomycota). J. Mol. Evol. 39:56-61.doi|pubmed

Bhattacharya, D., S.K. Stickel, and M.L. Sogin. 1993. Isolation and molecular phylogenetic analysis of actin coding regions from the prymnesiophyte alga, Emiliania huxleyi, using reverse transcriptase and PCR methods. Mol. Biol. Evol. 10:689-703.pubmed

Bhattacharya, D., J. Steinkötter, and M. Melkonian. 1993. Molecular cloning and evolutionary analysis of the calcium-modulated contractile protein, centrin, in green algae and land plants. Pl. Mol. Biol. 23:1243-1254.doi|pubmed

Bhattacharya, D., S.K. Stickel, and M.L. Sogin. 1991. Molecular phylogenetic analysis of actin genic regions from Achlya bisexualis (Oomycota) and Costaria costata (Chromophyta). J. Mol. Evol. 33:525-536.doi|pubmed