Debashish Bhattacharya

Summary

Affiliation: University of Iowa
Country: USA

Publications

  1. ncbi request reprint Actin phylogeny identifies Mesostigma viride as a flagellate ancestor of the land plants
    D Bhattacharya
    Department of Biological Sciences, University of Iowa, 239 Biology Building, Iowa City, IA 52242 1324, USA
    J Mol Evol 47:544-50. 1998
  2. ncbi request reprint Widespread occurrence of spliceosomal introns in the rDNA genes of ascomycetes
    D Bhattacharya
    Department of Biological Sciences, University of Iowa, Iowa City, 52242 1324, USA
    Mol Biol Evol 17:1971-84. 2000
  3. ncbi request reprint The SSU rDNA coding region of a filose amoeba contains a group I intron lacking the universally conserved G at the 3'-terminus
    D Bhattacharya
    University of Iowa, Department of Biological Sciences, Iowa City 52242 1324, USA
    J Eukaryot Microbiol 47:585-9. 2000
  4. ncbi request reprint Photosynthetic eukaryotes unite: endosymbiosis connects the dots
    Debashish Bhattacharya
    Department of Biological Sciences and Center for Comparative Genomics, University of Iowa, Iowa City, Iowa 52242 1324, USA
    Bioessays 26:50-60. 2004
  5. ncbi request reprint Group I intron lateral transfer between red and brown algal ribosomal RNA
    D Bhattacarya
    Department of Biological Sciences, University of Iowa, Iowa City 52242 1324, USA
    Curr Genet 40:82-90. 2001
  6. ncbi request reprint Vertical evolution and intragenic spread of lichen-fungal group I introns
    Debashish Bhattacharya
    Department of Biological Sciences and Center for Comparative Genomics, University of Iowa, 239 Biology Building, Iowa City, IA 52242 1324, USA
    J Mol Evol 55:74-84. 2002
  7. pmc The exon context and distribution of Euascomycetes rRNA spliceosomal introns
    Debashish Bhattacharya
    Department of Biological Sciences and Center for Comparative Genomics, University of Iowa, Iowa City, USA
    BMC Evol Biol 3:7. 2003
  8. ncbi request reprint Phylogenomic analysis supports the monophyly of cryptophytes and haptophytes and the association of rhizaria with chromalveolates
    Jeremiah D Hackett
    Department of Biological Sciences and Roy J Carver Center for Comparative Genomics, University of Iowa, IA, USA
    Mol Biol Evol 24:1702-13. 2007
  9. ncbi request reprint Chimeric plastid proteome in the Florida "red tide" dinoflagellate Karenia brevis
    Tetyana Nosenko
    The Roy J Carver Center for Comparative Genomics, Department of Biological Sciences, University of Iowa, IA, USA
    Mol Biol Evol 23:2026-38. 2006
  10. ncbi request reprint Tertiary endosymbiosis driven genome evolution in dinoflagellate algae
    Hwan Su Yoon
    Department of Biological Sciences and Roy J Carver Center for Comparative Genomics, University of Iowa, USA
    Mol Biol Evol 22:1299-308. 2005

Research Grants

Collaborators

Detail Information

Publications50

  1. ncbi request reprint Actin phylogeny identifies Mesostigma viride as a flagellate ancestor of the land plants
    D Bhattacharya
    Department of Biological Sciences, University of Iowa, 239 Biology Building, Iowa City, IA 52242 1324, USA
    J Mol Evol 47:544-50. 1998
    ..This result is supported by the existence of two conserved actin-coding region introns (positions 20-3, 152-1), and one intron in the 5'-untranslated region of the actin gene shared by Mesostigma and the embryophytes...
  2. ncbi request reprint Widespread occurrence of spliceosomal introns in the rDNA genes of ascomycetes
    D Bhattacharya
    Department of Biological Sciences, University of Iowa, Iowa City, 52242 1324, USA
    Mol Biol Evol 17:1971-84. 2000
    ..The clustered positions of spliceosomal introns on secondary structures suggest that particular rRNA regions are preferred sites for insertion through reverse-splicing...
  3. ncbi request reprint The SSU rDNA coding region of a filose amoeba contains a group I intron lacking the universally conserved G at the 3'-terminus
    D Bhattacharya
    University of Iowa, Department of Biological Sciences, Iowa City 52242 1324, USA
    J Eukaryot Microbiol 47:585-9. 2000
    ..The rDNA of N-Por contained a group I intron at the conserved 943 position that remarkably, had a U at the 3'-terminus rather than the universally conserved G...
  4. ncbi request reprint Photosynthetic eukaryotes unite: endosymbiosis connects the dots
    Debashish Bhattacharya
    Department of Biological Sciences and Center for Comparative Genomics, University of Iowa, Iowa City, Iowa 52242 1324, USA
    Bioessays 26:50-60. 2004
    ..This area of research has advanced rapidly and long-standing issues such as the chromalveolate hypothesis and the extent of endosymbiotic gene transfer have recently been clarified...
  5. ncbi request reprint Group I intron lateral transfer between red and brown algal ribosomal RNA
    D Bhattacarya
    Department of Biological Sciences, University of Iowa, Iowa City 52242 1324, USA
    Curr Genet 40:82-90. 2001
    ..The highly conserved primary and secondary structure of the extra P5b helix suggests that it is important, although its specific function is unknown. Our study attempts to understand the origin and movement of these IC1 introns...
  6. ncbi request reprint Vertical evolution and intragenic spread of lichen-fungal group I introns
    Debashish Bhattacharya
    Department of Biological Sciences and Center for Comparative Genomics, University of Iowa, 239 Biology Building, Iowa City, IA 52242 1324, USA
    J Mol Evol 55:74-84. 2002
    ..Detailed phylogenetic analyses of the introns and host cells are required, therefore, to distinguish this scenario from the alternative hypothesis of widespread and independent intron gains in the different lichen-fungal lineages...
  7. pmc The exon context and distribution of Euascomycetes rRNA spliceosomal introns
    Debashish Bhattacharya
    Department of Biological Sciences and Center for Comparative Genomics, University of Iowa, Iowa City, USA
    BMC Evol Biol 3:7. 2003
    ..We have studied spliceosomal introns in the ribosomal (r)RNA of fungi to discover the forces that guide their insertion and fixation...
  8. ncbi request reprint Phylogenomic analysis supports the monophyly of cryptophytes and haptophytes and the association of rhizaria with chromalveolates
    Jeremiah D Hackett
    Department of Biological Sciences and Roy J Carver Center for Comparative Genomics, University of Iowa, IA, USA
    Mol Biol Evol 24:1702-13. 2007
    ..The association of the two Rhizaria with chromalveolates is supported by the approximately unbiased (AU)-test and when the fastest evolving amino acid sites are removed from the 16-protein alignment...
  9. ncbi request reprint Chimeric plastid proteome in the Florida "red tide" dinoflagellate Karenia brevis
    Tetyana Nosenko
    The Roy J Carver Center for Comparative Genomics, Department of Biological Sciences, University of Iowa, IA, USA
    Mol Biol Evol 23:2026-38. 2006
    ..One of these genes is an electron transfer protein (plastocyanin) of green algal origin in K. brevis that likely allows this species to thrive under conditions of iron depletion...
  10. ncbi request reprint Tertiary endosymbiosis driven genome evolution in dinoflagellate algae
    Hwan Su Yoon
    Department of Biological Sciences and Roy J Carver Center for Comparative Genomics, University of Iowa, USA
    Mol Biol Evol 22:1299-308. 2005
    ..These results underline the remarkable ability of dinoflagellates to remodel their genomes through endosymbiosis and the considerable impact of this process on cell evolution...
  11. pmc Phylogenetic analyses suggest reverse splicing spread of group I introns in fungal ribosomal DNA
    Debashish Bhattacharya
    Department of Biological Sciences, Roy J Carver Center for Comparative Genomics, University of Iowa, Iowa City, IA 52242 1324, USA
    BMC Evol Biol 5:68. 2005
    ....
  12. ncbi request reprint A phylogenomic approach for studying plastid endosymbiosis
    Ahmed Moustafa
    Interdisciplinary Genetics Program, University of Iowa, Iowa City, IA 52242, USA
    Genome Inform 21:165-76. 2008
    ..This assertion awaits experimental validation. Whereas the current study is focused within the context of secondary endosymbiosis, our approach can be applied to large-scale detection of gene transfer in any system...
  13. pmc Insights into a dinoflagellate genome through expressed sequence tag analysis
    Jeremiah D Hackett
    Department of Biological Sciences and Roy J, Carver Center for Comparative Genomics, University of Iowa, Iowa City, IA 52242, USA
    BMC Genomics 6:80. 2005
    ..Previous analyses of these data have clarified plastid origin and here we study the gene content, annotate the ESTs, and analyze the genes that are putatively involved in DNA packaging...
  14. pmc Cyanobacterial ribosomal RNA genes with multiple, endonuclease-encoding group I introns
    Peik Haugen
    Department of Biological Sciences and Roy J, Carver Center for Comparative Genomics, University of Iowa, 446 Biology Building, Iowa City, IA 52242, USA
    BMC Evol Biol 7:159. 2007
    ..Group I introns are common in fungal and protist nuclear ribosomal RNA genes and in organellar genomes. In contrast, they are rare in all other organisms and genomes, including bacteria...
  15. ncbi request reprint A molecular timeline for the origin of photosynthetic eukaryotes
    Hwan Su Yoon
    Department of Biological Sciences and Center for Comparative Genomics, University of Iowa, Iowa, USA
    Mol Biol Evol 21:809-18. 2004
    ..e., acritarchs) from the early Mesoproterozoic (1,500 MYA) and with a major eukaryotic diversification in the very late Mesoproterozoic and Neoproterozoic, provide a molecular timeline for understanding algal evolution...
  16. pmc Host origin of plastid solute transporters in the first photosynthetic eukaryotes
    Heather M Tyra
    Department of Biological Sciences and Roy J Carver Center for Comparative Genomics, 446 Biology Building, University of Iowa, Iowa City, IA 52242 1324, USA
    Genome Biol 8:R212. 2007
    ..We postulate that the re-targeting of existing host solute transporters to the plastid fore-runner was critical for the early success of the primary endosymbiosis, allowing the host to harvest endosymbiont primary production...
  17. pmc Origin of saxitoxin biosynthetic genes in cyanobacteria
    Ahmed Moustafa
    Interdisciplinary Program in Genetics, University of Iowa, Iowa City, IA, USA
    PLoS ONE 4:e5758. 2009
    ..Here we focus on saxitoxin-producing cyanobacteria and their non-toxic sisters to elucidate the origin of genes involved in the putative STX biosynthetic pathway...
  18. doi request reprint Genomic footprints of a cryptic plastid endosymbiosis in diatoms
    Ahmed Moustafa
    Interdisciplinary Program in Genetics, University of Iowa, Iowa City, IA 52242, USA
    Science 324:1724-6. 2009
    ..Chromalveolates appear to have recruited genes from the two major existing algal groups to forge a highly successful, species-rich protist lineage...
  19. pmc The single, ancient origin of chromist plastids
    Hwan Su Yoon
    Department of Biological Sciences and Center for Comparative Genomics, University of Iowa, 210 Biology Building, Iowa City 52242, USA
    Proc Natl Acad Sci U S A 99:15507-12. 2002
    ..This finding is consistent with Chromista monophyly and implicates secondary endosymbiosis as an important force in generating eukaryotic biodiversity...
  20. pmc Broadly sampled multigene trees of eukaryotes
    Hwan Su Yoon
    Department of Biological Sciences, Smith College, Northampton, MA 01063, USA
    BMC Evol Biol 8:14. 2008
    ....
  21. pmc Multiple genes of apparent algal origin suggest ciliates may once have been photosynthetic
    Adrian Reyes-Prieto
    Department of Biological Sciences and Roy J Carver Center for Comparative Genomics, University of Iowa, Iowa City, Iowa 52242 1324, USA
    Curr Biol 18:956-62. 2008
    ....
  22. doi request reprint Interrelationships of chromalveolates within a broadly sampled tree of photosynthetic protists
    Valérie C Reeb
    Department of Biology and Roy J Carver Center for Comparative Genomics, University of Iowa, Iowa City, IA 52242, USA
    Mol Phylogenet Evol 53:202-11. 2009
    ..We assessed the Plastidophila hypothesis that is based on EF2 data and suggest this grouping may be explained by horizontal gene transfers involving the EF2 gene rather than indicating host relationships...
  23. pmc Single, ancient origin of a plastid metabolite translocator family in Plantae from an endomembrane-derived ancestor
    Andreas P M Weber
    Department of Biological Sciences and Roy J Carver Center for Comparative Genomics, University of Iowa, 446 Biology Building, Iowa City, IA 52242 1324, USA
    Eukaryot Cell 5:609-12. 2006
    ..Red algal secondary endosymbiosis has spread a translocator gene into the ancestor of the "chromalveolate" protists, where it has diversified into a novel clade of proteins...
  24. ncbi request reprint Cyanobacterial contribution to algal nuclear genomes is primarily limited to plastid functions
    Adrian Reyes-Prieto
    Department of Biological Sciences and Roy J Carver Center for Comparative Genomics, University of Iowa, 446 Biology Building, Iowa City, Iowa 52242, USA
    Curr Biol 16:2320-5. 2006
    ..Our data indicate that unlike plants, early-diverging algal groups appear to retain a smaller number of endosymbiont genes in their nucleus, with only a minor proportion of these recruited for nonplastid functions...
  25. ncbi request reprint Phylogenomic analysis identifies red algal genes of endosymbiotic origin in the chromalveolates
    Shenglan Li
    Department of Biological Sciences and Roy J Carver Center for Comparative Genomics, University of Iowa, USA
    Mol Biol Evol 23:663-74. 2006
    ..Our data demonstrate the existence of multiple red algal genes that are shared among different chromalveolates, suggesting that at least a subset of this group may share a common origin...
  26. ncbi request reprint Divergent histories of rDNA group I introns in the lichen family Physciaceae
    Dawn Simon
    Department of Biological Sciences and the Roy J Carver Center for Comparative Genomics, University of Iowa, 312 Biology Building, Iowa City, IA, 52242 1324, USA
    J Mol Evol 60:434-46. 2005
    ..In contrast, we suggest that the LSU rRNA may have fewer acceptable positions and therefore intron spread is limited in this gene...
  27. pmc PhyloSort: a user-friendly phylogenetic sorting tool and its application to estimating the cyanobacterial contribution to the nuclear genome of Chlamydomonas
    Ahmed Moustafa
    University of Iowa, Interdisciplinary Program in Genetics, 456 Biology Building, Iowa City, Iowa 52242, USA
    BMC Evol Biol 8:6. 2008
    ..To facilitate this procedure, we developed PhyloSort to rapidly search large collection of trees for monophyletic relationships. Here we present PhyloSort and its application to estimating EGT in Chlamydomonas...
  28. pmc Evidence of a chimeric genome in the cyanobacterial ancestor of plastids
    Jeferson Gross
    University of Iowa, Department of Biological Sciences and the Roy J, Carver Center for Comparative Genomics, 446 Biology Building, Iowa City, Iowa 52242, USA
    BMC Evol Biol 8:117. 2008
    ..Genetic remnants of the endosymbiont are still preserved in plastids as a highly reduced chromosome encoding 54 - 264 genes. These data provide an ideal target to assess genome chimericism in an ancient cyanobacterial lineage...
  29. ncbi request reprint Phylogeny and self-splicing ability of the plastid tRNA-Leu group I Intron
    Dawn Simon
    Department of Biological Sciences and Center for Comparative Genomics, University of Iowa, 210 Biology Building, Iowa City, IA 52242 1324, USA
    J Mol Evol 57:710-20. 2003
    ..The host dependence likely evolved once in the common ancestor of land plants. In all other plastid lineages, these ribozymes could either self-splice or complete only the first step of autocatalysis...
  30. ncbi request reprint Phylogeny of Calvin cycle enzymes supports Plantae monophyly
    Adrian Reyes-Prieto
    University of Iowa, Department of Biological Sciences and the Roy J Carver Center for Comparative Genomics, 446 Biology Building, Iowa City, IA 52242, USA
    Mol Phylogenet Evol 45:384-91. 2007
  31. ncbi request reprint Migration of the plastid genome to the nucleus in a peridinin dinoflagellate
    Jeremiah D Hackett
    Department of Biological Sciences and Center for Comparative Genomics, The University of Iowa, Iowa City, IA 52242, USA
    Curr Biol 14:213-8. 2004
    ..tamarense. The plastid-targeted genes have red and green algal origins. These results highlight the unique position of dinoflagellates as the champions of plastid gene transfer to the nucleus among photosynthetic eukaryotes...
  32. pmc Establishment of endolithic populations of extremophilic Cyanidiales (Rhodophyta)
    Hwan Su Yoon
    Department of Biological Sciences and Roy J, Carver Center for Comparative Genomics, University of Iowa, Iowa City, Iowa 52242, USA
    BMC Evol Biol 6:78. 2006
    ..Here, we conducted an environmental PCR survey of another extreme environment in Tuscany, Italy and contrasted Cyanidiales population structure at endolithic and interlithic habitats in Naples and Tuscany...
  33. doi request reprint Revaluating the evolution of the Toc and Tic protein translocons
    Jeferson Gross
    University of Iowa, Department of Biology and the Roy J Carver Center for Comparative Genomics, 446 Biology Building, Iowa City, IA 52242, USA
    Trends Plant Sci 14:13-20. 2009
    ..Multifunctionality seems to be a hallmark of the Tic complex, in which protein import is integrated with a broad array of plastid processes...
  34. pmc Long-term evolution of the S788 fungal nuclear small subunit rRNA group I introns
    Peik Haugen
    Department of Biological Sciences and Center for Comparative Genomics, University of Iowa, 210 Biology Building, Iowa City, IA 52242 1324, USA
    RNA 10:1084-96. 2004
    ..In summary, we demonstrate one possible fate of vertically inherited group I introns, the loss of secondary structure elements, lessened selective constraints in the intron core, and ultimately, dependence on host-mediated splicing...
  35. doi request reprint Mitochondrial and plastid evolution in eukaryotes: an outsiders' perspective
    Jeferson Gross
    Department of Biology, Roy J Carver Center for Comparative Genomics, University of Iowa, 446 Biology Building, Iowa City, Iowa 52242, USA
    Nat Rev Genet 10:495-505. 2009
    ..Such a convergent trajectory for mitochondrion and plastid establishment suggests a novel paradigm for organelle evolution that affects theories of eukaryogenesis...
  36. ncbi request reprint The evolution of homing endonuclease genes and group I introns in nuclear rDNA
    Peik Haugen
    Department of Biological Sciences and Center for Comparative Genomics, University of Iowa, USA
    Mol Biol Evol 21:129-40. 2004
    ..The S943 HEG is shown to be widely distributed as functional, inactivated, or remnant ORFs in S943 introns...
  37. ncbi request reprint The origin and establishment of the plastid in algae and plants
    Adrian Reyes-Prieto
    Department of Biological Sciences and Roy J Carver Center for Comparative Genomics, University of Iowa, Iowa City, IA 52242 1324, USA
    Annu Rev Genet 41:147-68. 2007
    ..Here we review these aspects of plastid evolution with a focus on understanding early events in plastid endosymbiosis...
  38. doi request reprint Good to the bone: microbial community thrives within bone cavities of a bison carcass at Yellowstone National Park
    Valérie Reeb
    Department of Biology, University of Iowa, Iowa City, IA 52242, USA
    Environ Microbiol 13:2403-15. 2011
    ..Rather these taxa and the bacteria appear to be opportunists that have colonized an isolated oasis that provides nutrients and protection from desiccation and UV radiation...
  39. ncbi request reprint The natural history of group I introns
    Peik Haugen
    Department of Biological Sciences and Roy J Carver Center for Comparative Genomics, University of Iowa, 312 Biology Building, Iowa City, IA 52242 1324, USA
    Trends Genet 21:111-9. 2005
    ....
  40. ncbi request reprint How do endosymbionts become organelles? Understanding early events in plastid evolution
    Debashish Bhattacharya
    Department of Biological Sciences and the Roy J Carver Center for Comparative Genomics, University of Iowa, Iowa City, IA 52242, USA
    Bioessays 29:1239-46. 2007
    ..Here we discuss the use of these terms in light of new data in order to highlight the unique aspects of plastids and mitochondria and underscore their central role in eukaryotic evolution...
  41. ncbi request reprint Evolution of a novel function: nutritive milk in the viviparous cockroach, Diploptera punctata
    Anna Williford
    Department of Biological Sciences, University of Iowa, Iowa City, Iowa 52242, USA
    Evol Dev 6:67-77. 2004
    ..The shared exon/intron structure of one of the Milk loci with lipocalin genes further supports a close evolutionary relationship between these sequences...
  42. pmc Horizontal gene transfer in chromalveolates
    Tetyana Nosenko
    University of Iowa, Department of Biological Sciences and the Roy J, Carver Center for Comparative Genomics, 446 Biology Building, Iowa City, Iowa 52242, USA
    BMC Evol Biol 7:173. 2007
    ....
  43. pmc A single origin of the peridinin- and fucoxanthin-containing plastids in dinoflagellates through tertiary endosymbiosis
    Hwan Su Yoon
    Department of Biological Sciences and Center for Comparative Genomics, University of Iowa, Iowa City, IA 85542 1324, USA
    Proc Natl Acad Sci U S A 99:11724-9. 2002
    ..Our findings imply that the presence of chlorophylls c(1) + c(2) and fucoxanthin, and the Form I rbcL gene are in fact the primitive (not derived, as widely believed) condition in dinoflagellates...
  44. ncbi request reprint Heterogeneity of intron presence or absence in rDNA genes of the lichen species Physcia aipolia and P. stellaris
    Dawn M Simon
    Department of Biological Sciences and Roy J Carver Center for Comparative Genomics, University of Iowa, 312 Biology Building, Iowa City, IA 52242 1324, USA
    Curr Genet 47:389-99. 2005
    ..Our results suggest that considerable care must be taken when interpreting intron presence/absence in lichen rDNA, an observation that has general implications for the study of rDNA intron evolution...
  45. pmc Chlamydiae has contributed at least 55 genes to Plantae with predominantly plastid functions
    Ahmed Moustafa
    Interdisciplinary Program in Genetics, University of Iowa, Iowa City, Iowa, United States of America
    PLoS ONE 3:e2205. 2008
    ..Despite the critical importance of primary plastid endosymbiosis, its ancient derivation has left behind very few "footprints" of early key events in organelle genesis...
  46. pmc The spread of LAGLIDADG homing endonuclease genes in rDNA
    Peik Haugen
    Department of Biological Sciences and Center for Comparative Genomics, University of Iowa, 210 Old Biology Building, Iowa City, IA 52242 1324, USA
    Nucleic Acids Res 32:2049-57. 2004
    ..Our data also suggest that a subset of the double-motif HEGs in rDNA originated from the duplication and fusion of a single-motif HEG encoded by present-day ribozymes in LSU rDNA...
  47. pmc Emergence of Xin demarcates a key innovation in heart evolution
    Shaun E Grosskurth
    Department of Biology, University of Iowa, Iowa City, Iowa, United States of America
    PLoS ONE 3:e2857. 2008
    ..We postulate that the emergence of the Xin paralogs and their functional differentiation may have played a key role in the evolutionary development of the heart...
  48. ncbi request reprint Frontiers in genomics: insights into protist evolutionary biology, University of Iowa, May 19-21, 2004
    Debashish Bhattacharya
    Department of Biological Sciences and Roy J Carver Center for Comparative Genomics, 312 Biology Building, University of Iowa, Iowa City, Iowa 52242, USA
    J Eukaryot Microbiol 52:170-2. 2005
    ..The findings of the workshop are presented here and in a white paper that provide a set of guidelines for organizing the protist community and for planning and executing a protist genome project...
  49. ncbi request reprint Extensive ribosomal DNA genic variation in the columnar cactus Lophocereus
    S Hartmann
    University of Iowa, Department of Biological Sciences, 239 Biology Building, Iowa City, IA 52242-1324, USA
    J Mol Evol 53:124-34. 2001
    ..8S rDNA coding region in the Functional operon in comparison to Pereskiopsis porteri (Cactaceae) and Portulaca molokiniensis (Portulacaceae) with Silene dioica and Spinacia oleracea as the outgroups...
  50. pmc Adenosine deamination in human transcripts generates novel microRNA binding sites
    Glen M Borchert
    Department of Internal Medicine, University of Iowa, Iowa City, IA 52242, USA
    Hum Mol Genet 18:4801-7. 2009
    ..Our results suggest the creation of miRNA regulatory sites as a novel function for ADAR activity. Consequently, many miRNA target sites may only be identifiable through examining expressed sequences...

Research Grants1