Debashish Bhattacharya

..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...

..The clustered positions of spliceosomal introns on secondary structures suggest that particular rRNA regions are preferred sites for insertion through reverse-splicing...

..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...

..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...

..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...

..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...

..We have studied spliceosomal introns in the ribosomal (r)RNA of fungi to discover the forces that guide their insertion and fixation...

..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...

..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...

..These results underline the remarkable ability of dinoflagellates to remodel their genomes through endosymbiosis and the considerable impact of this process on cell evolution...

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..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...

..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...

..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...

..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...

..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...

..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...

..Chromalveolates appear to have recruited genes from the two major existing algal groups to forge a highly successful, species-rich protist lineage...

..This finding is consistent with Chromista monophyly and implicates secondary endosymbiosis as an important force in generating eukaryotic biodiversity...

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..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...

..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...

..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...

..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...

..In contrast, we suggest that the LSU rRNA may have fewer acceptable positions and therefore intron spread is limited in this gene...

..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...

..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...

..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...

..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...

..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...

..Multifunctionality seems to be a hallmark of the Tic complex, in which protein import is integrated with a broad array of plastid processes...

..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...

..Such a convergent trajectory for mitochondrion and plastid establishment suggests a novel paradigm for organelle evolution that affects theories of eukaryogenesis...

..The S943 HEG is shown to be widely distributed as functional, inactivated, or remnant ORFs in S943 introns...

..Here we review these aspects of plastid evolution with a focus on understanding early events in plastid endosymbiosis...

..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...

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..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...

..The shared exon/intron structure of one of the Milk loci with lipocalin genes further supports a close evolutionary relationship between these sequences...

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..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...

..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...

..Despite the critical importance of primary plastid endosymbiosis, its ancient derivation has left behind very few "footprints" of early key events in organelle genesis...

..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...

..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...

..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...

..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...

..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...

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