Bodo saltans
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ABSTRACT:
PROVIDER: PRJNA1133846 | ENA |
REPOSITORIES: ENA
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Project description:Abstract: The Kinetoplastida (Euglenozoa) are unicellular flagellates that include the trypanosomatid parasites, most notably Trypanosoma brucei, T.cruzi and Leishmania spp. These organisms cause substantial mortality and morbidity in humans and their livestock worldwide as the causative agents of African sleeping sickness, Chagas disease and leishmaniasis respectively. Draft genome sequences are available for several species of both Trypanosoma and Leishmania. Bodo saltans is a free-living heterotroph found worldwide in freshwater and marine habitats, and it is among the closest bodonid relatives of the trypanosomatids. The purpose of a B. saltans genome sequence is to provide an 'out-group' for comparative genomic analysis of the trypanosomatid parasites. It will provide a model of the ancestral trypanosomatid to distinguish those derived parts of the parasite genomes (i.e., unique trypanosomatid adaptations) from those which are a legacy of the free-living ancestor. To aid annotation of the B.saltans genome sequence, total genomic RNA was extracted on four occasions from the total cellular mass of 160ml of B.saltans cell culture, for the purposes of transcription profiling by high throughput sequencing. Cells were unmodified. B.saltans cells were grown in water at 4oC. Total genomic RNA was extracted from a cell pellet using TRIZOL reagent and ethanol precipitated. Poly A+ mRNA was purified from total RNA using oligo dT dyna bead selection and libraries were created using the Illumina RNA-seq protocol. The samples were sequenced on an Illumina HiSeq 2000. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/
2012-07-13 | E-ERAD-88 | biostudies-arrayexpress
Project description:We have sequenced, assembled and annotated the genome of Bodo saltans strain Lake Konstanz
| PRJEB10421 | ENA
Project description:Pedobacter saltans DSM 12145 genome sequencing
| PRJNA49337 | ENA
Project description:The evolution of parasitism is a recurring event in the history of life and a core question in evolutionary biology. Trypanosomatids are important parasites including the human pathogens Trypanosoma brucei, T. cruzi and Leishmania spp., which have evolved complex life cycles to exploit a series of defined host environments after diverging from free-living, phagotrophic bodonids. However, the origins of genomic adaptations for transmission, disease and pathogenesis remain obscure because there has been no genomic comparison of parasitic and free-living species. Addressing this absence, we have produced a genome sequence for Bodo saltans, the closest known non-parasitic relative of trypanosomatids. Here we show how genomic reduction and innovation contributed to the character of trypanosomatid genomes. We find that despite a genetic ‘streamlining’ of diverse physiological functions, including macromolecular degradation and cellular homeostasis, the origin of trypanosomatid parasitism did not lead to a substantial reduction in genome function. Instead, we observe dramatic elaboration of gene families that facilitate host-parasite interactions and pathogenesis. We also show how parasite-specific proteins that characterize the enigmatic cell surfaces of Trypanosoma and Leishmania were derived from the same ancestral proteins, still represented in B. saltans. Our new evidence distinguishes adaptive innovations of trypanosomatids that post-date their parasitic origin from essentially kinetoplastid legacies of a free-living past. It shows that when the labile environment of a phagotrophic ancestor was replaced by the defined conditions of their various hosts, trypanosomatid physiology was reoriented towards host interaction, and ancestral structures were radically transformed to provide adaptations for obligate parasitism.
2018-10-24 | PXD002628 | Pride
Project description:Pedobacter saltans Steyn et al. 1998 is one of currently 32 species in the genus Pedobacter within the family Sphingobacteriaceae. The species is of interest for its isolated location in the tree of life. Like other members of the genus P. saltans is heparinolytic. Cells of P. saltans show a peculiar gliding, dancing motility and can be distinguished from other Pedobacter strains by their ability to utilize glycerol and the inability to assimilate D-cellobiose. The genome presented here is only the second completed genome sequence of a type strain from a member of the family Sphingobacteriaceae to be published. The 4,635,236 bp long genome with its 3,854 protein-coding and 67 RNA genes consists of one chromosome, and is a part of the Genomic Encyclopedia of Bacteria and Archaea project.
| S-EPMC3236043 | biostudies-literature
Project description:In parasitic kinetoplastid protozoa, mitochondrial (mt) mRNAs are post-transcriptionally edited by insertion and deletion of uridylate residues, the information being provided by guide (g) RNAs. In order to further explore the role and evolutionary history of this process, we searched for editing in mt RNAs of the free-living bodonid Bodo saltans. We found extensive editing in the transcript for NADH dehydrogenase (ND) subunit 5, which is unedited in trypanosomatids. In contrast, B.saltans cytochrome c oxidase (cox) subunit 2 and maxicircle unidentified reading frame (MURF) 2 RNAs display limited editing in the same regions as their trypanosomatid counterparts. A putative intramolecular cox2 gRNA and the gene for gMURF2-I directing the insertion of only one U in the 5' editing domain of MURF2 RNA, are conserved in B.saltans. This lends (further) evolutionary support to the proposed role of these sequences as gRNAs. Phylogenetic analysis showed that B.saltans is more closely related to trypanosomatids than the cryptobiids Trypanoplasma borreli and Cryptobia helicis, in line with the trypanosomatid-like cox2 and MURF2 RNA editing patterns. Nevertheless, other features like the apparent absence of a catenated mtDNA network, are shared with bodonid and cryptobiid species. ND5 RNA editing may represent yet another example of editing 'on the way out' during kinetoplastid evolution, but in view of the fact that cox2 RNA is unedited in T. borreli and C.helicis, we infer that the editing of this RNA may have arisen relatively recently. Our results provide the first examples of RNA editing in a free-living kinetoplastid, indicating that there is no direct link between U-insertion/deletion editing and a parasitic lifestyle.
| S-EPMC147379 | biostudies-other