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Transcriptome characterization via 454 pyrosequencing of the annelid Pristina leidyi, an emerging model for studying the evolution of regeneration

dc.contributor.authorNyberg, Kevin G.
dc.contributor.authorConte, Matthew A.
dc.contributor.authorKostyun, Jamie L.
dc.contributor.authorForde, Alison
dc.contributor.authorBely, Alexandra E.
dc.date.accessioned2013-01-07T19:36:13Z
dc.date.available2013-01-07T19:36:13Z
dc.date.issued2012-06-29
dc.identifier.citationNyberg, K.G., Conte, M.A., Kostyun, J.L. et al. Transcriptome characterization via 454 pyrosequencing of the annelid Pristina leidyi, an emerging model for studying the evolution of regeneration. BMC Genomics 13, 287 (2012).en_US
dc.identifier.urihttp://hdl.handle.net/1903/13342
dc.description.abstractBackground: The naid annelids contain a number of species that vary in their ability to regenerate lost body parts, making them excellent candidates for evolution of regeneration studies. However, scant sequence data exists to facilitate such studies. We constructed a cDNA library from the naid Pristina leidyi, a species that is highly regenerative and also reproduces asexually by fission, using material from a range of regeneration and fission stages for our library. We then sequenced the transcriptome of P. leidyi using 454 technology. Results: 454 sequencing produced 1,550,174 reads with an average read length of 376 nucleotides. Assembly of 454 sequence reads resulted in 64,522 isogroups and 46,679 singletons for a total of 111,201 unigenes in this transcriptome. We estimate that over 95% of the transcripts in our library are present in our transcriptome. 17.7% of isogroups had significant BLAST hits to the UniProt database and these include putative homologs of a number of genes relevant to regeneration research. Although many sequences are incomplete, the mean sequence length of transcripts (isotigs) is 707 nucleotides. Thus, many sequences are large enough to be immediately useful for downstream applications such as gene expression analyses. Using in situ hybridization, we show that two Wnt/β-catenin pathway genes (homologs of frizzled and β-catenin) present in our transcriptome are expressed in the regeneration blastema of P. leidyi, demonstrating the usefulness of this resource for regeneration research. Conclusions: 454 sequencing is a rapid and efficient approach for identifying large numbers of genes in an organism that lacks a sequenced genome. This transcriptome dataset will be a valuable resource for molecular analyses of regeneration in P. leidyi and will serve as a starting point for comparisons to non-regenerating naids. It also contributes significantly to the still limited genomic resources available for annelids and lophotrochozoans more generally.en_US
dc.description.urihttps://doi.org/10.1186/1471-2164-13-287
dc.language.isoen_USen_US
dc.subjectTranscriptomeen_US
dc.subject454 pyrosequencingen_US
dc.subjectRegenerationen_US
dc.subjectEvolutionen_US
dc.subjectAsexual reproductionen_US
dc.subjectFissionen_US
dc.subjectAnneliden_US
dc.subjectPristina leidyien_US
dc.subjectCell signalingen_US
dc.subjectWnt signalingen_US
dc.titleTranscriptome characterization via 454 pyrosequencing of the annelid Pristina leidyi, an emerging model for studying the evolution of regenerationen_US
dc.typeArticleen_US
dc.relation.isAvailableAtCollege of Computer, Mathematical & Physical Sciencesen_us
dc.relation.isAvailableAtDigital Repository at the University of Marylanden_us
dc.relation.isAvailableAtBiologyen_us
dc.relation.isAvailableAtUniversity of Maryland (College Park, MD)en_us


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