Transcriptome characterization via 454 pyrosequencing of the annelid Pristina leidyi, an emerging model for studying the evolution of regeneration
Transcriptome characterization via 454 pyrosequencing of the annelid Pristina leidyi, an emerging model for studying the evolution of regeneration
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Date
2012-06-29
Authors
Nyberg, Kevin G.
Conte, Matthew A.
Kostyun, Jamie L.
Forde, Alison
Bely, Alexandra E.
Advisor
Citation
Nyberg, 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).
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Abstract
Background: 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.