Open Access Research article

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

Kevin G Nyberg1, Matthew A Conte1, Jamie L Kostyun13, Alison Forde2 and Alexandra E Bely1*

Author affiliations

1 Department of Biology, University of Maryland, College Park, MD, 20742, USA

2 Department of Integrative Biology, University of Guelph, Guelph, ON, N1G 2W1, Canada

3 Current address: Department of Biology, Indiana University, Bloomington, IN, 47401, USA

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Citation and License

BMC Genomics 2012, 13:287  doi:10.1186/1471-2164-13-287

Published: 29 June 2012

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.

Keywords:
Transcriptome; 454 pyrosequencing; Regeneration; Evolution; Asexual reproduction; Fission; Annelid; Pristina leidyi; Cell signaling; Wnt signaling