Transcriptome characterization via 454 pyrosequencing of the annelid <it>Pristina leidyi</it>, an emerging model for studying the evolution of regeneration
<p>Abstract</p> <p>Background</p> <p>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 st...
| Main Authors: | , , , , |
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| Format: | Article |
| Language: | English |
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BMC
2012-06-01
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| Series: | BMC Genomics |
| Subjects: | |
| Online Access: | http://www.biomedcentral.com/1471-2164/13/287 |
| _version_ | 1830282388018561024 |
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| author | Nyberg Kevin G Conte Matthew A Kostyun Jamie L Forde Alison Bely Alexandra E |
| author_facet | Nyberg Kevin G Conte Matthew A Kostyun Jamie L Forde Alison Bely Alexandra E |
| author_sort | Nyberg Kevin G |
| collection | DOAJ |
| description | <p>Abstract</p> <p>Background</p> <p>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 <it>Pristina leidyi</it>, 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 <it>P. leidyi</it> using 454 technology.</p> <p>Results</p> <p>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 <it>frizzled</it> and <it>β-catenin</it>) present in our transcriptome are expressed in the regeneration blastema of <it>P. leidyi</it>, demonstrating the usefulness of this resource for regeneration research.</p> <p>Conclusions</p> <p>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 <it>P. leidyi</it> 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.</p> |
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| institution | Directory Open Access Journal |
| issn | 1471-2164 |
| language | English |
| last_indexed | 2024-12-19T02:37:07Z |
| publishDate | 2012-06-01 |
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| spelling | doaj.art-e5d9cb433f324875a56eb20b724753d62022-12-21T20:39:20ZengBMCBMC Genomics1471-21642012-06-0113128710.1186/1471-2164-13-287Transcriptome characterization via 454 pyrosequencing of the annelid <it>Pristina leidyi</it>, an emerging model for studying the evolution of regenerationNyberg Kevin GConte Matthew AKostyun Jamie LForde AlisonBely Alexandra E<p>Abstract</p> <p>Background</p> <p>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 <it>Pristina leidyi</it>, 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 <it>P. leidyi</it> using 454 technology.</p> <p>Results</p> <p>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 <it>frizzled</it> and <it>β-catenin</it>) present in our transcriptome are expressed in the regeneration blastema of <it>P. leidyi</it>, demonstrating the usefulness of this resource for regeneration research.</p> <p>Conclusions</p> <p>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 <it>P. leidyi</it> 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.</p>http://www.biomedcentral.com/1471-2164/13/287Transcriptome454 pyrosequencingRegenerationEvolutionAsexual reproductionFissionAnnelid<it>Pristina leidyi</it>Cell signalingWnt signaling |
| spellingShingle | Nyberg Kevin G Conte Matthew A Kostyun Jamie L Forde Alison Bely Alexandra E Transcriptome characterization via 454 pyrosequencing of the annelid <it>Pristina leidyi</it>, an emerging model for studying the evolution of regeneration BMC Genomics Transcriptome 454 pyrosequencing Regeneration Evolution Asexual reproduction Fission Annelid <it>Pristina leidyi</it> Cell signaling Wnt signaling |
| title | Transcriptome characterization via 454 pyrosequencing of the annelid <it>Pristina leidyi</it>, an emerging model for studying the evolution of regeneration |
| title_full | Transcriptome characterization via 454 pyrosequencing of the annelid <it>Pristina leidyi</it>, an emerging model for studying the evolution of regeneration |
| title_fullStr | Transcriptome characterization via 454 pyrosequencing of the annelid <it>Pristina leidyi</it>, an emerging model for studying the evolution of regeneration |
| title_full_unstemmed | Transcriptome characterization via 454 pyrosequencing of the annelid <it>Pristina leidyi</it>, an emerging model for studying the evolution of regeneration |
| title_short | Transcriptome characterization via 454 pyrosequencing of the annelid <it>Pristina leidyi</it>, an emerging model for studying the evolution of regeneration |
| title_sort | transcriptome characterization via 454 pyrosequencing of the annelid it pristina leidyi it an emerging model for studying the evolution of regeneration |
| topic | Transcriptome 454 pyrosequencing Regeneration Evolution Asexual reproduction Fission Annelid <it>Pristina leidyi</it> Cell signaling Wnt signaling |
| url | http://www.biomedcentral.com/1471-2164/13/287 |
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