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dc.contributor.authorZeng, Victor
dc.contributor.authorVillanueva, Karina E
dc.contributor.authorEwen-Campen, Benjamin Scott
dc.contributor.authorAlwes, Frederike
dc.contributor.authorBrowne, William E
dc.contributor.authorExtavour, Cassandra G.
dc.date.accessioned2013-10-24T17:22:08Z
dc.date.issued2011
dc.identifier.citationZeng, Victor, Karina E. Villanueva, Ben S. Ewen-Campen, Frederike Alwes, William E. Browne, and Cassandra G. Extavour. 2011. De novo assembly and characterization of a maternal and developmental transcriptome for the emerging model crustacean Parhyale hawaiensis. BMC Genomics 12:581.en_US
dc.identifier.issn1471-2164en_US
dc.identifier.urihttp://nrs.harvard.edu/urn-3:HUL.InstRepos:11208939
dc.description.abstractBackground: Arthropods are the most diverse animal phylum, but their genomic resources are relatively few. While the genome of the branchiopod Daphnia pulex is now available, no other large-scale crustacean genomic resources are available for comparison. In particular, genomic resources are lacking for the most tractable laboratory model of crustacean development, the amphipod Parhyale hawaiensis. Insight into shared and divergent characters of crustacean genomes will facilitate interpretation of future developmental, biomedical, and ecological research using crustacean models. Results: To generate a transcriptome enriched for maternally provided and zygotically transcribed developmental genes, we created cDNA from ovaries and embryos of P. hawaiensis. Using 454 pyrosequencing, we sequenced over 1.1 billion bases of this cDNA, and assembled them de novo to create, to our knowledge, the second largest crustacean genomic resource to date. We found an unusually high proportion of C2H2 zinc finger-containing transcripts, as has also been reported for the genome of the pea aphid Acyrthosiphon pisum. Consistent with previous reports, we detected trans-spliced transcripts, but found that they did not noticeably impact transcriptome assembly. Our assembly products yielded 19,067 unique BLAST hits against nr (E-value cutoff e-10). These included over 400 predicted transcripts with significant similarity to D. pulex sequences but not to sequences of any other animal. Annotation of several hundred genes revealed P. hawaiensis homologues of genes involved in development, gametogenesis, and a majority of the members of six major conserved metazoan signaling pathways. Conclusions: The amphipod P. hawaiensis has higher transcript complexity than known insect transcriptomes, and trans-splicing does not appear to be a major contributor to this complexity. We discuss the importance of a reliable comparative genomic framework within which to consider findings from new crustacean models such as D. pulex and P. hawaiensis, as well as the need for development of further substantial crustacean genomic resources.en_US
dc.description.sponsorshipOrganismic and Evolutionary Biologyen_US
dc.language.isoen_USen_US
dc.publisherBioMed Centralen_US
dc.relation.isversionofdoi://10.1186/1471-2164-12-581en_US
dc.relation.hasversionhttp://www.ncbi.nlm.nih.gov/pmc/articles/PMC3282834/pdf/en_US
dash.licenseLAA
dc.titleDe Novo Assembly and Characterization of a Maternal and Developmental Transcriptome for the Emerging Model Crustacean Parhyale hawaiensisen_US
dc.typeJournal Articleen_US
dc.description.versionVersion of Recorden_US
dc.relation.journalBMC Genomicsen_US
dash.depositing.authorExtavour, Cassandra G.
dc.date.available2013-10-24T17:22:08Z
dc.identifier.doi10.1186/1471-2164-12-581*
dash.contributor.affiliatedEwen-Campen, Benjamin
dash.contributor.affiliatedExtavour, Cassandra


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