De novo assembly and characterization of a maternal and developmental transcriptome for the emerging model crustacean Parhyale hawaiensis

Victor Zeng, Karina E. Villanueva, Ben S. Ewen-Campen, Frederike Alwes, William Browne, Cassandra G. Extavour

Research output: Contribution to journalArticle

65 Citations (Scopus)

Abstract

Background: 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.

Original languageEnglish
Article number581
JournalBMC Genomics
Volume12
DOIs
StatePublished - Nov 25 2011

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Transcriptome
Amphipoda
Mothers
Genome
Complementary DNA
Trans-Splicing
Gametogenesis
Developmental Genes
Daphnia
Aphids
Arthropods
Peas
Genes
Insects
Biomedical Research
Ovary
Embryonic Structures

ASJC Scopus subject areas

  • Biotechnology
  • Genetics

Cite this

De novo assembly and characterization of a maternal and developmental transcriptome for the emerging model crustacean Parhyale hawaiensis. / Zeng, Victor; Villanueva, Karina E.; Ewen-Campen, Ben S.; Alwes, Frederike; Browne, William; Extavour, Cassandra G.

In: BMC Genomics, Vol. 12, 581, 25.11.2011.

Research output: Contribution to journalArticle

Zeng, Victor ; Villanueva, Karina E. ; Ewen-Campen, Ben S. ; Alwes, Frederike ; Browne, William ; Extavour, Cassandra G. / De novo assembly and characterization of a maternal and developmental transcriptome for the emerging model crustacean Parhyale hawaiensis. In: BMC Genomics. 2011 ; Vol. 12.
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