High through-put sequencing of the Parhyale hawaiensis mRNAs and microRNAs to aid comparative developmental studies

Blythe, Martin J.; Malla, Sunir; Everall, Richard; Shih, Yu-huan; Lemay, Virginie; Moreton, Joanna; Wilson, Raymond; Aboobaker, Aziz

Abstract

Understanding the genetic and evolutionary basis of animal morphological diversity will require comparative developmental studies that use new model organisms. This necessitates development of tools for the study of genetics and also the generation of sequence information of the organism to be studied. The development of next generation sequencing technology has enabled quick and cost effective generation of sequence information. Parhyale hawaiensis has emerged as a model organism of choice due to the development of advanced molecular tools, thus P. hawaiensis genetic information will help drive functional studies in this organism.

Here we present a transcriptome and miRNA collection generated using next generation sequencing platforms. We generated approximately 1.7 million reads from a P. hawaiensis cDNA library constructed from embryos up to the germ band stage. These reads were assembled into a dataset comprising 163,501 transcripts.

Using the combined annotation of Annot8r and pfam2go, Gene Ontology classifications was assigned to 20,597 transcripts. Annot8r was used to provide KEGG orthology to our transcript dataset. A total of 25,292 KEGG pathway assignments were defined and further confirmed with reciprocal blast against the NCBI nr protein database. This has identified many P. hawaiensis gene orthologs of key conserved signalling pathways involved in development. We also generated small RNA sequences from P. hawaiensis, identifying 55 conserved miRNAs. Sequenced small RNAs that were not annotated by stringent comparison to mirBase were used to search the Daphnia pulex for possible novel miRNAs. Using a conservative approach, we have identified 51 possible miRNA candidates conserved in the Daphnia pulex genome, which could be potential crustacean/arthropod specific miRNAs. Our study presents gene and miRNA discovery in a new model organism that does not have a sequenced genome. The data provided by our work will be valuable for the P. hawaiensis community as well as the wider evolutionary developmental biology community.

Citation

Blythe, M. J., Malla, S., Everall, R., Shih, Y.-H., Lemay, V., Moreton, J., Wilson, R., & Aboobaker, A. (2012). High through-put sequencing of the Parhyale hawaiensis mRNAs and microRNAs to aid comparative developmental studies. PLoS ONE, 7(3), Article e33784. https://doi.org/10.1371/journal.pone.0033784

• Journal Article Type: Article
• Publication Date: Mar 20, 2012
• Deposit Date: Apr 25, 2014
• Publicly Available Date: Apr 25, 2014
• Journal: PLoS ONE
• Electronic ISSN: 1932-6203
• Publisher: Public Library of Science
• Peer Reviewed: Peer Reviewed
• Volume: 7
• Issue: 3
• Article Number: e33784
• DOI: https://doi.org/10.1371/journal.pone.0033784
• Public URL: https://nottingham-repository.worktribe.com/output/709696
• Publisher URL: http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0033784