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De novo assembly and characterization of the invasive Northern Pacific Seastar transcriptome

Richardson, Mark F. and Sherman, Craig D. H. 2015, De novo assembly and characterization of the invasive Northern Pacific Seastar transcriptome, PLoS one, vol. 10, no. 11, Article number: e0142003, pp. 1-18, doi: 10.1371/journal.pone.0142003.

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Title De novo assembly and characterization of the invasive Northern Pacific Seastar transcriptome
Formatted title De novo assembly and characterization of the invasive Northern Pacific Seastar transcriptome
Author(s) Richardson, Mark F.ORCID iD for Richardson, Mark F. orcid.org/0000-0002-1650-0064
Sherman, Craig D. H.ORCID iD for Sherman, Craig D. H. orcid.org/0000-0003-2099-0462
Journal name PLoS one
Volume number 10
Issue number 11
Season Article number: e0142003
Start page 1
End page 18
Total pages 18
Publisher Public Library of Science
Place of publication San Francisco, Calif.
Publication date 2015-11-03
ISSN 1932-6203
Keyword(s) echinoderm transcriptomes
invasive species
genomic resources
Summary Invasive species are a major threat to global biodiversity but can also serve as valuable model systems to examine important evolutionary processes. While the ecological aspects of invasions have been well documented, the genetic basis of adaptive change during the invasion process has been hampered by a lack of genomic resources for the majority of invasive species. Here we report the first larval transcriptomic resource for the Northern Pacific Seastar, Asterias amurensis, an invasive marine predator in Australia. Approximately 117.5 million 100 base-pair (bp) paired-end reads were sequenced from a single RNA-Seq library from a pooled set of full-sibling A. amurensis bipinnaria larvae. We evaluated the efficacy of a pre-assembly error correction pipeline on subsequent de novo assembly. Error correction resulted in small but important improvements to the final assembly in terms of mapping statistics and core eukaryotic genes representation. The error-corrected de novo assembly resulted in 115,654 contigs after redundancy clustering. 41,667 assembled contigs were homologous to sequences from NCBI's non-redundant protein and UniProt databases. We assigned Gene Ontology, KEGG Orthology, Pfam protein domain terms and predicted protein-coding sequences to > 36,000 contigs. The final transcriptome dataset generated here provides functional information for 18,319 unique proteins, comprising at least 11,355 expressed genes. Furthermore, we identified 9,739 orthologs to P. miniata proteins, evaluated our annotation pipeline and generated a list of 150 candidate genes for responses to several environmental stressors that may be important for adaptation of A. amurensis in the invasive range. Our study has produced a large set of A. amurensis RNA contigs with functional annotations that can serve as a resource for future comparisons to other echinoderm transcriptomes and gene expression studies. Our data can be used to study the genetic basis of adaptive change and other important evolutionary processes during a successful invasion.
Language eng
DOI 10.1371/journal.pone.0142003
Field of Research 050103 Invasive Species Ecology
Socio Economic Objective 970105 Expanding Knowledge in the Environmental Sciences
HERDC Research category C1 Refereed article in a scholarly journal
ERA Research output type C Journal article
Copyright notice ©2015, The Authors
Free to Read? Yes
Use Rights Creative Commons Attribution licence
Persistent URL http://hdl.handle.net/10536/DRO/DU:30082139

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Every reasonable effort has been made to ensure that permission has been obtained for items included in DRO. If you believe that your rights have been infringed by this repository, please contact drosupport@deakin.edu.au.