Optimizing hybrid de novo transcriptome assembly and extending genomic resources for giant freshwater prawns (Macrobrachium rosenbergii): The identification of genes and markers associated with reproduction

Jung, Hyungtaek, Yoon, Byoung-Ha, Kim, Woo-Jin, Kim, Dong-Wook, Hurwood, David A., Lyons, Russell E., Salin, Krishna R., Kim, Heui-Soo, Baek, Il Seon, Chand, Vincent, & Mather, Peter B. (2016) Optimizing hybrid de novo transcriptome assembly and extending genomic resources for giant freshwater prawns (Macrobrachium rosenbergii): The identification of genes and markers associated with reproduction. International Journal of Molecular Sciences, 17(5), Article Number-690.

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Abstract

The giant freshwater prawn, Macrobrachium rosenbergii, a sexually dimorphic decapod crustacean is currently the world's most economically important cultured freshwater crustacean species. Despite its economic importance, there is currently a lack of genomic resources available for this species, and this has limited exploration of the molecular mechanisms that control the M. rosenbergii sex-differentiation system more widely in freshwater prawns. Here, we present the first hybrid transcriptome from M. rosenbergii applying RNA-Seq technologies directed at identifying genes that have potential functional roles in reproductive-related traits. A total of 13,733,210 combined raw reads (1720 Mbp) were obtained from Ion-Torrent PGM and 454 FLX. Bioinformatic analyses based on three state-of-the-art assemblers, the CLC Genomic Workbench, Trans-ABySS, and Trinity, that use single and multiple k-mer methods respectively, were used to analyse the data. The influence of multiple k-mers on assembly performance was assessed to gain insight into transcriptome assembly from short reads. After optimisation, de novo assembly resulted in 44,407 contigs with a mean length of 437 bp, and the assembled transcripts were further functionally annotated to detect single nucleotide polymorphisms and simple sequence repeat motifs. Gene expression analysis was also used to compare expression patterns from ovary and testis tissue libraries to identify genes with potential roles in reproduction and sex differentiation. The large transcript set assembled here represents the most comprehensive set of transcriptomic resources ever developed for reproduction traits in M. rosenbergii, and the large number of genetic markers predicted should constitute an invaluable resource for future genetic research studies on M. rosenbergii and can be applied more widely on other freshwater prawn species in the genus Macrobrachium.

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ID Code: 99621
Item Type: Journal Article
Refereed: Yes
Keywords: Macrobrachium rosenbergii, crustacean, prawn, de novo assembly, hybrid transcriptome, optimization, reproduction
DOI: 10.3390/ijms17050690
ISSN: 1422-0067
Divisions: Current > Research Centres > Centre for Tropical Crops and Biocommodities
Current > Schools > School of Earth, Environmental & Biological Sciences
Current > Institutes > Institute for Future Environments
Current > QUT Faculties and Divisions > Science & Engineering Faculty
Copyright Owner: Copyright 2016 The Author(s)
Copyright Statement: licensee MDPI, Basel, Switzerland. This article is an open access
article distributed under the terms and conditions of the Creative Commons Attribution
(CC-BY) license (http://creativecommons.org/licenses/by/4.0/).
Deposited On: 29 Sep 2016 23:29
Last Modified: 04 Oct 2016 23:01

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