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, Byung-Ha, Kim, Woo-Jin, Kim, Dong-Wook, Hurwood, David A., Lyons, Russell E., Salin, Krishna R., Kim, Heui-Soo, Baek, Ilseon, Chand, Vincent and 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: 1-21. doi:10.3390/ijms17050690


Author Jung, Hyungtaek
Yoon, Byung-Ha
Kim, Woo-Jin
Kim, Dong-Wook
Hurwood, David A.
Lyons, Russell E.
Salin, Krishna R.
Kim, Heui-Soo
Baek, Ilseon
Chand, Vincent
Mather, Peter B.
Title 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
Formatted title
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
Journal name International Journal of Molecular Sciences   Check publisher's open access policy
ISSN 1422-0067
Publication date 2016-05-07
Year available 2016
Sub-type Article (original research)
DOI 10.3390/ijms17050690
Open Access Status DOI
Volume 17
Issue 5
Start page 1
End page 21
Total pages 21
Place of publication Basel, Switzerland
Publisher MDPI AG
Language eng
Subject 1503 Catalysis
1312 Molecular Biology
1607 Spectroscopy
1706 Computer Science Applications
1606 Physical and Theoretical Chemistry
1605 Organic Chemistry
1604 Inorganic Chemistry
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.
Formatted 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.
Keyword Macrobrachium rosenbergii
Crustacean
Prawn
De novo assembly
Hybrid transcriptome
Optimization
Reproduction
Q-Index Code C1
Q-Index Status Provisional Code
Institutional Status UQ

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Sub-type: Article (original research)
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