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.
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.
authors.affiliation: Centre for Tropical Crops and Biocommodities, Science and Engineering Faculty, Queensland University of Technology, Queensland 4000, Australia. h7.jung@qut.edu.au.
authors.forename: Hyungtaek
authors.initials: H
authors.lastname: Jung
authors.affiliation: Korean Bioinformation Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 305806, Korea. cogate@kribb.re.kr.|Department of Bioinformatics, University of Science and Technology, Daejeon 305333, Korea. cogate@kribb.re.kr.
authors.forename: Byung-Ha
authors.initials: BH
authors.lastname: Yoon
authors.affiliation: Biotechnology Research Division, National Institute of Fisheries Science, Busan 46083, Korea. wj2464@korea.kr.
authors.forename: Woo-Jin
authors.initials: WJ
authors.lastname: Kim
authors.affiliation: All Bio Technology Co., LTD, Internet Business Incubation Center, Mokweon University, Daejeon 302729, Korea. kdw9017@naver.com.
authors.forename: Dong-Wook
authors.initials: DW
authors.lastname: Kim
authors.affiliation: Earth, Environmental and Biological Sciences, Science and Engineering Faculty, Queensland University of Technology, Queensland 4000, Australia. d.hurwood@qut.edu.au.
authors.forename: David A
authors.initials: DA
authors.lastname: Hurwood
authors.affiliation: School of Veterinary Science, University of Queensland, Queensland 4067, Australia. r.lyons2@uq.edu.au.
authors.forename: Russell E
authors.initials: RE
authors.lastname: Lyons
authors.affiliation: School of Environment, Resources and Development, Asian Institute of Technology, Pathumthani 12120, Thailand. salinkr@gmail.com.
authors.forename: Krishna R
authors.initials: KR
authors.lastname: Salin
authors.affiliation: Department of Biological Sciences, College of Natural Sciences, Pusan National University, Busan 609735, Korea. khs307@pusan.ac.kr.
authors.forename: Heui-Soo
authors.initials: HS
authors.lastname: Kim
authors.affiliation: Division of Marine Technology, Chonnam National University, Yeosu 550250, Korea. chitago@naver.com.
authors.forename: Ilseon
authors.initials: I
authors.lastname: Baek
authors.affiliation: Earth, Environmental and Biological Sciences, Science and Engineering Faculty, Queensland University of Technology, Queensland 4000, Australia. v.chand@qut.edu.au.
authors.forename: Vincent
authors.initials: V
authors.lastname: Chand
authors.affiliation: Earth, Environmental and Biological Sciences, Science and Engineering Faculty, Queensland University of Technology, Queensland 4000, Australia. p.mather@qut.edu.au.
authors.forename: Peter B
authors.initials: PB
authors.lastname: Mather
mesh_terms: D000465:Algorithms; D000818:Animals; D033364:Decapoda / Q000235:genetics* / Q000378:metabolism / Q000502:physiology; D005819:Genetic Markers; D016678:Genome; D058977:Molecular Sequence Annotation / Q000379:methods; D020641:Polymorphism, Single Nucleotide; D012098:Reproduction / Q000235:genetics*; D017423:Sequence Analysis, RNA / Q000379:methods*; D059467:Transcriptome
chemical_list: D005819:Genetic Markers
keywords: Macrobrachium rosenbergii; crustacean; de novo assembly; hybrid transcriptome; optimization; prawn; reproduction