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
| Autor: | Vincent Chand, Dong-Wook Kim, Hyungtaek Jung, Il Seon Baek, David A. Hurwood, Russell E. Lyons, Krishna R. Salin, Byoung-Ha Yoon, Heui-Soo Kim, Peter B. Mather, Woo-Jin Kim |
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| Jazyk: | angličtina |
| Rok vydání: | 2016 |
| Předmět: |
0301 basic medicine
prawn Genetic Markers Macrobrachium rosenbergii De novo transcriptome assembly Sequence assembly Computational biology Biology de novo assembly Bioinformatics hybrid transcriptome Polymorphism Single Nucleotide Catalysis Article Inorganic Chemistry Transcriptome lcsh:Chemistry 03 medical and health sciences Decapoda Animals Physical and Theoretical Chemistry Molecular Biology Gene lcsh:QH301-705.5 Spectroscopy Macrobrachium Genome Sequence Analysis RNA Reproduction Organic Chemistry Molecular Sequence Annotation 04 agricultural and veterinary sciences General Medicine biology.organism_classification Computer Science Applications 030104 developmental biology lcsh:Biology (General) lcsh:QD1-999 Genetic marker 040102 fisheries Prawn 0401 agriculture forestry and fisheries crustacean optimization reproduction Algorithms |
| Zdroj: | International Journal of Molecular Sciences; Volume 17; Issue 5; Pages: 690 International Journal of Molecular Sciences International Journal of Molecular Sciences, Vol 17, Iss 5, p 690 (2016) |
| ISSN: | 1422-0067 |
| DOI: | 10.3390/ijms17050690 |
| Popis: | 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. |
| Databáze: | OpenAIRE |
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