title: Transcriptome Analysis and Differential Gene Expression on the Testis of Orange Mud Crab, Scylla olivacea, during Sexual Maturation.
abstract: Adequate genetic information is essential for sustainable crustacean fisheries and aquaculture management. The commercially important orange mud crab, Scylla olivacea, is prevalent in Southeast Asia region and is highly sought after. Although it is a suitable aquaculture candidate, full domestication of this species is hampered by the lack of knowledge about the sexual maturation process and the molecular mechanisms behind it, especially in males. To date, data on its whole genome is yet to be reported for S. olivacea. The available transcriptome data published previously on this species focus primarily on females and the role of central nervous system in reproductive development. De novo transcriptome sequencing for the testes of S. olivacea from immature, maturing and mature stages were performed. A total of approximately 144 million high-quality reads were generated and de novo assembled into 160,569 transcripts with a total length of 142.2 Mb. Approximately 15-23% of the total assembled transcripts were annotated when compared to public protein sequence databases (i.e. UniProt database, Interpro database, Pfam database and Drosophila melanogaster protein database), and GO-categorised with GO Ontology terms. A total of 156,181 high-quality Single-Nucleotide Polymorphisms (SNPs) were mined from the transcriptome data of present study. Transcriptome comparison among the testes of different maturation stages revealed one gene (beta crystallin like gene) with the most significant differential expression-up-regulated in immature stage and down-regulated in maturing and mature stages. This was further validated by qRT-PCR. In conclusion, a comprehensive transcriptome of the testis of orange mud crabs from different maturation stages were obtained. This report provides an invaluable resource for enhancing our understanding of this species' genome structure and biology, as expressed and controlled by their gonads.
authors.affiliation: Institute of Tropical Aquaculture, Universiti Malaysia Terengganu, Kuala Terengganu, Terengganu, Malaysia.
authors.forename: Khor
authors.initials: K
authors.lastname: Waiho
authors.affiliation: Institute of Tropical Aquaculture, Universiti Malaysia Terengganu, Kuala Terengganu, Terengganu, Malaysia.
authors.forename: Hanafiah
authors.initials: H
authors.lastname: Fazhan
authors.affiliation: Institute of Tropical Aquaculture, Universiti Malaysia Terengganu, Kuala Terengganu, Terengganu, Malaysia.|School of Fisheries and Aquaculture Sciences, Universiti Malaysia Terengganu, Kuala Terengganu, Terengganu, Malaysia.
authors.forename: Md Sheriff
authors.initials: MS
authors.lastname: Shahreza
authors.affiliation: Institute of Tropical Aquaculture, Universiti Malaysia Terengganu, Kuala Terengganu, Terengganu, Malaysia.
authors.forename: Julia Hwei Zhong
authors.initials: JH
authors.lastname: Moh
authors.affiliation: Institute of Tropical Aquaculture, Universiti Malaysia Terengganu, Kuala Terengganu, Terengganu, Malaysia.
authors.forename: Shaibani
authors.initials: S
authors.lastname: Noorbaiduri
authors.affiliation: Institute of Tropical Aquaculture, Universiti Malaysia Terengganu, Kuala Terengganu, Terengganu, Malaysia.
authors.forename: Li Lian
authors.initials: LL
authors.lastname: Wong
authors.affiliation: Institute of Marine Biotechnology, Universiti Malaysia Terengganu, Kuala Terengganu, Terengganu, Malaysia.
authors.forename: Saranya
authors.initials: S
authors.lastname: Sinnasamy
authors.affiliation: Institute of Tropical Aquaculture, Universiti Malaysia Terengganu, Kuala Terengganu, Terengganu, Malaysia.
authors.forename: Mhd
authors.identifier: http://orcid.org/0000-0002-2632-3612
authors.initials: M
authors.lastname: Ikhwanuddin
mesh_terms: D000818:Animals; D003386:Brachyura / Q000235:genetics* / Q000502:physiology*; D016000:Cluster Analysis; D020869:Gene Expression Profiling / Q000379:methods*; D063990:Gene Ontology; D008297:Male; D058977:Molecular Sequence Annotation; D020641:Polymorphism, Single Nucleotide / Q000235:genetics; D012333:RNA, Messenger / Q000235:genetics / Q000378:metabolism; D012015:Reference Standards; D015203:Reproducibility of Results; D012098:Reproduction / Q000235:genetics; D012741:Sexual Maturation / Q000235:genetics*; D013737:Testis / Q000378:metabolism*; D059467:Transcriptome / Q000235:genetics; D038204:beta-Crystallins / Q000235:genetics / Q000378:metabolism
chemical_list: D012333:RNA, Messenger; D038204:beta-Crystallins