title: Optimizing de novo transcriptome assembly and extending genomic resources for striped catfish (Pangasianodon hypophthalmus).
abstract: Striped catfish (Pangasianodon hypophthalmus) is a commercially important freshwater fish used in inland aquaculture in the Mekong Delta, Vietnam. The culture industry is facing a significant challenge however from saltwater intrusion into many low topographical coastal provinces across the Mekong Delta as a result of predicted climate change impacts. Developing genomic resources for this species can facilitate the production of improved culture lines that can withstand raised salinity conditions, and so we have applied high-throughput Ion Torrent sequencing of transcriptome libraries from six target osmoregulatory organs from striped catfish as a genomic resource for use in future selection strategies. We obtained 12,177,770 reads after trimming and processing with an average length of 97bp. De novo assemblies were generated using CLC Genomic Workbench, Trinity and Velvet/Oases with the best overall contig performance resulting from the CLC assembly. De novo assembly using CLC yielded 66,451 contigs with an average length of 478bp and N50 length of 506bp. A total of 37,969 contigs (57%) possessed significant similarity with proteins in the non-redundant database. Comparative analyses revealed that a significant number of contigs matched sequences reported in other teleost fishes, ranging in similarity from 45.2% with Atlantic cod to 52% with zebrafish. In addition, 28,879 simple sequence repeats (SSRs) and 55,721 single nucleotide polymorphisms (SNPs) were detected in the striped catfish transcriptome. The sequence collection generated in the current study represents the most comprehensive genomic resource for P. hypophthalmus available to date. Our results illustrate the utility of next-generation sequencing as an efficient tool for constructing a large genomic database for marker development in non-model species.
authors.affiliation: International University - VNU HCMC, Quarter 6, Linh Trung Ward, Thu Duc District, Ho Chi Minh City, Viet Nam. Electronic address: nmthanh@hcmiu.edu.vn.
authors.forename: Nguyen Minh
authors.initials: NM
authors.lastname: Thanh
authors.affiliation: Centre for Tropical Crops and Biocommodities, Queensland University of Technology, GPO Box 2434, Brisbane, QLD 4001, Australia; Science and Engineering Faculty, Queensland University of Technology, GPO Box 2434, Brisbane, QLD 4001, Australia. Electronic address: h7.jung@qut.edu.au.
authors.forename: Hyungtaek
authors.initials: H
authors.lastname: Jung
authors.affiliation: Animal Genetics Laboratory, School of Veterinary Science, University of Queensland, Gatton, QLD 4343, Australia. Electronic address: r.lyons2@uq.edu.au.
authors.forename: Russell E
authors.initials: RE
authors.lastname: Lyons
authors.affiliation: Centre for Tropical Crops and Biocommodities, Queensland University of Technology, GPO Box 2434, Brisbane, QLD 4001, Australia. Electronic address: i.njaci@qut.edu.au.
authors.forename: Isaac
authors.initials: I
authors.lastname: Njaci
authors.affiliation: Medical Genomics Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 305-806, Republic of Korea; Department of Functional Genomics, Korea University of Science and Technology, Daejoen 305-333, Republic of Korea. Electronic address: cogate@kribb.re.kr.
authors.forename: Byoung-Ha
authors.initials: BH
authors.lastname: Yoon
authors.affiliation: Science and Engineering Faculty, Queensland University of Technology, GPO Box 2434, Brisbane, QLD 4001, Australia. Electronic address: v.chand@qut.edu.au.
authors.forename: Vincent
authors.initials: V
authors.lastname: Chand
authors.affiliation: Science and Engineering Faculty, Queensland University of Technology, GPO Box 2434, Brisbane, QLD 4001, Australia. Electronic address: viettuan.nguyen@student.qut.edu.au.
authors.forename: Nguyen Viet
authors.initials: NV
authors.lastname: Tuan
authors.affiliation: International University - VNU HCMC, Quarter 6, Linh Trung Ward, Thu Duc District, Ho Chi Minh City, Viet Nam. Electronic address: vtmthu@hcmiu.edu.vn.
authors.forename: Vo Thi Minh
authors.initials: VT
authors.lastname: Thu
authors.affiliation: Science and Engineering Faculty, Queensland University of Technology, GPO Box 2434, Brisbane, QLD 4001, Australia. Electronic address: p.mather@qut.edu.au.
authors.forename: Peter
authors.initials: P
authors.lastname: Mather
mesh_terms: D000818:Animals; D002397:Catfishes / Q000235:genetics*; D020224:Expressed Sequence Tags; D029941:Fish Proteins / Q000235:genetics / Q000378:metabolism; D005786:Gene Expression Regulation / Q000502:physiology; D023281:Genomics; D020641:Polymorphism, Single Nucleotide; D017434:Protein Structure, Tertiary; D054712:Salinity; D059467:Transcriptome
chemical_list: D029941:Fish Proteins
keywords: Ion Torrent; Pangasianodon hypophthalmus; Salinity tolerance; Simple sequence repeat; Single nucleotide polymorphism; Transcriptome