Thanh Nguyen Minh, Jung Hyungtaek, Lyons Russell E, Njaci Isaac, Yoon Byoung-Ha, Chand Vincent, Tuan Nguyen Viet, Thu Vo Thi Minh, Mather Peter
International University - VNU HCMC, Quarter 6, Linh Trung Ward, Thu Duc District, Ho Chi Minh City, Viet Nam.
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.
Mar Genomics. 2015 Oct;23:87-97. doi: 10.1016/j.margen.2015.05.001. Epub 2015 May 12.
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.
条纹鲶鱼（Pangasianodon hypophthalmus）是越南湄公河三角洲内陆水产养殖中具有重要商业价值的淡水鱼。然而，由于预计的气候变化影响，海水入侵湄公河三角洲许多地势低洼的沿海省份，该养殖业正面临重大挑战。开发该物种的基因组资源有助于培育出能耐受更高盐度条件的改良养殖品系，因此我们对条纹鲶鱼六个目标渗透压调节器官的转录组文库进行了高通量离子激流测序，作为未来选择策略中使用的基因组资源。经过修剪和处理后，我们获得了12,177,770条 reads，平均长度为97bp。使用CLC基因组工作台、Trinity和Velvet/Oases进行从头组装，其中CLC组装的整体重叠群性能最佳。使用CLC进行从头组装产生了66,451个重叠群，平均长度为478bp，N50长度为506bp。共有37,969个重叠群（57%）与非冗余数据库中的蛋白质具有显著相似性。比较分析表明，大量重叠群与其他硬骨鱼类报道的序列匹配，相似性范围从与大西洋鳕鱼的45.2%到与斑马鱼的52%。此外，在条纹鲶鱼转录组中检测到28,879个简单序列重复（SSR）和55,721个单核苷酸多态性（SNP）。本研究中生成的序列集合代表了迄今为止可获得的最全面的条纹鲶鱼基因组资源。我们的结果说明了下一代测序作为构建非模式物种标记开发大型基因组数据库的有效工具的实用性。
