Du Min, Li Na, Niu Baozhen, Liu Yanhong, You Dongjing, Jiang Defu, Ruan Congquan, Qin Zhengquan, Song Taowen, Wang Wentao
Key Lab for Quality, Efficient Cultivation and Security Control of Crops in Colleges and University of Yunnan Province, Honghe University, Mengzi, Yunnan Province, P.R. China.
College of Life Science and Technology, Honghe University, Mengzi, Yunnan Province, P.R. China.
PLoS One. 2018 Feb 9;13(2):e0190343. doi: 10.1371/journal.pone.0190343. eCollection 2018.
The yellow sisorid catfish (Bagarius yarrelli) is a carnivorous freshwater fish that inhabits the Honghe River, Lanchangjiang River and Nujiang River of southern China and other Southeast Asian countries. However, the publicly available genomic data for B. yarrelli are limited.
Illumina Solexa paired-end technology produced 1,706,456 raw reads from muscle, liver and caudal fin tissues of B. yarrelli. Nearly 5 Gb of data were acquired, and de novo assembly generated 14,607 unigenes, with an N50 of 2006 bp. A total of 9093 unigenes showed significant similarities to known proteins in public databases: 4477 and 6391 of B. yarrelli unigenes were mapped to the Gene Ontology (GO) and Clusters of Orthologous Groups (COG) databases, respectively. Moreover, 9635 unigenes were assigned to 242 Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways. In addition, 8568 microsatellites (simple sequence repeats, SSRs) were detected, and 31 pairs of polymorphic primers were characterized using wild populations of B. yarrelli from the Nujiang River, Yunnan Province, China.
CONCLUSION/SIGNIFICANCE: These sequences enrich the genomic resources for B. yarrelli and will benefit future investigations into the evolutionary and biological processes of this and related Bagarius species. The SSR markers developed in this study will facilitate construction of genetic maps, investigations of genetic structures and germplasm polymorphism assessments in B. yarrelli.
黄斑褶鮡是一种肉食性淡水鱼，栖息于中国南方的红河、澜沧江和怒江以及其他东南亚国家。然而，公开可得的黄斑褶鮡基因组数据有限。
利用Illumina Solexa双末端技术从黄斑褶鮡的肌肉、肝脏和尾鳍组织中产生了1,706,456条原始 reads。获得了近5 Gb的数据，从头组装产生了14,607个单基因，N50为2006 bp。共有9093个单基因与公共数据库中的已知蛋白质具有显著相似性：黄斑褶鮡单基因分别有4477个和6391个被映射到基因本体论（GO）和直系同源簇（COG）数据库。此外，9635个单基因被分配到242条京都基因与基因组百科全书（KEGG）通路。另外，检测到8568个微卫星（简单序列重复，SSRs），并使用来自中国云南省怒江的黄斑褶鮡野生种群对31对多态性引物进行了表征。
结论/意义：这些序列丰富了黄斑褶鮡的基因组资源，将有助于未来对该物种及相关褶鮡属物种的进化和生物学过程进行研究。本研究开发的SSR标记将有助于构建黄斑褶鮡的遗传图谱、研究其遗传结构和评估种质多态性。
