Abstract
BackgroundThe 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.Methodology and principal findingsIllumina 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/SignificanceThese 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.
Highlights
The yellow sisorid catfish (Bagarius yarrelli, Osteichthyes, Siluriformes, Sisoridae) [1] is distributed mainly in southwestern China, including the Nujiang, Lanchangjiang, and Yuanjiang Rivers, Southeast Asia, including Vietnam, Laos, Thailand and Burma, South Asia, and India [2]
1,706,456 raw reads were obtained from muscle, fin and liver tissues of B. yarrelli specimens obtained from the Honghe River in Hekou County, Yunnan Province, China
Raw reads were processed to eliminate lowquality reads and de novo assembled into 151,911 contigs using Trinity software, with an average length of 644 bp
Summary
The yellow sisorid catfish (Bagarius yarrelli, Osteichthyes, Siluriformes, Sisoridae) [1] is distributed mainly in southwestern China, including the Nujiang, Lanchangjiang, and Yuanjiang Rivers, Southeast Asia, including Vietnam, Laos, Thailand and Burma, South Asia, and India [2]. Though wild resources of B. yarrelli are currently under threat of population decline due to environmental changes and overfishing, the fish is consumed by locals, which has resulted in a high price. Mitochondrial and nuclear DNA sequencing have been utilized to study the species’ genetic phylogeny, including 16S rRNA [6], cytochrome oxidase [7], ND6 [8] and rag and rag2 [9]. Random amplified polymorphic DNA (RAPD) and microsatellite (simple sequence repeat, SSR) marker technologies have been applied to study the population genetic diversity of B. yarrelli [10,11]. The available gene sequences and molecular markers are extremely limited, and as of August 15, 2017, only 37 nucleotide sequences were available in the NCBI GenBank database
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