High-quality genome assembly of channel catfish, Ictalurus punctatus

Abstract

BackgroundThe channel catfish (Ictalurus punctatus), a species native to North America, is one of the most important commercial freshwater fish in the world, especially in the United States’ aquaculture industry. Since its introduction into China in 1984, both cultivation area and yield of this species have been dramatically increased such that China is now the leading producer of channel catfish. To aid genomic research in this species, data sets such as genetic linkage groups, long-insert libraries, physical maps, bacterial artificial clones (BAC) end sequences (BES), transcriptome assemblies, and reference genome sequences have been generated. Here, using diverse assembly methods, we provide a comparable high-quality genome assembly for a channel catfish from a breeding stock inbred in China for more than three generations, which was originally imported to China from North America.FindingsApproximately 201.6 gigabases (Gb) of genome reads were sequenced by the Illumina HiSeq 2000 platform. Subsequently, we generated high quality, cost-effective and easily assembled sequences of the channel catfish genome with a scaffold N50 of 7.2 Mb and 95.6 % completeness. We also predicted that the channel catfish genome contains 21,556 protein-coding genes and 275.3 Mb (megabase pairs) of repetitive sequences.ConclusionsWe report a high-quality genome assembly of the channel catfish, which is comparable to a recent report of the “Coco” channel catfish. These generated genome data could be used as an initial platform for molecular breeding to obtain novel catfish varieties using genomic approaches.

Applications of genotyping by sequencing in aquaculture breeding and genetics

“…; channel catfish, Chen et al . ), and new sequencing data will improve genome quality and annotation. Therefore, reference‐guided RAD‐Seq approaches are likely to be increasingly utilized.…”

“…Therefore, in original RAD experiments using Stacks, the P2 read is typically used for quality control (e.g. removal of PCR duplicates), and for constructing paired-end 'mini-contigs' which facilitate BLAST alignment and genotyping assay design Chen et al 2016), and new sequencing data will improve genome quality and annotation. Therefore, referenceguided RAD-Seq approaches are likely to be increasingly utilized.…”

The draft genome of blunt snout bream (Megalobrama amblycephala) reveals the development of intermuscular bone and adaptation to herbivorous diet

“…This growth of fish production is meanwhile solely accomplished by an extension of aquaculture as over the past 30 years the total mass of captured fish has remained almost constant [ 1 ]. As a consequence of this emphasis on fish breeding, the genomes of various economically important fish species, e.g., Atlantic cod ( Gadus morhua ) [ 2 ], rainbow trout ( Oncorhynchus mykiss ) [ 3 ], European sea bass ( Dicentrarchus labrax ) [ 4 ], yellow croaker ( Larimichthys crocea ) [ 5 ], half-smooth tongue sole ( Cynoglossus semilaevis ) [ 6 ], tilapia ( Oreochromis niloticus ) [ 7 ], and channel catfish ( Ictalurus punctatus ) [ 8 ], have been sequenced. Yet, the majority of these species are carnivorous, requiring large inputs of protein from wild caught fish or other precious feed.…”

Rearranged T Cell Receptor Sequences in the Germline Genome of Channel Catfish Are Preferentially Expressed in Response to Infection

“…The I. punctatus genome has been sequenced to ~97% completeness, but the projected sizes of the two reference genomes range between 0.84 Gb and 1.01 Gb ( 10 , 11 ). Estimates of repetitive sequences range between 275 Mb and 418 Mb, or 33 % to 44 % of the genome ( 11 , 27 ). The Tc1-mariner family DNA transposon is the most abundant class of TEs and accounts for ~9 % of the genome ( 11 , 27 , 28 ).…”

“…cDNA sequences for twelve Vβ genes, organized in five families, have been determined ( 8 , 9 ). Although the channel catfish genome has been sequenced, the TCRβ genes have not been annotated ( 10 , 11 ). We have mapped the TCRβ genes to chromosome 9, spanning a region of ~204 kb, arranged in a translocon organization (Figure 1 ).…”