The First Generation Genome Sequence Assembly for Channel Catfish, Ictalurus punctatus

Catfish production is the leading aquaculture industry in the United States. In order to facilitate genomic analyses and genomic selection of catfish broodstock, we have produced a first draft whole genome sequence assembly for channel catfish. Illumina sequence from a doubled haploid channel catfish was produced on the HiSeq 2000 and NextSeq500 platforms; 750 M paired reads from 400bp fragments, 17.8 M mate pairs from 3kb fragments, 4.7 M mate pairs from 8 kb fragments, and 1.6 M paired reads from 34 kb fragments. After scaffold assembly using MaSuRCA, Illumina and Illumina-corrected PacBio sequences (1.6 kb avg. length) were queried to fill scaffold gaps using MaSuRCA’s gap closing pipeline. 95% of the assembled bases (N95) were contained in 14,590 contigs of > 7.7 kb that were aligned in 690 scaffolds of > 124 kb. Half of the assembled bases (N50) were contained in 2,861 contigs of > 76.6 kb that were aligned in 113 scaffolds of > 1.88 Mb.  Substitution of 400bp-insert paired sequences from a traditional Illumina library with those from a PCR-Free library almost doubled the average contig and scaffold lengths and halved the scaffold number. The MaSuRCA gap closing pipeline filled 27,367 scaffold gaps (1.4 Mb) with Illumina sequences and an additional 34,468 gaps (3.0 Mb) with PacBio sequences. Mapping of 28,477 SNP markers to 878 scaffolds permitted placement of 737 Mb (93.6%) of scaffolded sequence on the high density channel catfish genetic map.