A 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, 4.6 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, C2 chemistry) were queried to fill scaffold gaps using MaSuRCA’s gap closing pipeline. 95% of the assembled bases (N95) were contained in 14,526 contigs of ≥ 7.7 kb that were aligned in 686 scaffolds of ≥ 126 kb. Half of the assembled bases (N50) were contained in 2,600 contigs of ≥ 84.6 kb that were aligned in 114 scaffolds of ≥ 1.88 Mb. Substitution of 400bp-insert paired sequences from a traditional Illumina library with those from a PCR-Free library led to a 3-fold increase in contig length, an 18-fold increase in scaffold length, and an 11-fold reduction in scaffold number. The MaSuRCA gap closing pipeline filled 18,675 scaffold gaps (7.5 Mb) with Illumina sequences and an additional 29,059 gaps (26.1 Mb) with PacBio sequences. Mapping of 28,737 SNP markers on 949 scaffolds permitted placement of 735.6 Mb (93%) of scaffolded sequence on the high density channel catfish genetic map.