The channel catfish genome sequence provides insights into the evolution of scale formation in teleosts

Abstract

Catfish represent 12% of teleost or 6.3% of all vertebrate species, and are of enormous economic value. Here we report a high-quality reference genome sequence of channel catfish (Ictalurus punctatus), the major aquaculture species in the US. The reference genome sequence was validated by genetic mapping of 54,000 SNPs, and annotated with 26,661 predicted protein-coding genes. Through comparative analysis of genomes and transcriptomes of scaled and scaleless fish and scale regeneration experiments, we address the genomic basis for the most striking physical characteristic of catfish, the evolutionary loss of scales and provide evidence that lack of secretory calcium-binding phosphoproteins accounts for the evolutionary loss of scales in catfish. The channel catfish reference genome sequence, along with two additional genome sequences and transcriptomes of scaled catfishes, provide crucial resources for evolutionary and biological studies. This work also demonstrates the power of comparative subtraction of candidate genes for traits of structural significance.

The liver transcriptome of suckermouth armoured catfish (Pterygoplichthys anisitsi, Loricariidae): Identification of expansions in defensome gene families

“…The raw Illumina reads and the assembled transcriptome are available for expanded analyses, and provide a valuable genomic resource for future studies ranging from gene discovery and molecular phylogenetics to control of invasive populations and molecular ecology. Indeed, during the final review of this manuscript a draft genome of the related species Pterygoplichthys pardalis was released along with the annotated genome of the channel catfish, Ictalurus punctatus (Liu et al, 2016). The genomic data provided by Liu et al, 2016 together with the transcriptomic data provided here can now be used in an iterative process to extend our findings on the diversity of defensome genes in this important group of fish.…”

Development of a 690 K SNP array in catfish and its application for genetic mapping and validation of the reference genome sequence

“…Channel catfish ( Ictalurus punctatus ) and blue catfish ( I. furcatus ) are the two most important species in catfish farming industry due to their high tolerance in a wide range of environmental conditions. They have been also used as models for comparative immunology and environmental toxicology1. In the past decades, various genetic and genomic resources have been produced to facilitate catfish genetic improvement and breeding programs, including development of molecular markers2345, BAC-based physical maps678, expression sequence tags (ESTs)9101112131415 and transcriptome sequencing using RNA-Seq1617181920212223, genetic linkage maps242526272829, and generation of whole genome reference sequences1.…”

“…As a result, there were limitations with equal spacing of marker intervals and complete genome coverage. The recent catfish reference genome assembly1 provided a platform for the construction of a high-density SNP array with improved genome coverage. In addition, independent genetic analyses using linkage mapping should allow greater levels of integration of the reference genome sequence with linkage maps, validation of the reference genome sequence, and correction of potential mistakes in the reference genome sequence.…”

High-quality genome assembly of channel catfish, Ictalurus punctatus

“…The calculated genome size is 0.839 Gb, which is shorter than that (1 Gb) from a 2016 report of an American-native channel catfish [3]. …”

“…Gaps were closed using approximately 480 million of Illumina paired-end reads generated from the three libraries with insert sizes of 250, 500 and 800 bp as the input for GapCloser (v1.12-r6, default parameters and −p set to 25) [2]. A final genome assembly of 0.845 Gb in length was obtained (Table 1), which is slightly shorter than that (0.942 Gb) of a recently reported a American-native channel catfish genome [3]. The calculated contig N50 was 48.5 kilobases (kb), and the scaffold N50 was 7.2 Mb (Table 1).…”