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.

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A high-density genetic linkage map is essential for the studies of comparative genomics and gene mapping, and can facilitate assembly of reference genome. Herein, we constructed a high-density genetic linkage map with 8,094 SNPs selected from 113 sequenced fish of a F1 family. Ultimately, the consensus map spanned 3818.24 cM and covered nearly the whole genome (99.4%) with a resolution of 0.47 cM. 1,457 scaffolds spanning 435.15 Mb were anchored onto 24 linkage groups, accounting for 80.7% of the draft genome assembly of the yellow drum. Comparative genomic analyses with medaka and zebrafish genomes showed superb chromosome-scale synteny between yellow drum and medaka. QTL mapping and association analysis congruously revealed 22 QTLs for growth-related traits and 13 QTLs for sex dimorphism. Some important candidate genes such as PLA2G4A, BRINP3 and P2RY1 were identified from these growth-related QTL regions. A gene family including DMRT1, DMRT2 and DMRT3 was identified from these sex-related QTL regions on the linkage group LG9. We demonstrate that this linkage map can facilitate the ongoing marker-assisted selection and genomic and genetic studies for yellow drum.

The aim of the present study was to perform a preliminary analysis of the characterization and diversity of Y-chromosome haplotypes/haplogroups in yak of Qinghai Province, China. A total of 322 male yaks from nine populations belonging to three officially recognized breeds (Gaoyuan, Huanhu and Datong) were sampled. Animals were genotyped using six previously reported Y-SNPs present in the SRY, USP9Y, UTY, AMELY and OFD1Y genes and four new Y-SNPs in the OFD1Y gene (g.569A>C, g.578A>C, g.608G>T and g.653G>C) identified in this study. Seven Y-chromosome haplotypes (H1-H7) were identified according to the combination of the 10 Y-SNPs. H1, H2 and H6 were the most common and shared haplotypes across all yak populations/breeds. Private haplotypes H3 and H7 were detected in the Datong breed; H4 in Guoleimude, Qumalai, Qilian, Tianjun and Ganglong populations; and H5 in Qumalai of Gaoyuan breed. Haplotype clustering and network analyses inferred two haplogroups, Y1 and Y2, indicating two divergent lineages of paternal origins of Qinghai yak. The analysis of molecular variance showed a significant difference among individuals (P < 0.0001) with more than 93% of the total genetic variation present within populations, suggesting a weak genetic structure among Qinghai yak populations. The overall Y-haplotype diversity was 0.538 ± 0.028, showing a relatively high diversity in Qinghai yak. The Gaoyuan and Datong breeds had similar haplotype diversities (0.547 ± 0.030 and 0.553 ± 0.083, respectively), which were higher than that of the Huanhu breed (0.441 ± 0.098). Our results support the conservation and sustainable use of unique yak genetic resources in Qinghai.

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Yellow drum (Nibea albiflora) is an important fish species in capture fishery and aquaculture in East Asia. We herein report the first and near‐complete genome assembly of an ultra‐homologous gynogenic female yellow drum using Illumina short sequencing reads. In summary, a total of 154.2 Gb of raw reads were generated via whole‐genome sequencing and were assembled to 565.3 Mb genome with a contig N50 size of 50.3 kb and scaffold N50 size of 2.2 Mb (BUSCO completeness of 97.7%), accounting for 97.3%–98.6% of the estimated genome size of this fish. We further identified 22,448 genes using combined methods of ab initio prediction, RNAseq annotation, and protein homology searching, of which 21,614 (96.3%) were functionally annotated in NCBI nr, trEMBL, SwissProt, and KOG databases. We also investigated the nucleotide diversity (around 1/390) of aquacultured individuals and found the genetic diversity of the aquacultured population decreased due to inbreeding. Evolutionary analyses illustrated significantly expanded and extracted gene families, such as myosin and sodium: neurotransmitter symporter (SNF), could help explain swimming motility of yellow drum. The presented genome will be an important resource for future studies on population genetics, conservation, understanding of evolutionary history and genetic breeding of the yellow drum and other Nibea species.

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