Additional file 2: Table S2. of Comparative genome analysis of 52 fish species suggests differential associations of repetitive elements with their living aquatic environments

Distribution of repetitive elements among species. (XLS 96 kb

The annotation of repetitive elements in the genome of channel catfish (<i>Ictalurus punctatus</i>)

<div><p>Channel catfish (<i>Ictalurus punctatus</i>) is a highly adaptive species and has been used as a research model for comparative immunology, physiology, and toxicology among ectothermic vertebrates. It is also economically important for aquaculture. As such, its reference genome was generated and annotated with protein coding genes. However, the repetitive elements in the catfish genome are less well understood. In this study, over 417.8 Megabase (MB) of repetitive elements were identified and characterized in the channel catfish genome. Among them, the DNA/TcMar-Tc1 transposons are the most abundant type, making up ~20% of the total repetitive elements, followed by the microsatellites (14%). The prevalence of repetitive elements, especially the mobile elements, may have provided a driving force for the evolution of the catfish genome. A number of catfish-specific repetitive elements were identified including the previously reported <i>Xba</i> elements whose divergence rate was relatively low, slower than that in untranslated regions of genes but faster than the protein coding sequences, suggesting its evolutionary restrictions.</p></div

The divergence distribution of channel catfish Xba elements (blue) and DNA/TcMar-Tc1 transposons (pink).

<p>The X-axis represents the average number of substitutions per site (%), and the Y-axis represents the percentage sequences that comprise the whole genome (%).</p

The proportion of major categories of repetitive elements within the channel catfish repeatome.

<p>The proportion of major categories of repetitive elements within the channel catfish repeatome.</p

The major novel repetitive elements and their characteristics in the channel catfish repeatome.

<p>The major novel repetitive elements and their characteristics in the channel catfish repeatome.</p

The distribution of Tc1/Mariner transposons cross channel catfish genome.

<p>Color key is indicated at the lower right of the figure, with blue color to indicate low and red color to indicate high levels of the transposons in the chromosomal regions. Each color bar represented a physical distance of 1 Mb DNA.</p

Identification and Analysis of Genome-Wide SNPs Provide Insight into Signatures of Selection and Domestication in Channel Catfish (<i>Ictalurus punctatus</i>)

<div><p>Domestication and selection for important performance traits can impact the genome, which is most often reflected by reduced heterozygosity in and surrounding genes related to traits affected by selection. In this study, analysis of the genomic impact caused by domestication and artificial selection was conducted by investigating the signatures of selection using single nucleotide polymorphisms (SNPs) in channel catfish (<i>Ictalurus punctatus</i>). A total of 8.4 million candidate SNPs were identified by using next generation sequencing. On average, the channel catfish genome harbors one SNP per 116 bp. Approximately 6.6 million, 5.3 million, 4.9 million, 7.1 million and 6.7 million SNPs were detected in the Marion, Thompson, USDA103, Hatchery strain, and wild population, respectively. The allele frequencies of 407,861 SNPs differed significantly between the domestic and wild populations. With these SNPs, 23 genomic regions with putative selective sweeps were identified that included 11 genes. Although the function for the majority of the genes remain unknown in catfish, several genes with known function related to aquaculture performance traits were included in the regions with selective sweeps. These included hypoxia-inducible factor 1β· <i>HIF</i>ι<i>β ¨</i> and the transporter gene ATP-binding cassette sub-family B member 5 (<i>ABCB5</i>). HIF1β· is important for response to hypoxia and tolerance to low oxygen levels is a critical aquaculture trait. The large numbers of SNPs identified from this study are valuable for the development of high-density SNP arrays for genetic and genomic studies of performance traits in catfish.</p></div

Optimization of criteria for SNP identification in channel catfish, including minimum reads, maximum reads and minor allele count.

<p>Optimization of criteria for SNP identification in channel catfish, including minimum reads, maximum reads and minor allele count.</p

Genome-wide distribution of significant SNPs.

<p>Physical positions of all catfish 29 chromosomes are presented on the x-axis, and significant SNP numbers within a window size of 200 Kb is given on the y axis.</p

Summary of strain-SNPs in channel catfish, including quality SNPs in the strain, strain-specific SNPs and the percentage of strain-specific SNPs.

<p>Summary of strain-SNPs in channel catfish, including quality SNPs in the strain, strain-specific SNPs and the percentage of strain-specific SNPs.</p