Characterization of genome-wide segmental duplications reveals a common genomic feature of association with immunity among domestic animals

Abstract

BackgroundSegmental duplications (SDs) commonly exist in plant and animal genomes, playing crucial roles in genomic rearrangement, gene innovation and the formation of copy number variants. However, they have received little attention in most livestock species.ResultsAiming at characterizing SDs across the genomes of diverse livestock species, we mapped genome-wide SDs of horse, rabbit, goat, sheep and chicken, and also enhanced the existing SD maps of cattle and pig genomes based on the most updated genome assemblies. We adopted two different detection strategies, whole genome analysis comparison and whole genome shotgun sequence detection, to pursue more convincing findings. Accordingly we identified SDs for each species with the length of from 21.7 Mb to 164.1 Mb, and 807 to 4,560 genes were harboured within the SD regions across different species. More interestingly, many of these SD-related genes were involved in the process of immunity and response to external stimuli. We also found the existence of 59 common genes within SD regions in all studied species except goat. These common genes mainly consisted of both UDP glucuronosyltransferase and Interferon alpha families, implying the connection between SDs and the evolution of these gene families.ConclusionsOur findings provide insights into livestock genome evolution and offer rich genomic sources for livestock genomic research.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-017-3690-x) contains supplementary material, which is available to authorized users.

Functional and population genetic features of copy number variations in two dairy cattle populations

“…The CNVRs were compared together with SD and SNP density in. The SDs detected by Feng et al [80] based on UMD3.1 were remapped to ARS-UCD1.2 using NCBI Genome Remapping Service. Afterwards, the density of SDs and SNPs were calculate for 5 Mb bin using BEDtools [81].…”

Screening of duplicated loci reveals hidden divergence patterns in a complex salmonid genome

“…We demonstrated the use of a novel method to perform genome scans of nonduplicated and duplicated loci throughout a complex polyploid‐origin genome with mixed levels of disomic and tetrasomic inheritance. This method would be equally valuable for scans for adaptive variation in tandem and segmental gene duplications present in diploid plants and animals; these duplications are precursors to families of adaptively important genes (Dennis & Eichler, ; Feng et al., ; Yer, Baloglu, Ziplar, Ayan, & Unver, ).…”

Genome-Wide Identification, Characterization and Expression Analysis of Non-Arginine Aspartate Receptor like kinase gene family under Colletotrichum truncatum stress conditions in Hot pepper

“…Genes were mapped onto chromosome at their genomic position and drawn manually. Duplicated genes were identified by Blast P search against each other when both their identity and query coverage was >80% of their partner sequence [19]. Tandem duplication in genes was identified by occurrence of homologous genes located in single region(<100kb) within a chromosome, while segmental duplication occurs among homologous or non-homologous genes with > 1kb in length and more than 90% sequence similarity dispersed but present on same or different chromosomes from the same clade as described by Feng et al (2017) [20].…”