Comparative analyses of copy number variations between Bos taurus and Bos indicus

Abstract

Background Bos taurus and Bos indicus are two main sub-species of cattle. However, the differential copy number variations (CNVs) between them are not yet well studied. Results Based on the new high-quality cattle reference genome ARS-UCD1.2, we identified 13,234 non-redundant CNV regions (CNVRs) from 73 animals of 10 cattle breeds (4 Bos taurus and 6 Bos indicus), by integrating three detection strategies. While 6990 CNVRs (52.82%) were shared by Bos taurus and Bos indicus, large CNV differences were discovered between them and these differences could be used to successfully separate animals into two subspecies. We found that 2212 and 538 genes uniquely overlapped with either indicine-specific CNVRs and or taurine-specific CNVRs, respectively. Based on FST, we detected 16 candidate lineage-differential CNV segments (top 0.1%) under selection, which overlapped with eight genes (CTNNA1, ENSBTAG00000004415, PKN2, BMPER, PDE1C, DNAJC18, MUSK, and PLCXD3). Moreover, we obtained 1.74 Mbp indicine-specific sequences, which could only be mapped on the Bos indicus reference genome UOA_Brahman_1. We found these sequences and their associated genes were related to heat resistance, lipid and ATP metabolic process, and muscle development under selection. We further analyzed and validated the top significant lineage-differential CNV. This CNV overlapped genes related to muscle cell differentiation, which might be generated from a retropseudogene of CTH but was deleted along Bos indicus lineage. Conclusions This study presents a genome wide CNV comparison between Bos taurus and Bos indicus. It supplied essential genome diversity information for understanding of adaptation and phenotype differences between the Bos taurus and Bos indicus populations.

Population differentiated copy number variation of Bos taurus, Bos indicus and their African hybrids

“…The muscle development related gene CTNNA1 was overlapped with indicine-specific deletion. This result was mostly agreed by Hu et al [ 46 ] except for the lower copy number in our AFT individuals. The low copy number in Bos taurus indicus while normal or little change in Bos taurus taurus suggest that the sequence is likely to be specific to Bos taurus taurus .…”

“…AFH whose ancestry of selection signature skewed toward indicine was also suggested to be adapted to heat stress by indicine introgression into local taurine [ 11 ]. In our analyses, one of the heat shock protein family coding gene, DNAJC18 is found to be overlapped with indicine-specific deletion, which is consistent with the CNVR identified in a previous study [ 46 ]. The DnaJ family binds to HSP70s for regulating their client capture and drives HSP70s toward specific client [ 47 ].…”

Copy number variations with adaptive potential in caribou (Rangifer tarandus): genome architecture and new annotated genome assembly

“…First, genetic polymorphisms are usually found in higher numbers when more individuals are studied, and CNV diversity is strongly related to the number of tested individuals (Bickhart et al 2012;Conrad et al 2010). Second, a hierarchical population structure is expected at the entire species distribution level with some CNVs being peculiar to specific populations (Conrad et al 2010;Sudmant et al 2015) or lineages (Hu et al 2020;Yang et al 2018). Alleles thus remain undetected when testing individuals from a fraction of the species range.…”

“…CNVs have been investigated in a number of domestic mammal species including cattle (Fadista et al 2010;Hu et al 2020), swine (Wang et al 2013), horses (Wang et al 2014), sheep (Fontanesi 2011) and goats (Fontanesi 2010). These early genome-wide CNV studies revealed relatively few CNVs (37 to 368) per genome with length averaging 127 kbp to 10.7 Mbp due to the low resolution inherent in detection methods based on array comparative genomic hybridization (aCGH) or SNP chips (Clop, Vidal, and Amills 2012).…”

Atomic-Level Investigation of Reactant Recognition Mechanism and Thermodynamic Property in Glucosamine 6-Phosphate Deaminase Catalysis

“…GlcN6P deaminase is expressed in many different organisms, while it is absent from several green plants and eukaryotic lineages ( Burki et al, 2020 ). The enzyme was originally described in extracts of pig kidney ( Yu et al, 2020 ) then subsequently in a number of other organisms, including Escherichia coli ( Jang et al, 2017 ), Candida albicans ( Arkowitz and Bassilana, 2019 ), Musca domestica ( de Jonge et al, 2020 ), Plasmodium falciparum ( Neveu et al, 2020 ), Canis familiaris ( Guedes et al, 2021 ), Bos Taurus ( Hu et al, 2020 ), and Homo sapiens ( Weni 2020 ). Over the years, the crystal structure of the NagB hexamer was elucidated in Escherichia coli and Homo sapiens , while the crystal structure of the NagB monomer was obtained from Bacillus subtilis and Streptococcus mutans ( Liu et al, 2008 ).…”