Dataset Information

Patterns of DNA variation between the autosomes, the X chromosome and the Y chromosome in Bos taurus genome.

ABSTRACT: The new ARS-UCD1.2 assembly of the bovine genome has considerable improvements over the previous assembly and thus more accurate identification of patterns of genetic variation can be achieved with it. We explored differences in genetic variation between autosomes, the X chromosome, and the Y chromosome. In particular, variant densities, annotations, lengths (only for InDels), nucleotide divergence, and Tajima's D statistics between chromosomes were considered. Whole-genome DNA sequences of 217 individuals representing different cattle breeds were examined. The analysis included the alignment to the new reference genome and variant identification. 23,655,295 SNPs and 3,758,781 InDels were detected. In contrast to autosomes, both sex chromosomes had negative values of Tajima's D and lower nucleotide divergence. That implies a correlation between nucleotide diversity and recombination rate, which is obviously reduced for sex chromosomes. Moreover, the accumulation of nonsynonymous mutations on the Y chromosome could be associated with loss of recombination. Also, the relatively lower effective population size for sex chromosomes leads to a lower expected density of variants.

SUBMITTER: Czech B

PROVIDER: S-EPMC7423949 | biostudies-literature | 2020 Aug

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

Patterns of DNA variation between the autosomes, the X chromosome and the Y chromosome in Bos taurus genome.

Czech Bartosz B Guldbrandtsen Bernt B Szyda Joanna J

Scientific reports 20200812 1

The new ARS-UCD1.2 assembly of the bovine genome has considerable improvements over the previous assembly and thus more accurate identification of patterns of genetic variation can be achieved with it. We explored differences in genetic variation between autosomes, the X chromosome, and the Y chromosome. In particular, variant densities, annotations, lengths (only for InDels), nucleotide divergence, and Tajima's D statistics between chromosomes were considered. Whole-genome DNA sequences of 217 ...[more]

PMID: 32788585

Similar Datasets

Project description:Proteins are the major constituents of muscle and are key molecules regulating the metabolic changes during conversion of muscle to meat. Brazil is one of the largest exporters of beef and most Brazilian cattle are composed by zebu (Nellore) genotype. Bos indicus beef is generally leaner and tougher than Bos taurus such as Angus. The aim of this study was to compare the muscle proteomic and phosphoproteomic profile of Angus and Nellore. Seven animals of each breed previously subjected the same growth management were confined for 84 days. Proteins were extracted from Longissimus lumborum samples collected immediately after slaughter and separated by two-dimensional electrophoresis. Pro-Q Diamond stain was used in phosphoproteomics. Proteins identification was performed using matrix assisted laser desorption/ionization time-of-flight mass spectrometry. Tropomyosin alpha-1 chain, troponin-T, myosin light chain-1 fragment, cytoplasmic malate dehydrogenase, alpha-enolase and 78 kDa glucose-regulated protein were more abundant in Nellore, while myosin light chain 3, prohibitin, mitochondrial stress-70 protein and heat shock 70 kDa protein 6 were more abundant in Angus (P<0.05). Nellore had higher phosphorylation of myosin regulatory light chain-2, alpha actin-1, triosephosphate isomerase and 14-3-3 protein epsilon. However, Angus had greater phosphorylation of phosphoglucomutase-1 and troponin-T (P<0.05). Therefore, proteins involved in contraction and muscle organization, myofilaments expressed in fast or slow-twitch fibers and heat shock proteins localized in mitochondria or sarcoplasmic reticulum and involved in cell flux of calcium and apoptosis might be associated with differences in beef quality between Angus and Nellore. Furthermore, prohibitin appears to be a potential biomarker of intramuscular fat in cattle. Additionally, differences in phosphorylation of myofilaments and glycolytic enzymes could be involved with differences in muscle contraction force, susceptibility to calpain, apoptosis and postmortem glycolysis, which might also be related to differences in beef quality among Angus and Nellore.

Dataset Information

Patterns of DNA variation between the autosomes, the X chromosome and the Y chromosome in Bos taurus genome.

Publications

Patterns of DNA variation between the autosomes, the X chromosome and the Y chromosome in Bos taurus genome.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets