The x-axis indicates the position around gene bodies, and the y-axis indicates the normalized read number. Although the domestication of chickens dates back over 10, years Xiang et al. The breed originated in Tibet and immigrated to other places.
Numerous studies have provided insights into the origin and genomic characters of high-altitude natives Bigham et al. All effective reads from each sample were initially clustered into OTUs by Uparse software Uparse v7.
Numbers of reads within a peak were compared between TC and CH using a chi-square test, in which p values were corrected by a false discovery rate to avoid false positives. The rich factor is the ratio of differentially methylated gene DMG numbers annotated in this pathway term to the total gene numbers annotated in this pathway term.
Cecal microbiota have been compared with intestinal microflora Barnes Raw reads must be quality filtered to some degree before downstream analysis. Bacteroides and the RC9 gut group were the two most abundant genera.
The distribution of allele frequencies of nonsynonymous single nucleotide polymorphisms between highland and lowland populations was analyzed using chi-square test, which showed that several differentially distributed genes with missense mutations were enriched in several functional categories, especially in blood vessel development and adaptations to hypoxia and intense radiation.
This article has been cited by other articles in PMC. Through quality control using Qiime Version 1.
Unlike their lowland counterparts, Tibetan chickens have several physiological parameters that efficiently promote the blood oxygen-carrying capacity, such as larger organs heart, liver, and lungslower arterial oxygen partial pressure, lower venous blood pH, higher venous CO2 partial pressure, and higher hemoglobin concentration Gou et al.
Filtering typically involved removing some reads based on length, quality score, ambiguous bases, homopolymers, and chimeric sequences. We speculated that the Tibetan Chicken was geographically distributed on the plateau at different altitudes, allowing the establishment of unique intestinal microflora, which would significantly contribute to their survival in the region.
This study was designed to investigate the unique structure of the intestinal flora in Tibetan Chickens under their normal habitat conditions.
Adaptation to hypoxia in animals is a complex trait that involves multigenes and multi-channel regulatory mechanisms. However, the regulatory mechanisms of these hypoxic adaptive genes remain unclear. Epigenetic DNA methylation affects many biological processes, including hypoxic adaptation; however, the regulatory genes for DNA methylation in hypoxic adaptation remain unknown.
The Tibetan chicken Gallus gallusa unique breed native to the Qinghai—Tibet Plateau, shows distinctive genetic adaptation to the high-altitude environment in which it is found.
This is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited. Three individual female embryo libraries each were prepared as biological replicates for TC and CH.
RNA sequencing revealed that several differentially expressed genes were enriched in gene ontology terms related to blood vessel and respiratory system development.Here, we assembled a de novo genome of a Tibetan chicken, and re-sequenced whole genomes of 32 additional chickens, including Tibetan chickens, village chickens, game fowl, and Red Junglefowl, and found that the Tibetan chickens could broadly be placed into two groups.
Genome methylation and regulatory functions for hypoxic adaptation in Tibetan chicken embryos Yawen Zhang, Wenyu Gou, Jun Ma, Hongliang Zhang, Ying Zhang, Hao Zhang National Engineering Laboratory for Animal Breeding/Beijing Key Laboratory for Animal Genetic Improvement, China Agricultural University, Beijing, China.
Study on Tibetan Chicken embryonic adaptability to chronic hypoxia by revealing differential gene expression in heart tissue. Sci China C Life Sci. 52 (3)– Li M., et al. Genomic analyses identify distinct patterns of selection in domesticated pigs and. Profiling the genome-wide DNAmethylation pattern of Tibetan chicken using whole genome bisulfite sequencing.
Keywords Tibetan chicken, Hypoxia adaption, MeDIP-seq, DNA methylation, Regulatory genes INTRODUCTION The molecular mechanisms underlying hypoxic. Genome methylation and regulatory functions for hypoxic adaptation in Tibetan chicken embryos. Zhang Y. et al. Tibetan chickens have unique adaptations to the extreme high-altitude environment that they inhabit.
Epigenetic DNA methylation affects many biological processes, including hypoxic adaptation; however, the regulatory genes for DNA methylation in hypoxic adaptation remain unknown.Download