Genetic responses to seasonal variation in altitudinal stress: whole-genome resequencing of great tit in eastern Himalayas

Qu, Yanhua; Tian, Shilin; Han, Ning; Zhao, Hongwei; Gao, Bin; Fu, Jun; Cheng, Yanhao; Song, Gang; Ericson, Per G. P.; Zhang, Yong E.; Wang, Dawei; Qing, Quan; Jiang, Zhi; Li, Ruiqiang; Lei, Fumin

doi:10.1038/srep14256

Cited by 40 publications

(45 citation statements)

References 57 publications

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“…Analysis using genome sequencing and ChIP has shown that the ITGA2 gene assists hypoxic adaptation in Tibetan pigs and great tits in the highlands (Ai et al, 2014; Qu et al, 2015). In the present study, ITGA2 was down-methylated in promoter regions, resulting in the upregulation of gene expression in TC compared to CH.…”

Section: Discussionmentioning

confidence: 99%

Genome methylation and regulatory functions for hypoxic adaptation in Tibetan chicken embryos

Zhang

Gou

et al. 2017

PeerJ

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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. In this study, methylated DNA immunoprecipitation with high-throughput sequencing (MeDIP-seq) was used to provide an atlas of the DNA methylomes of the heart tissue of hypoxic highland Tibetan and lowland Chahua chicken embryos. A total of 31.2 gigabases of sequence data were generated from six MeDIP-seq libraries. We identified 1,049 differentially methylated regions (DMRs) and 695 related differentially methylated genes (DMGs) between the two chicken breeds. The DMGs are involved in vascular smooth muscle contraction, VEGF signaling pathway, calcium signaling pathway, and other hypoxia-related pathways. Five candidate genes that had low methylation (EDNRA, EDNRB2, BMPR1B, BMPRII, and ITGA2) might play key regulatory roles in the adaptation to hypoxia in Tibetan chicken embryos. Our study provides significant explanations for the functions of genes and their epigenetic regulation for hypoxic adaptation in Tibetan chickens.

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Section: Discussionmentioning

confidence: 99%

Genome methylation and regulatory functions for hypoxic adaptation in Tibetan chicken embryos

Zhang

Gou

et al. 2017

PeerJ

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“…Gene families were identified using TreeFam (Li et al, 2006) with default settings from 16 animal genomes [bar-headed goose (Anser indicus), swan goose (Anser cygnoides) (Lu et al, 2015), crested ibis (Nipponia nippon) , mallard (Anas platyrhynchos) (Huang et al, 2013), red junglefowl (Gallus gallus) (International Chicken Genome Sequencing Consortium, 2004), turkey (Meleagris gallopavo) (Dalloul et al, 2010), common cuckoo (Cuculus canorus) (https://www.ncbi.nlm.nih.gov/assembly/GCF_000709325.1/), rock pigeon (Columba livia) (Shapiro et al, 2013), ground tit (Pseudopodoces humilis) (Qu et al, 2013), bananaquit (Coereba flaveola) (Antonides, Ricklefs & DeWoody, 2017), great tit (Parus major) (Qu et al, 2015), zebra finch (Taeniopygia guttata) (Warren et al, 2010), ruff (Philomachus pugnax) (Lamichhaney et al, 2016), peregrine falcon (Falco peregrinus) (Zhan et al, 2013), yak (Bos mutus) (Qiu et al, 2012) and tibetan antelope (Pantholops hodgsonii) (Ge et al, 2013)]. A total of 2,888 single-copy orthologs, shared by these 16 species, were finally identified.…”

Section: Comparative Genome Analysismentioning

confidence: 99%

“…Understanding how vertebrates cope with these harsh conditions can provide important insights into the process of adaptive evolution (Zhang et al, 2016a;Zhang et al, 2016b). Among the high-altitude-adapted vertebrates, birds in general have excellent hypoxia tolerance and can maintain the highest basal metabolic rates during hypoxia too severe for most mammals to survive (Tucker, 1968;Faraci, 1991;Monge & Leon-Velarde, 1991), and are therefore especially compelling subjects for studies of high-altitude adaptation (Projecto-Garcia et al, 2013;Qu et al, 2013;Qu et al, 2015;Zhu et al, 2018).…”

Section: Introductionmentioning

confidence: 99%

First de novo whole genome sequencing and assembly of the bar-headed goose

Wang

Hao

et al. 2020

PeerJ

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Background The bar-headed goose (Anser indicus) mainly inhabits the plateau wetlands of Asia. As a specialized high-altitude species, bar-headed geese can migrate between South and Central Asia and annually fly twice over the Himalayan mountains along the central Asian flyway. The physiological, biochemical and behavioral adaptations of bar-headed geese to high-altitude living and flying have raised much interest. However, to date, there is still no genome assembly information publicly available for bar-headed geese. Methods In this study, we present the first de novo whole genome sequencing and assembly of the bar-headed goose, along with gene prediction and annotation. Results 10X Genomics sequencing produced a total of 124 Gb sequencing data, which can cover the estimated genome size of bar-headed goose for 103 times (average coverage). The genome assembly comprised 10,528 scaffolds, with a total length of 1.143 Gb and a scaffold N50 of 10.09 Mb. Annotation of the bar-headed goose genome assembly identified a total of 102 Mb (8.9%) of repetitive sequences, 16,428 protein-coding genes, and 282 tRNAs. In total, we determined that there were 63 expanded and 20 contracted gene families in the bar-headed goose compared with the other 15 vertebrates. We also performed a positive selection analysis between the bar-headed goose and the closely related low-altitude goose, swan goose (Anser cygnoides), to uncover its genetic adaptations to the Qinghai-Tibetan Plateau. Conclusion We reported the currently most complete genome sequence of the bar-headed goose. Our assembly will provide a valuable resource to enhance further studies of the gene functions of bar-headed goose. The data will also be valuable for facilitating studies of the evolution, population genetics and high-altitude adaptations of the bar-headed geese at the genomic level.

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“…MAPK1 has been reported to be involved in accelerated selection in the highland great tit during the hypoxia adaptation [21]. MAPK1 only bound to miR-19b-3p of the 14 miRNAs predicted by both TargetScan and miRanda software.…”

Section: Resultsmentioning

confidence: 99%

“…In the southwestern mountains (SWM), the great tit is distributed between 2000 and 4500 meters above sea level. The high-altitude population of great tits shows an accelerated genetic selection for carbohydrate energy metabolism and the hypoxia response (e.g., the MAPK signaling pathway) compared to lowland populations [21]. Due to the crucial role of the MAPK signaling pathway in the hypoxia response in the great tit, we chose MAPK1 as a candidate gene.…”

Section: Introductionmentioning

confidence: 99%

MiR-19b-3p Regulates MAPK1 Expression in Embryonic Fibroblasts from the Great Tit (Parus Major) Under Hypoxic Conditions

Chen

Cheng

et al. 2018

Cell Physiol Biochem

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Background/Aims: Genomic adaptations to high altitudes have been well studied in the last several years; however, the roles of microRNAs (miRNAs), which are essential modulators of a variety of genes and key cellular processes, have rarely been explored. Here, we explored the interactions between miRNAs and their target genes as an adaptation to high altitude in an avian species, the great tit (Parus major), which is widely distributed across the Eurasian continent at altitudes between 4500 m and sea level. Because the MAPK signaling pathway plays a crucial role in the hypoxia response in the great tit, we chose MAPK1 as a target candidate gene. Methods: We established a great tit embryonic fibroblast line and subsequently studied the relationship between miRNA-19b-3p and MAPK1 in normoxia and hypoxia groups. Meanwhile, the great tit embryonic fibroblasts (GEFs) were treated or transfected with miR-19b-3p mimics, inhibitors, or si-MAPK1, and their proliferation was subsequently assessed using the MTT assay. The expression of the miRNAs and MAPK1 was measured by real-time PCR and Western blotting. Results: We identified 14 miRNAs in the cardiac tissues of great tits that are related to hypoxia adaptation. MAPK1 binds only to miR-19b-3p of the 14 miRNAs predicted by both TargetScan and miRanda software. Specifically, we validated the computational prediction of miR-19b-3p binding to the 3’UTR of MAPK1 using a luciferase reporter assay. Our results show that miR-19b-3p promotes GEFs proliferation and up-regulates MAPK1 expression. Moreover, miR-19b-3p mimics and MAPK1 knockdown induce GEFs apoptosis and regulate the cell cycle under hypoxic conditions. Conclusions: Our study is the first to describe an important miRNA-mediated regulatory mechanism of high altitude adaptation in a non-model wild songbird and highlights the importance of studies on miRNA-mediated mechanisms of hypoxic adaptations in other animals.

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Genetic responses to seasonal variation in altitudinal stress: whole-genome resequencing of great tit in eastern Himalayas

Cited by 40 publications

References 57 publications

Genome methylation and regulatory functions for hypoxic adaptation in Tibetan chicken embryos

Genome methylation and regulatory functions for hypoxic adaptation in Tibetan chicken embryos

First de novo whole genome sequencing and assembly of the bar-headed goose

MiR-19b-3p Regulates MAPK1 Expression in Embryonic Fibroblasts from the Great Tit (Parus Major) Under Hypoxic Conditions

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