Genome-wide analysis sheds light on the high-altitude adaptation of the buff-throated partridge (Tetraophasis szechenyii)

Zhou, Chuang; James, Jake George; Xu, Yu; Tu, Hongmei; He, Xingcheng; Wen, Qinchao; Price, Megan; Yang, Nan; Wu, Yongjie; Ran, Jianghong; Yang, Meng; Yue, Bisong

doi:10.1007/s00438-019-01601-8

Cited by 13 publications

(17 citation statements)

References 81 publications

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“…The genome size of L. relictus was similar to those of some other Aves, such as P. pugnax (1.25 Gb) [18]. The GC content of the L. relictus genome was similar to that of other Aves, such as 41.43% in Tetraophasis szechenyii [19], an average of 42.5% in P. pugnax and an average of 41.5% in G. gallus [18]. This proportion of repeat sequences is similar to that found in previous studies, in which almost all avian genomes contained lower levels of repeat elements than other animal genomes, with percentages of approximately 4-10% [16].…”

Section: Genomic Characteristics and Evolutionsupporting

confidence: 58%

Genome-Wide Analyses of the Relict Gull (Larus Relictus) Insights Into Evolutionary Implications

Liu

Wang

et al. 2020

Preprint

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BackgroundThe relict gull (Larus relictus), one of the least known Aves, was classified as vulnerable on the IUCN Red List and is a first-class national protected bird in China. Genomic resources for L. relictus are lacking, which limits the study of its evolution and its conservation.ResultsIn this study, based on the Illumina and PacBio sequencing platforms, we successfully assembled the genome of L. relictus, the first reference genome of the genus Larus. The size of the final assembled genome was 1.21 Gb, with a contig N50 of 8.11 Mb. A total of 18,454 protein-coding genes were predicted from the assembly results, with 16,967 (91.94%) of these genes annotated. The genome contained 92.52 Mb of repeat sequence, accounting for 7.63% of the assembly. The phylogenetic tree was constructed using 7,339 single-copy orthologous genes, which showed Charadriiformes located at the basal position and Philomachus pugnax as the closest relative of L. relictus. The divergence time between L. relictus and P. pugnax was ~68.44 Mya. The population dynamics of the Ordos breeding subpopulation in Hongjian Nur is a good confirmation that these birds are suffering from habitat loss and fragmentation.ConclusionsThis assembled genome will be a valuable genomic resource for a range of genomic and conservation studies of L. relictus and helps to establish a foundation for further studies investigating whether the other three breeding subpopulations have combined with the Ordos breeding subpopulation. As the species is threatened by habitat loss and fragmentation, actions to protect L. relictus are suggested to improve the fragmentation of breeding populations.

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Section: Genomic Characteristics and Evolutionsupporting

confidence: 58%

Genome-Wide Analyses of the Relict Gull (Larus Relictus) Insights Into Evolutionary Implications

Liu

Wang

et al. 2020

Preprint

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“…The average GC content of the bar-headed goose genome was around 41.87%, similar to that of the other birds such as Sichuan white goose (Anser cygnoides Linn. var domestica) (Gao et al, 2016) and buff-throated partridge (Tetraophasis szechenyii) (Zhou et al, 2019). Repeat sequences comprised approximately 8.9% of the bar-headed goose genome, which was higher than that of the Sichuan white goose genome at 6.9%.…”

Section: Discussionmentioning

confidence: 97%

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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“…Indeed, most environmental variables used in GEA studies are related to temperature and precipitation, while other variables such as solar radiation, daylight hours, evaporation, and wind, that could also play a role in adaptation are not widely used. Solar radiation, and more specifically UV‐B radiation, could be relevant as DNA damage responses are known to play a role in adaptation of several species such as birds, insects or fungi (Körner, 2007; Svetec et al, 2016; Wu et al, 2019; Zhou et al, 2020). Daylight hours is related to the circadian rhythm, which for example is known to play a role in Drosophila behavioural adaptation to high latitudes (Helfrich‐Förster et al, 2020).…”

Section: Introductionmentioning

confidence: 99%

Temperature, rainfall and wind variables underlie environmental adaptation in natural populations of Drosophila melanogaster

et al. 2021

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While several studies in a diverse set of species have shed light on the genes underlying adaptation, our knowledge on the selective pressures that explain the observed patterns lags behind. Drosophila melanogaster is a valuable organism to study environmental adaptation because this species originated in Southern Africa and has recently expanded worldwide, and also because it has a functionally well‐annotated genome. In this study, we aimed to decipher which environmental variables are relevant for adaptation of D. melanogaster natural populations in Europe and North America. We analysed 36 whole‐genome pool‐seq samples of D. melanogaster natural populations collected in 20 European and 11 North American locations. We used the BayPass software to identify single nucleotide polymorphisms (SNPs) and transposable elements (TEs) showing signature of adaptive differentiation across populations, as well as significant associations with 59 environmental variables related to temperature, rainfall, evaporation, solar radiation, wind, daylight hours, and soil type. We found that in addition to temperature and rainfall, wind related variables are also relevant for D. melanogaster environmental adaptation. Interestingly, 23%–51% of the genes that showed significant associations with environmental variables were not found overly differentiated across populations. In addition to SNPs, we also identified 10 reference transposable element insertions associated with environmental variables. Our results showed that genome‐environment association analysis can identify adaptive genetic variants that are undetected by population differentiation analysis while also allowing the identification of candidate environmental drivers of adaptation.

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Genome-wide analysis sheds light on the high-altitude adaptation of the buff-throated partridge (Tetraophasis szechenyii)

Cited by 13 publications

References 81 publications

Genome-Wide Analyses of the Relict Gull (Larus Relictus) Insights Into Evolutionary Implications

Genome-Wide Analyses of the Relict Gull (Larus Relictus) Insights Into Evolutionary Implications

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

Temperature, rainfall and wind variables underlie environmental adaptation in natural populations of Drosophila melanogaster

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