Large-scale ruminant genome sequencing provides insights into their evolution and distinct traits

Chen, Lei; Qiu, Qiang; Jiang, Yu; Wang, Kun; Wang, Qisheng; Li, Zhipeng; Bibi, Faysal; Yang, Yongzhi; Wang, Jinhuan; Nie, Wei; Su, Wencheng; Liu, Guichun; Li, Qiye; Fu, Weiwei; Pan, Xiangyu; Liu, Chang; Yang, Jie; Zhang, Chenzhou; Yin, Yuan; Wang, Yu; Zhao, Yue; Wang, Zhongkai; Qin, Yanli; Liu, Wei; Bao, Wang; Ren, Yandong; Zhang, Ru; Zeng, Yan; Fonseca, Rute R. da; Wei, Bin; Li, Ran; Wan, Wenting; Zhao, Ruoping; Zhu, Wenbo; Wang, Yutao; Duan, Shengchang; Gao, Yun; Zhang, Yong E.; Chen, Chunyan; Hvilsom, Christina; Epps, Clinton W.; Chemnick, Leona G.; Dong, Yang; Mirarab, Siavash; Siegismund, Hans R.; Ryder, Oliver A.; Gilbert, M. Thomas P.; Lewin, Harris A.; Zhang, Guojie; Heller, Rasmus; Wang, Wen

doi:10.1126/science.aav6202

Cited by 332 publications

(366 citation statements)

References 184 publications

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“…Our reindeer genome assembly is 2.66 Gb in size and represents ~91% of the estimated 2.92 Gb genome size according to the k-mer analysis. The estimated genome size of reindeer in our study is slightly higher than that in two recent studies, i.e., 2.86 48 19 ). In addition, the number of protein-coding annotated genes (>27,000) in our genome assembly draft is higher than that typically predicted in the latest assemblies of several other domesticated mammalian species (~21,000) [18][19][20]25,33 and in the first genome draft of reindeer (21,555) 21 .…”

Section: Discussioncontrasting

confidence: 80%

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Genome sequence and comparative analysis of reindeer (Rangifer tarandus) in northern Eurasia

Weldenegodguad

Pokharel

Yao

et al. 2019

Preprint

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18Reindeer are semi-domesticated ruminants that have adapted to the challenging northern 19 Eurasian environment characterized by long winters and marked annual fluctuations in daylight. 20We explored the genetic makeup behind their unique characteristics by de novo sequencing the 21 genome of a male reindeer and conducted gene family analyses with nine other mammalian 22 species. We performed a population genomics study of 23 additional reindeer representing both 23 domestic and wild populations and several ecotypes from various geographic locations. We 24 assembled 2.66 Gb (N50 scaffold of 5 Mb) of the estimated 2.92 Gb reindeer genome, 25comprising 27,332 genes. The results from the demographic history analysis suggested marked 26 changes in the effective population size of reindeer during the Pleistocene period. We detected 27 160 reindeer-specific and expanded genes, of which zinc finger proteins (n=42) and olfactory 28 receptors (n=13) were the most abundant. Comparative genome analyses revealed several genes 29 that may have promoted the adaptation of reindeer, such as those involved in recombination and 30 speciation (PRDM9), vitamin D metabolism (TRPV5, TRPV6), retinal development (PRDM1, 31 OPN4B), circadian rhythm (GRIA1), immunity (CXCR1, CXCR2, CXCR4, IFNW1), tolerance to 32 cold-triggered pain (SCN11A) and antler development (SILT2). The majority of these 33 characteristic reindeer genes have been reported for the first time here. Moreover, our population 34 genomics analysis suggested at least two independent reindeer domestication events with genetic 35 lineages originating from different refugial regions after the Last Glacial Maximum. Taken 36 together, our study has provided new insights into the domestication, evolution and adaptation of 37 reindeer and has promoted novel genomic research of reindeer. 38

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Section: Discussioncontrasting

confidence: 80%

“…Our phylogeny suggests that reindeer diverged from four other domestic ruminants ca. 36 million years ago, which is earlier than previously estimated 21,48 . The demographic analysis (Fig.…”

Section: Discussionmentioning

confidence: 66%

Genome sequence and comparative analysis of reindeer (Rangifer tarandus) in northern Eurasia

Weldenegodguad

Pokharel

Yao

et al. 2019

Preprint

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“…Similarly, bones of leopard ( Panthera pardus ) have been found associated with hunting by prehistoric humans throughout Europe (reviewed by Sommer & Benecke, ). Additionally, the decline of ruminants since 100–50 kya has been partially attributed to human activities, rather than climatic oscillations (Chen et al, ), and hence the lynx decline during the Late Pleistocene could also be indirectly attributable to humans through negative effects on prey. Our hypothesis is in line with previous work that supports the idea that anthropogenic impacts in combination with climatic oscillations were one of the main drivers of the decline, and in some cases the extinction, of fauna and flora during the Late Pleistocene and early Holocene (Braje & Erlandson, ; Chen et al, ; Gretzinger et al, ; Lorenzen et al, ).…”

Section: Discussionmentioning

confidence: 99%

Genomic patterns in the widespread Eurasian lynx shaped by Late Quaternary climatic fluctuations and anthropogenic impacts

et al. 2020

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Disentangling the contribution of long‐term evolutionary processes and recent anthropogenic impacts to current genetic patterns of wildlife species is key to assessing genetic risks and designing conservation strategies. Here, we used 80 whole nuclear genomes and 96 mitogenomes from populations of the Eurasian lynx covering a range of conservation statuses, climatic zones and subspecies across Eurasia to infer the demographic history, reconstruct genetic patterns, and discuss the influence of long‐term isolation and/or more recent human‐driven changes. Our results show that Eurasian lynx populations shared a common history until 100,000 years ago, when Asian and European populations started to diverge and both entered a period of continuous and widespread decline, with western populations, except Kirov, maintaining lower effective sizes than eastern populations. Population declines and increased isolation in more recent times probably drove the genetic differentiation between geographically and ecologically close westernmost European populations. By contrast, and despite the wide range of habitats covered, populations are quite homogeneous genetically across the Asian range, showing a pattern of isolation by distance and providing little genetic support for the several proposed subspecies. Mitogenomic and nuclear divergences and population declines starting during the Late Pleistocene can be mostly attributed to climatic fluctuations and early human influence, but the widespread and sustained decline since the Holocene is more probably the consequence of anthropogenic impacts which intensified in recent centuries, especially in western Europe. Genetic erosion in isolated European populations and lack of evidence for long‐term isolation argue for the restoration of lost population connectivity.

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“…A major goal of evolutionary biology is to elucidate the genomic underpinnings of phenotypic innovations across the tree of life. Over the past decade, comparative genomics has been used as a powerful tool to begin to elucidate the genetic basis of phenotypic innovations and adaptation in a wide range of organisms (Xu et al 2017;Gou et al 2014;Zhang et al 2014;Chen et al 2019;Exposito-Alonso et al 2018;Gaither et al 2018;Goodman et al 2009;Wang et al 2019;Wu et al 2014). These studies have often identified changes in gene repertoire (e.g., expansions of certain gene families) or genomic signatures of molecular evolution at orthologous genes, by comparing the genomes of species with and without a phenotype of interest (Xu et al 2017;Gou et al 2014;Gaither et al 2018;Goodman et al 2009;Wang et al 2019;Wu et al 2014).…”

Section: Introductionmentioning

confidence: 99%

Comparative genomics identifies putative signatures of sociality in spiders

Tong

Najm

Pinter‐Wollman

et al. 2019

Preprint

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Comparative genomics has begun to elucidate the genomic basis of social life in insects but insight into the genomic basis of spider sociality has lagged behind. To begin to characterize genomic signatures associated with the evolution of social life in spiders, we performed one of the first spider comparative genomics studies including five solitary species and two social species, representing two independent origins of sociality in the genus Stegodyphus. We found that the two social spider species had a large expansion of gene families associated with transport and metabolic processes and an elevated genomewide rate of molecular evolution compared with the five solitary spider species. Genes that were rapidly evolving in the two social species relative to the five solitary species were enriched for transport, behavior, and immune functions, while genes that were rapidly evolving in the solitary species were enriched for energy metabolism processes. Most rapidly evolving genes in the social species S. dumicola were broadly expressed across four tissues and enriched for transport functions, but 12 rapidly evolving genes showed brain-specific expression and were enriched for social behavioral processes. Altogether, our study identifies putative genomic signatures and potential candidate genes associated with spider sociality. These results indicate that future spider comparative genomic studies, including broader sampling and additional independent origins of sociality, can further clarify the genomic causes and consequences of social life.

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Large-scale ruminant genome sequencing provides insights into their evolution and distinct traits

Cited by 332 publications

References 184 publications

Genome sequence and comparative analysis of reindeer (Rangifer tarandus) in northern Eurasia

Genome sequence and comparative analysis of reindeer (Rangifer tarandus) in northern Eurasia

Genomic patterns in the widespread Eurasian lynx shaped by Late Quaternary climatic fluctuations and anthropogenic impacts

Comparative genomics identifies putative signatures of sociality in spiders

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