Camelid genomes reveal evolution and adaptation to desert environments

Wu, Huiguang; Guang, Xuanmin; Al-Fageeh, Mohamed B.; Cao, Junwei; Pan, Shengkai; Zhou, Huanmin; Zhang, Li; Abutarboush, Mohammed H.; Xing, Yanping; Xie, Zhiyuan; Alshanqeeti, Ali S.; Zhang, Yanru; Yao, Qizheng; Al-Shomrani, Badr M.; Zhang, Dong; Jiang, Li; Manee, Manee M.; Yang, Zidong; Yang, L.; Liu, Yiyi; Zhang, Jilin; Altammami, Musaad A.; Wang, Shenyuan; Yu, Lili; Zhang, Wenbin; Liu, Sanyang; Ba, La; Liu, Chunxia; Yang, Xukui; Meng, Fengyan; Wang, Shaowei; Li, Lü; Li, Erli; Li, Xueqiong; Wu, Keyue; Shu, Zhang; Wang, Junyi; Yin, Ye; Yang, Huanming; Al-Swailem, Abdulaziz M.; Wang, Jun

doi:10.1038/ncomms6188

Cited by 230 publications

(322 citation statements)

References 63 publications

(49 reference statements)

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“…This appears to be common among species that are adapted to desert and desert-like environments. For instance, in a comparative genomic analysis, Wu et al (2014) revealed complex features, such as fat and water metabolism, stress response to heat and aridity, intense ultraviolet radiation and chocking dust, in the genome architecture of camelids that are related to adaptation to desert environments.…”

Section: Discussionmentioning

confidence: 99%

Multiple genomic signatures of selection in goats and sheep indigenous to a hot arid environment

et al. 2015

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Goats and sheep are versatile domesticates that have been integrated into diverse environments and production systems. Natural and artificial selection have shaped the variation in the two species, but natural selection has played the major role among indigenous flocks. To investigate signals of natural selection, we analyzed genotype data generated using the caprine and ovine 50K SNP BeadChips from Barki goats and sheep that are indigenous to a hot arid environment in Egypt's Coastal Zone of the Western Desert. We identify several candidate regions under selection that spanned 119 genes. A majority of the genes were involved in multiple signaling and signal transduction pathways in a wide variety of cellular and biochemical processes. In particular, selection signatures spanning several genes that directly or indirectly influenced traits for adaptation to hot arid environments, such as thermo-tolerance (melanogenesis) (FGF2, GNAI3, PLCB1), body size and development (BMP2, BMP4, GJA3, GJB2), energy and digestive metabolism (MYH, TRHDE, ALDH1A3), and nervous and autoimmune response (GRIA1, IL2, IL7, IL21, IL1R1) were identified. We also identified eight common candidate genes under selection in the two species and a shared selection signature that spanned a conserved syntenic segment to bovine chromosome 12 on caprine and ovine chromosomes 12 and 10, respectively, providing, most likely, the evidence for selection in a common environment in two different but closely related species. Our study highlights the importance of indigenous livestock as model organisms for investigating selection sweeps and genome-wide association mapping.

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Section: Discussionmentioning

confidence: 99%

Multiple genomic signatures of selection in goats and sheep indigenous to a hot arid environment

et al. 2015

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“…These animals have served for traditional technologies since the very early era of domestication (Elsik et al 2009;Archibald et al 2010;Dong et al 2013;Wu et al 2014). In addition, some of domestic even-toed ungulates are now used as animal models in biomedical researches to investigate the genetic basis of complex traits, to produce transgenic peptide medicines, and to come up with some special form of antibody offering particular advantages in various medical and biotechnological applications (Kastelic et al 2009;Jirimutu et al 2012).…”

Section: Introductionmentioning

confidence: 99%

Genome-wide analysis of CpG islands in some livestock genomes and their relationship with genomic features

Barazandeh¹,

Mohammadabadi²,

Ghaderi–Zefrehei³

et al. 2016

CZECH J ANIM SCI

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CpG islands (CGIs) are an important group of CpG dinucleotides in the guanine-and cytosinerich regions as they harbour functionally relevant epigenetic loci for whole genome studies. As a matter of fact, since there has not been a formal comparative analysis of CGIs in domestic even-toed ungulate genomes, this study was performed to serve this comparison. The Hidden Markov Model was used to detect CGIs in the genomes. The results indicated that the CGIs number and CGI densities had scant variations across genomes. The goat genome had the highest number of CGIs (99 070), whereas the alpaca genome had the highest CGI density (43.39 CGIs/Mb). Significant positive correlations were observed among CGI densities with chromosome pair number, observed CpG/expected CpG, recombination rate, and gene density. When the size of chromosomes increased, the CGI densities decreased and a trend of higher CGI densities in the telomeric regions was observed. Only 10.96% of CGIs were methylated underscoring this postulation that the majority of CGIs remains to be unmethylated. The highest amount of the methylated CGIs was observed in the introns, intergenic, and coding (CDS) regions and the lowest amount of the methylated CGIs was observed in the promoter regions, implying that the DNA methylation of CGIs may control gene expression at the genome level. Detected differences between even-toed ungulate and other vertebrate genomes showed that CGI densities varied greatly among the genomes. These findings would contribute to better understanding the even-toed ungulate (epi) genomes, the role of CGIs in epigenomic functions and molecular evolution.

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“…This multipurpose animal has outperformed all other domestic mammals, including the donkey, in arid environments and continues to provide basic commodities to millions of people inhabiting marginal agro-ecological zones. In the current context of advancing desertification and global climate change, there is renewed interest in the biology and production traits of the species (2), with the first annotated genome drafts having been recently released (3,4).…”

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confidence: 99%

Ancient and modern DNA reveal dynamics of domestication and cross-continental dispersal of the dromedary

Almathen

Charruau

Mohandesan

et al. 2016

Proc. Natl. Acad. Sci. U.S.A.

106

128

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Dromedaries have been fundamental to the development of human societies in arid landscapes and for long-distance trade across hostile hot terrains for 3,000 y. Today they continue to be an important livestock resource in marginal agro-ecological zones. However, the history of dromedary domestication and the influence of ancient trading networks on their genetic structure have remained elusive. We combined ancient DNA sequences of wild and early-domesticated dromedary samples from arid regions with nuclear microsatellite and mitochondrial genotype information from 1,083 extant animals collected across the species' range. We observe little phylogeographic signal in the modern population, indicative of extensive gene flow and virtually affecting all regions except East Africa, where dromedary populations have remained relatively isolated. In agreement with archaeological findings, we identify wild dromedaries from the southeast Arabian Peninsula among the founders of the domestic dromedary gene pool. Approximate Bayesian computations further support the "restocking from the wild" hypothesis, with an initial domestication followed by introgression from individuals from wild, now-extinct populations. Compared with other livestock, which show a long history of gene flow with their wild ancestors, we find a high initial diversity relative to the native distribution of the wild ancestor on the Arabian Peninsula and to the brief coexistence of early-domesticated and wild individuals. This study also demonstrates the potential to retrieve ancient DNA sequences from osseous remains excavated in hot and dry desert environments.anthropogenic admixture | Camelus dromedarius | demographic history | paleogenetics | wild dromedary T he dromedary (Camelus dromedarius) is one of the largest domestic ungulates and one of the most recent additions to livestock. Known as the "ship of the desert" (1), it enabled the transportation of people and valuable goods (e.g., salt, incense, spices) over long distances connecting Arabia, the Near East, and North Africa. This multipurpose animal has outperformed all other domestic mammals, including the donkey, in arid environments and continues to provide basic commodities to millions of people inhabiting marginal agro-ecological zones. In the current context of advancing desertification and global climate change, there is renewed interest in the biology and production traits of the species (2), with the first annotated genome drafts having been recently released (3, 4). SignificanceThe dromedary is one of the largest domesticates, sustainably used in arid and hostile environments. It provides food and transport to millions of people in marginal agricultural areas. We show how important long-distance and back-and-forth movements in ancient caravan routes shaped the species' genetic diversity. Using a global sample set and ancient mitochondrial DNA analyses, we describe the population structure in modern dromedaries and their wild extinct ancestors. Phylogenetic analyses of ancient and modern dro...

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Camelid genomes reveal evolution and adaptation to desert environments

Cited by 230 publications

References 63 publications

Multiple genomic signatures of selection in goats and sheep indigenous to a hot arid environment

Multiple genomic signatures of selection in goats and sheep indigenous to a hot arid environment

Genome-wide analysis of CpG islands in some livestock genomes and their relationship with genomic features

Ancient and modern DNA reveal dynamics of domestication and cross-continental dispersal of the dromedary

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