Whole-genome sequencing of 128 camels across Asia reveals origin and migration of domestic Bactrian camels

Liang, Ming; Yuan, Liyun; Li, Yang; Ding, Guohui; Hasi, Surong; Chen, Gangliang; Jambl, Tuyatsetseg; Hedayat-Evright, Nemat; Batmunkh, Mijiddorj; Badmaevna, Garyaeva Khongr; Gan-Erdene, Tudeviin; Ts, Batsukh; Zhang, Wenbin; Zulipikaer, Azhati; Hosblig,; Erdemt,; Натыров, А.К.; Mamay, Prmanshayev; Narenbatu,; Meng, Gendalai; Choijilsuren, Narangerel; Khongorzul, Orgodol; He, Jing; Hải, Lê Thanh; Lin, Weili; Sirendalai,; Sarentuya,; Aiyisi,; Li, Yixue; Wang, Zhen; Jirimutu,

doi:10.1038/s42003-019-0734-6

Cited by 433 publications

(459 citation statements)

References 49 publications

(61 reference statements)

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“…Similar to the principal components analysis, the results indicated that a small amount (6.0%) of C. dromedarius ancestry is present in a C. bactrianus individual, and larger amount of C. bactrianus ancestry in a C. ferus individual (16.6%). These values are markedly similar to values reported by Ming et al 23 , where C. dromedarius ancestry in C. bactrianus ranged between 1 and 10%, and C. bactrianus ancestry in three C. ferus individuals ranged between 7 and 15%. Introgression from the domestic species into both Mongolian and Chinese populations of the Critically Endangered wild camel has been reported elsewhere using mitochondrial DNA 29 , microsatellites 30 and the Y chromosome 31 , potentially jeopardizing the wild camel's genomic integrity and evolutionary independence (~1.1 million years) 14 .…”

Section: Resultssupporting

confidence: 90%

“…Within C. dromedarius sequences aligned to the intraspecific reference, both Ts/Tv (2.49) and the number of SNPs (2,818,163) were comparable with the interspecific alignment ( Table 1). The large number of SNPs shared between the domesticated species is consistent with known introgression events and has been observed in other genomic studies of camels 23 . Anthropogenic hybridization between the domesticated dromedary and Bactrian camel, especially in central Asia, is a widely practiced tradition of cross-breeding aimed at improving milk production (F1 backcrossed with dromedary), wool and meat yield, cold resistance (F1 backcrossed with Bactrian camel), or for camel wrestling 24,25 .…”

Section: Resultssupporting

confidence: 87%

“…These patterns of genetic variation and heterozygosity are consistent with the relative differences observed between single genomes of the same species [15][16][17][18] . Interestingly, Ming et al 23 reported similar patterns of genetic variation in C. bactrianus (π = 0.95 × 10 −3 − 1.1 × 10 −3 ) and C. ferus (π = 0.88 × 10 −3 compared with 0.71 × 10 −3 in this study), but nearly threefold higher levels in C. dromedarius (π = 1.5 × 10 −3 ). Although this finding by Ming et al conflicts with our results and that of the previously mentioned studies [15][16][17][18] , the authors attributed this to the small sample size (n = 4) and being sampled from Iran where hybridization with C. bactrianus is commonplace.…”

Section: Resultssupporting

confidence: 75%

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Genomic signatures of domestication in Old World camels

et al. 2020

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Domestication begins with the selection of animals showing less fear of humans. In most domesticates, selection signals for tameness have been superimposed by intensive breeding for economical or other desirable traits. Old World camels, conversely, have maintained high genetic variation and lack secondary bottlenecks associated with breed development. By resequencing multiple genomes from dromedaries, Bactrian camels, and their endangered wild relatives, here we show that positive selection for candidate genes underlying traits collectively referred to as 'domestication syndrome' is consistent with neural crest deficiencies and altered thyroid hormone-based signaling. Comparing our results with other domestic species, we postulate that the core set of domestication genes is considerably smaller than the pandomestication setand overlapping genes are likely a result of chance and redundancy. These results, along with the extensive genomic resources provided, are an important contribution to understanding the evolutionary history of camels and the genomic features of their domestication.

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Section: Resultssupporting

confidence: 90%

Section: Resultssupporting

confidence: 87%

Section: Resultssupporting

confidence: 75%

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Genomic signatures of domestication in Old World camels

et al. 2020

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“…One possible explanation for these results is that the wild camel suffered strong population declines leading to the current status of "critically endangered" species (by the International Union for Conservation of Nature (IUCN)). Thus, with the number of individuals decreasing, loss of genetic diversity is unfortunately real [42,43]. Another possible explanation is that domestic Bactrian camels are under higher pathogenic pressure compared to the wild species.…”

Section: Nucleotide Diversity In Important Immune Gene Groupsmentioning

confidence: 99%

Nucleotide diversity of functionally different groups of immune response genes in Old World camels based on newly annotated and reference-guided assemblies

Lado¹,

Elbers²,

Rogers

et al. 2020

BMC Genomics

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Background: Immune-response (IR) genes have an important role in the defense against highly variable pathogens, and therefore, diversity in these genomic regions is essential for species' survival and adaptation. Although current genome assemblies from Old World camelids are very useful for investigating genome-wide diversity, demography and population structure, they have inconsistencies and gaps that limit analyses at local genomic scales. Improved and more accurate genome assemblies and annotations are needed to study complex genomic regions like adaptive and innate IR genes. Results: In this work, we improved the genome assemblies of the three Old World camel speciesdomestic dromedary and Bactrian camel, and the two-humped wild camelvia different computational methods. The newly annotated dromedary genome assembly CamDro3 served as reference to scaffold the NCBI RefSeq genomes of domestic Bactrian and wild camels. These upgraded assemblies were then used to assess nucleotide diversity of IR genes within and between species, and to compare the diversity found in immune genes and the rest of the genes in the genome. We detected differences in the nucleotide diversity among the three Old World camelid species and between IR gene groups, i.e., innate versus adaptive. Among the three species, domestic Bactrian camels showed the highest mean nucleotide diversity. Among the functionally different IR gene groups, the highest mean nucleotide diversity was observed in the major histocompatibility complex.

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“…Thus, with the number of individuals decreasing, loss of genetic diversity is unfortunately real [34,35].…”

Section: Old World Camelids Genome Assemblies´ Improvementmentioning

confidence: 99%

Nucleotide diversity of functionally different groups of immune response genes in Old World camels based on newly annotated and reference-guided assemblies

Lado¹,

Elbers²,

Rogers

et al. 2020

Preprint

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Background Immune-response (IR) genes have an important role in the defense against highly variable pathogens, and therefore, genetic diversity in these genomic regions is essential for species’ survival and adaptation. Although current genome assemblies from Old World camelids are very useful for investigating genome-wide diversity, demography and population structure, they have inconsistencies and gaps that limit analyses at local genomic scales. Improved and more accurate genome assemblies and annotations are needed to study complex genomic regions like adaptive and innate IR genes. Results In this work, we improved the genome assemblies in the three Old World camel species – domestic dromedary and Bactrian camel, and the two-humped wild camel – via different computational methods. The newly annotated dromedary genome assembly CamDro3 served as reference to scaffold the NCBI RefSeq genomes of domestic Bactrian and wild camels. These upgraded assemblies were then used to assess nucleotide diversity of IR genes within and between species, and to compare the diversity found in immune genes and the rest of the genes in the genome. We detected differences in the nucleotide diversity among the three Old World camelid species and between IR gene groups, i.e., innate versus adaptive. Among the three species, domestic Bactrian camels showed the highest mean nucleotide diversity. Among the functionally different IR gene groups, the highest mean nucleotide diversity was observed in the major histocompatibility complex. Conclusions The new camel genome assemblies were greatly improved in terms of contiguity and increased size with fewer scaffolds, which is of general value for the scientific community. This allowed us to perform in-depth studies on genetic diversity in immunity-related regions of the genome. Our results suggest that differences of diversity across classes of genes appear compatible with being caused by a combination of population history coupled with possible distinct exposures to pathogens and consequent different selective pressures.

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Whole-genome sequencing of 128 camels across Asia reveals origin and migration of domestic Bactrian camels

Cited by 433 publications

References 49 publications

Genomic signatures of domestication in Old World camels

Genomic signatures of domestication in Old World camels

Nucleotide diversity of functionally different groups of immune response genes in Old World camels based on newly annotated and reference-guided assemblies

Nucleotide diversity of functionally different groups of immune response genes in Old World camels based on newly annotated and reference-guided assemblies

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