Whole-Genome Sequencing of African Dogs Provides Insights into Adaptations against Tropical Parasites

Yan-hu, Liu; Wang, Lu; Xu, Tao; Guo, Xin; Yang, Li; Yin, Tingting; Yang, Hongshan; Hu, Yang; Adeola, Adeniyi C.; Sanke, Oscar J; Otecko, Newton O.; Wang, Meng; Ma, Yaping; Charles, Olaogun S; Sinding, Mikkel‐Holger S.; Gopalakrishnan, Shyam; Samaniego, José A.; Hansen, Anders J.; Fernandes, Carlos; Gaubert, Philippe; Budd, Jane; Dawuda, P.M.; Rueness, Eli Knispel; Jiang, Lubin; Zhai, Weiwei; Gilbert, M. Thomas P.; Peng, Min‐Sheng; Qi, Xiaopeng; Wang, Guodong; Zhang, Yaping

doi:10.1093/molbev/msx258

Cited by 46 publications

(46 citation statements)

References 90 publications

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“…A mutation rate of 2.2 × 10 −9 per site per year with a generation time of 3 years was assumed. Since our demographic analysis did not include wolves and European breeds, the effective population sizes and split time for wolves and European breeds were taken from Wang et al 3 and Liu et al 83 .…”

Section: Methodsmentioning

confidence: 99%

Genomic regions under selection in the feralization of the dingoes

Zhang

Wang

et al. 2020

Nat Commun

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Dingoes are wild canids living in Australia, originating from domestic dogs. They have lived isolated from both the wild and the domestic ancestor, making them a unique model for studying feralization. Here, we sequence the genomes of 10 dingoes and 2 New Guinea Singing Dogs. Phylogenetic and demographic analyses show that dingoes originate from dogs in southern East Asia, which migrated via Island Southeast Asia to reach Australia around 8300 years ago, and subsequently diverged into a genetically distinct population. Selection analysis identifies 50 positively selected genes enriched in digestion and metabolism, indicating a diet change during feralization of dingoes. Thirteen of these genes have shifted allele frequencies compared to dogs but not compared to wolves. Functional assays show that an A-to-G mutation in ARHGEF7 decreases the endogenous expression, suggesting behavioral adaptations related to the transitions in environment. Our results indicate that the feralization of the dingo induced positive selection on genomic regions correlated to neurodevelopment, metabolism and reproduction, in adaptation to a wild environment.

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Section: Methodsmentioning

confidence: 99%

Genomic regions under selection in the feralization of the dingoes

Zhang

Wang

et al. 2020

Nat Commun

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“…Furthermore, outside of ESS, there have been no breed-specific analyses. Considering that different WGS efforts in dogs have recently proven to be advantageous in elucidating genetic susceptibility to disease [22][23][24][25][26][27], differences in body types [28], as well as adaptions against parasites [29], we have compiled and processed WGS data to begin the exploration of breed-specific CMT-risk alleles and, in this initial report, to specifically reveal the coding variants detected in orthologs of the high-risk human breast cancer susceptibility genes.…”

Section: Introductionmentioning

confidence: 99%

Whole genome sequencing for the investigation of canine mammary tumor inheritance - an initial assessment of high-risk breast cancer genes reveal BRCA2 and STK11 variants potentially associated with risk in purebred dogs

Huskey

Goebel

Lloveras-Fuentes

et al. 2020

Canine Genet Epidemiol

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Background: Although, in general, cancer is considered a multifactorial disease, clustering of particular cancers in pedigrees suggests a genetic predisposition and could explain why some dog breeds appear to have an increased risk of certain cancers. To our knowledge, there have been no published reports of whole genome sequencing to investigate inherited canine mammary tumor (CMT) risk, and with little known about CMT genetic susceptibility, we carried out whole genome sequencing on 14 purebred dogs diagnosed with mammary tumors from four breedspecific pedigrees. Following sequencing, each dog's data was processed through a bioinformatics pipeline. This initial report highlights variants in orthologs of human breast cancer susceptibility genes. Results: The overall whole genome and exome coverage averages were 26.0X and 25.6X, respectively, with 96.1% of the genome and 96.7% of the exome covered at least 10X. Of the average 7.9 million variants per dog, initial analyses involved surveying variants in orthologs of human breast cancer susceptibility genes, BRCA1, BRCA2, CDH1, PTEN, STK11, and TP53, and identified 19 unique coding variants that were validated through PCR and Sanger sequencing. Statistical analyses identified variants in BRCA2 and STK11 that appear to be associated with CMT, and breed-specific analyses revealed the breeds at the highest risk. Several additional BRCA2 variants showed trends toward significance, but have conflicting interpretations of pathogenicity, and correspond to variants of unknown significance in humans, which require further investigation. Variants in other genes were noted but did not appear to be associated with disease.

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“…Little is still known about basic biological and ecological aspects of the African wolf because of its previous misidentification as a golden jackal (Canis aureus). Recent phylogenetic studies conducted on the species identified two main populations in Northwestern and in Eastern Africa [12][13][14][15]21,22]. The demographic history of the species, however, remains unknown to date.…”

Section: Introductionmentioning

confidence: 99%

Demographic expansion of an African opportunistic carnivore during the Neolithic revolution

et al. 2020

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The diffusion of Neolithic technology together with the Holocene Climatic Optimum fostered the spread of human settlements and pastoral activities in North Africa, resulting in profound and enduring consequences for the dynamics of species, communities and landscapes. Here, we investigate the demographic history of the African wolf ( Canis lupaster ), a recently recognized canid species, to understand if demographic trends of this generalist and opportunistic carnivore reflect the increase in food availability that emerged after the arrival of the Neolithic economy in North Africa. We screened nuclear and mitochondrial DNA in samples collected throughout Algeria and Tunisia, and implemented coalescent approaches to estimate the variation of effective population sizes from present to ancestral time. We have found consistent evidence supporting the hypothesis that the African wolf population experienced a meaningful expansion concurring with a period of rapid population expansion of domesticates linked to the advent of agricultural practices.

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Whole-Genome Sequencing of African Dogs Provides Insights into Adaptations against Tropical Parasites

Cited by 46 publications

References 90 publications

Genomic regions under selection in the feralization of the dingoes

Genomic regions under selection in the feralization of the dingoes

Whole genome sequencing for the investigation of canine mammary tumor inheritance - an initial assessment of high-risk breast cancer genes reveal BRCA2 and STK11 variants potentially associated with risk in purebred dogs

Demographic expansion of an African opportunistic carnivore during the Neolithic revolution

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