Donkey genomes provide new insights into domestication and selection for coat color

  title={Donkey genomes provide new insights into domestication and selection for coat color},
  author={Changfa Wang and Hai-Jun Li and Yu Guo and Jinming Huang and Yan Sun and Jiumeng Min and Jinpeng Wang and Xiaodong Fang and Zicheng Zhao and Shuai Wang and Yanlin Zhang and Qingfeng Liu and Qiang Jiang and Xiuge Wang and Yijun Guo and Chunhong Yang and Yinchao Wang and Fang Tian and Guilong Zhuang and Yanna Fan and Qican Gao and Yuhua Li and Zhihua Ju and Jianbin Li and Rongling Li and Ming-hai Hou and Guiwen Yang and Guiqin Liu and Wenqiang Liu and Jiao Guo and Shanshan Pan and Guangyi Fan and Wei Zhang and Ruitao Zhang and Jie Yu and Xinhao Zhang and Qi Yin and Chuanliang Ji and Yuanchun Jin and Guidong Yue and Mei Liu and Jiake Xu and Shimin Liu and Jordi Jordana and Antonia Noce and Marcel Amills and Dong-Dong Wu and Shuaicheng Li and Xiangshan Zhou and Jifeng Zhong},
  journal={Nature Communications},
Current knowledge about the evolutionary history of donkeys is still incomplete due to the lack of archeological and whole-genome diversity data. To fill this gap, we have de novo assembled a chromosome-level reference genome of one male Dezhou donkey and analyzed the genomes of 126 domestic donkeys and seven wild asses. Population genomics analyses indicate that donkeys were domesticated in Africa and conclusively show reduced levels of Y chromosome variability and discordant paternal and… 

Ancient Mitogenomes Provide New Insights into the Origin and Early Introduction of Chinese Domestic Donkeys

Bayesian analysis shows that the split of the two donkey maternal lineages is dated at 0.323 Ma (95% CI: 0.583–0.191 Ma) using root-tip dating calibrations based on near-complete mitogenomes, supporting the hypothesis that modern domestic donkeys go back to at least two independent domestication events.

Genome collinearity analysis illuminates the evolution of donkey chromosome 1 and horse chromosome 5 in perissodactyls: A comparative study

The cytogenetic nomenclature is identified, the direction of the chromosome-length sequence of the donkey genome is corrected, and the genome-wide chromosomal rearrangements between the donkey and horse are analyzed, which supports the correctness of the existing Equus phylogeny to an extent.

The genomic history and global expansion of domestic donkeys.

A strong phylogeographic structure in modern donkeys is found that supports a single domestication in Africa ~5000 BCE, followed by further expansions in this continent and Eurasia and ultimately returning to Africa.

Comparative Transcriptomics Uncover the Uniqueness of Oocyte Development in the Donkey

It is concluded that, compared to other species, donkey oocytes express a large number of genes related to RNA metabolism to maintain normal oocyte development during the period from GV to MII.

Genetic architectures and selection signatures of body height in Chinese indigenous donkeys revealed by next-generation sequencing.

Donkeys are widely distributed labour animals in the world. During the process of the domestication and artificial selection of domestic donkeys, body sizes show significant differences among

Transcriptome Atlas of 16 Donkey Tissues

Transcriptomics was used to describe the transcriptome landscape, classify the tissue-specific gene expression across all primary donkey tissues, and present supplementary analyses on the protein level of additional donkey milk samples.

Chromosome-Level Haplotype Assembly for Equus asinu

The hybrid single individual assembled haplotype of the Dezhou donkey based on the high-depth sequencing data from single-molecule real-time sequencing, Illumina short-read sequencing, and high-throughput chromosome conformation capture is described.

Whole Genome Sequencing Provides New Insights Into the Genetic Diversity and Coat Color of Asiatic Wild Ass and Its Hybrids

The heatmap was able to show the clear difference in the haplotype of the KITLG gene between the Kulan hybrids and Asiatic wild ass group and the Guanzhong black donkey group, which is a powerful demonstration of the key role of KIT LG in donkey color.

Genomes reveal selective sweeps in kiang and donkey for high-altitude adaptation

It is indicated that despite the short evolutionary time scale since the arrival of donkeys on the Tibetan Plateau, as well as the existence of a closely related species already adapted to hypoxia, Tibetan donkeys did not acquire adaptation via admixture but instead evolved adaptations via a different biological pathway.

MTaxi : A comparative tool for taxon identification of ultra low coverage ancient genomes

MTaxi provides a straightforward approach to classify closely related species that are compelling to distinguish through zooarchaeological methods using low coverage aDNA data, especially when similar quality reference genomes are unavailable.



Improved de novo genomic assembly for the domestic donkey

A new high-quality donkey genome assembly obtained using the Chicago HiRise assembly technology, providing scaffolds of subchromosomal size is presented, allowing fine-scale chromosomal rearrangements between the horse and the donkey that likely played an active role in their divergence and, ultimately, speciation to be identified.

Genetic diversity of donkey populations from the putative centers of domestication.

The results support previously proposed northeast Africa as a putative center of origin for the domestic donkey, but the high levels of unique diversity in Yemen opens the possibility of considering this region as yet another center oforigin for this species.

Donkey genome and insight into the imprinting of fast karyotype evolution

The donkey, like the horse, is a promising model for exploring karyotypic instability and expanded miRNA families and five newly discovered miRNA target genes involved in meiosis may be associated with fast karyotype evolution.

Convergent genomic signatures of domestication in sheep and goats

Comparing the genomes of wild Asiatic mouflon and Bezoar ibex with that of domestics from local, traditional and improved breeds finds common targets of selection related to domestication and improvement in sheep and goats.

Ancient DNA from Nubian and Somali wild ass provides insights into donkey ancestry and domestication

These findings resolve the long-standing issue of the role of the Nubian wild ass in the domestication of the donkey, but raise new questions regarding the second ancestor for the donkey.

Decline of genetic diversity in ancient domestic stallions in Europe

The results show that the lack of multiple stallion lineages in the extant domestic population is caused by neither a founder effect nor random demographic effects but instead is the result of artificial selection—initially during the Iron Age by nomadic people from the Eurasian steppes and later during the Roman period.

A comparative view of the evolution of grasses under domestication.

The history of domesticated grasses is reviewed and how domestication affected their phenotypic and genomic diversity is reviewed, and the role of mating systems in the domestication process is revisited.

The Genetic Architecture of Domestication in Animals

  • D. Wright
  • Biology
    Bioinformatics and biology insights
  • 2015
This review focuses on what is currently known about the genetic architecture of domesticated animal species, if genes of large effect are prevalent in driving the domestication phenotype, and whether pleiotropy can explain the loci underpinning these diverse traits being colocated.