Potential dual expansion of domesticated donkeys revealed by worldwide analysis on mitochondrial sequences

Molecular studies on donkey mitochondrial sequences have clearly defined two distinct maternal lineages involved in domestication.However,domestication histories of these two lineages remain enigmatic.We therefore compared several population characteristics between these two lineages based on global sampling,which included 171 sequences obtained in this study(including Middle Asian,East Asian,and African samples)plus 536 published sequences(including European,Asian,and African samples).The two lineages were clearly separated from each other based on whole mitochondrial genomes and partial non-coding displacement loop(D-loop)sequences,respectively.The Clade I lineage experienced an increase in population size more than 8000 years ago and shows a complex haplotype network.In contrast,the population size of the Clade II lineage has remained relatively constant,with a simpler haplotype network.Although the distribution of the two lineages was almost equal across the Eurasian mainland,they still presented discernible but complex geographic bias in most parts of Africa,which are known as their domestication sites.Donkeys from sub-Saharan Africa tended to descend from the Clade I lineage,whereas the Clade II lineage was dominant along the East and North coasts of Africa.Furthermore,the migration routes inferred from diversity decay suggested different expansion across China between the two lineages.Altogether,these differences indicated non-simultaneous domestication of the two lineages,which was possibly influenced by the response of pastoralists to the desertification of the Sahara and by the social expansion and trade of ancient humans in Northeast Africa,respectively.

Capture Probe: a java tool for designing probes for capture Hi-C applications

DEAR EDITOR,Many functional elements associated with traits and diseases are located in non-coding regions and act on distant target genes via chromatin looping and folding,making it difficult for scientists to reveal the genetic regulatory mechanisms.Capture Hi-C is a newly developed chromosome conformation capture technology based on hybridization capture between probes and target genomic regions.It can identify interactions among target loci and all other loci in a genome with low cost and high resolution.Here,we developed CaptureProbe,a user-friendly,graphical Java tool for the design of capture probes across a range of target sites or regions.Numerous parameters helped to achieve and optimize the designed probes.Design testing of CaptureProbe showed high efficiency in the design success ratio of target loci and probe specificity.Hence,this program will help scientists conduct genome spatial interaction research.

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

Over the last several hundred years,donkeys have adapted to high-altitude conditions on the Tibetan Plateau.Interestingly,the kiang,a closely related equid species,also inhabits this region.Previous reports have demonstrated the importance of specific genes and adaptive introgression in divergent lineages for adaptation to hypoxic conditions on the Tibetan Plateau.Here,we assessed whether donkeys and kiangs adapted to the Tibetan Plateau via the same or different biological pathways and whether adaptive introgression has occurred.We assembled a de novo genome from a kiang individual and analyzed the genomes of five kiangs and 93 donkeys(including 24 from the Tibetan Plateau).Our analyses suggested the existence of a strong hard selective sweep at the EPAS1 locus in kiangs.In Tibetan donkeys,however,another gene,i.e.,EGLN1,was likely involved in their adaptation to high altitude.In addition,admixture analysis found no evidence for interspecific gene flow between kiangs and Tibetan donkeys.Our findings indicate 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.

OrthReg:a tool to predict cis-regulatory elements based on cross-species orthologous sequence conservation

DEAR EDITOR,Cis-regulatory elements play an important role in the development of traits and disease in organisms(Ma et al.,2020;Woolfe et al., 2005) and their annotation could facilitate genetic studies. The Encyclopedia of DNA Elements(ENCODE)(Davis et al., 2018) and Functional Annotation of Animal Genomes(FAANG)(FAANG Consortium et al., 2015)offer pioneering data on regulatory elements in several species. Currently, however, regulatory element annotation data remain limited for most organisms.