Scientists who sequenced the genome of two donkeys named Peppe and Pippo found more similarities with the horse genome than previous research has suggested.
The Italian research involved one of the first uses of an Ion Proton sequencer – a next-generation semiconductor-based sequencing platform – to investigate a complex and large genome.
The scientists from the universities of Bologna and Messina obtained the genetic make-up of the two unrelated male donkeys from Sicily and compared the data with information available from the previously mapped donkey draft genome from an animal reared at the Copenhagen Zoo, as well as EquCab2.0 horse genome.
Luca Fontanesi and his colleagues found that the genomes of Peppe and Pippo were more closely aligned with the horse genome than the draft donkey genome.
Regions with low divergence between the horse and donkey were identified in several autosomal chromosomes and in the whole chromosome X.
“These regions might be evolutionally important in equids,” the research team reported in the open-access peer-reviewed journal, PLOS ONE.
The scientists said they identified variants in the Y-chromosome regions that could be useful in tracking donkey paternal lineages.
They said they identified about 4.8 million DNA sequence variations, known as single nucleotide polymorphisms. These amounted to a useful resource to describe variability at the genetic level in donkeys and to establish monitoring systems for the conservation of donkey genetic resources.
This may well prove important, with the reported decline in donkey numbers across Europe.
The donkey (Equus asinus) was probably domesticated by African pastoralists who started to breed Nubian (and possibly Somali) wild asses to cover their need for transportation and movements as the Sahara region grew increasingly dry about 6000 years ago.
Its domestication contributed to the expansion of overland trade in Africa and western Asia and the rise of the Egyptian state at that time.
Donkeys spread into Europe from about 4000 years ago, and subsequently into other continents.
They have been mainly employed as pack and working animals without any substantial changes in their use and without any particular improvement, the researchers noted.
It is estimated that about 95 percent of the current 43.5 million donkeys in the world (mainly in developing countries and China) are kept specifically for work and for the production of other working animals.
“In Europe the number of donkeys is rapidly decreasing, due to the mechanization of transport and agriculture, and many populations or breeds, generated mainly by geographical isolation, are highly endangered and close to extinction or already extinct,” the research team said.
They noted that few studies had investigated the donkey at the genetic level.
“It is clear,” they said, “that most of the studies that investigated donkey genes or DNA markers can be considered, to some extent, byproducts or were linked to related investigations that started from the horse or included this latter species in some way …”
Despite horses and donkeys having different numbers of chromosomes – 64 in the horse and 62 in the donkey – as well as other rearrangements identified by genetic mapping, they were closely related. Hybrids – mules and hinnies – were viable and in a few cases were not completely sterile.
A recent re-estimation based on molecular data indicated that all Equus species diverged from a common ancestor about 4 million to 4.5 million years ago.
Fontanesi was joined in the research by Francesca Bertolini, Concetta Scimone, Claudia Geraci, Giuseppina Schiavo, Valerio Joe Utzeri and Vincenzo Chiofalo.
Bertolini F, Scimone C, Geraci C, Schiavo G, Utzeri VJ, Chiofalo V, et al. (2015) Next Generation Semiconductor Based Sequencing of the Donkey (Equus asinus) Genome Provided Comparative Sequence Data against the Horse Genome and a Few Millions of Single Nucleotide Polymorphisms. PLoS ONE 10(7): e0131925. doi:10.1371/journal.pone.0131925
The full study can be read here.