Dynamic evolutionary processes and complex structure make the Y chromosome among the most diverse and least understood regions in mammalian genomes. Here, we present an annotated assembly of the male specific region of the horse Y chromosome (eMSY), representing the first comprehensive Y assembly in odd-toed ungulates. The eMSY comprises single-copy, equine specific multi-copy, PAR transposed, and novel ampliconic sequence classes. The eMSY gene density approaches that of autosomes with the highest number of retained X–Y gametologs recorded in eutherians, in addition to novel Y-born and transposed genes. Horse, donkey and mule testis RNAseq reveals several candidate genes for stallion fertility. A novel testis-expressed XY ampliconic sequence class, ETSTY7, is shared with the parasite Parascaris genome, providing evidence for eukaryotic horizontal transfer and inter-chromosomal mobility. Our study highlights the dynamic nature of the Y and provides a reference sequence for improved understanding of equine male development and fertility.

Highland pastoralism provides economic sustainability to the tribal livelihoods and is endemic to the yak-rearing tracts of India. Transhumant pastoralists of Arunachal Pradesh (in India) have centuries-old deep socio-religious and economic connections with this unique bovine species. As a result of their conservation efforts, Arunachali was recognized as the first and is still the lone breed (to date) of yaks in the country. A survey was conducted on the pastoral production system in the region to enable the phenotypic characterization of yaks and to understand the prevailing husbandry practices. Arunachali yaks are medium-sized bovines that are predominantly black with dense and long hairs hanging down the body and are docile in temperament. They have a convex head with horizontal ears and distinctly curved horns with pointed tips. The average milk yield is 0.98–1.04 kg milk/day with 7.45% fat and 11.5% SNF and the peak milk yield/day is 1.1–1.6 kg. The average ages of clipping of coarse hairs and down fibres are 12–18 months and 12 months, respectively, with average yields of 1.5 kg and 0.5 kg/clipping/animal, respectively. Value addition of yak milk and fibre presents a unique opportunity for the economic rejuvenation of yak pastoralism. However, winter feed scarcity, inbreeding, extreme climate events and the non-availability of essential services are still major challenges for yak production in the country. Our findings acknowledge that pastoral sustainability is critical for the conservation of yaks and yak rearing. This calls for pastoralism-centric governance and research efforts in the highlands to curb the declining population and to put Indian yaks on the road to sustainability.

Japanese encephalitis viruses (JEVs) are globally prevalent as deadly pathogens in humans and animals, including pig, horse and cattle. Japanese encephalitis (JE) still remains an important cause of epidemic encephalitis worldwide and exists in a zoonotic transmission cycle. Assam is one of the highly endemic states for JE in India. In the present study, to understand the epidemiological status of JE circulating in pigs and mosquito, particularly in Assam, India, molecular detection of JEV and the genome sequencing of JEV isolates from pigs and mosquitoes was conducted. The genome analysis of two JEV isolates from pigs and mosquitoes revealed 7 and 20 numbers of unique points of polymorphism of nucleotide during alignment of the sequences with other available sequences, respectively. Phylogenetic analysis revealed that the isolates of the present investigation belong to genotype III and are closely related with the strains of neighboring country China. This study highlights the transboundary nature of the JEV genotype III circulation, which maintained the same genotype through mosquito-swine transmission cycles.