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.

Mononuclear molybdoenzymes of the dimethyl sulfoxide reductase (DMSoR) family catalyze a number of reactions essential to the carbon, nitrogen, sulfur, arsenic, and selenium biogeochemical cycles. these enzymes are also ancient, with many lineages likely predating the divergence of the last universal common ancestor into the Bacteria and Archaea domains. We have constructed rooted phylogenies for over 1,550 representatives of the DMSOR family using maximum likelihood methods to investigate the evolution of the arsenic biogeochemical cycle. the phylogenetic analysis provides compelling evidence that formylmethanofuran dehydrogenase B subunits, which catalyze the reduction of co 2 to formate during hydrogenotrophic methanogenesis, constitutes the most ancient lineage. our analysis also provides robust support for selenocysteine as the ancestral ligand for the Mo/W atom. finally, we demonstrate that anaerobic arsenite oxidase and respiratory arsenate reductase catalytic subunits represent a more ancient lineage of DMSoRs compared to aerobic arsenite oxidase catalytic subunits, which evolved from the assimilatory nitrate reductase lineage. this provides substantial support for an active arsenic biogeochemical cycle on the anoxic Archean earth. our work emphasizes that the use of chalcophilic elements as substrates as well as the Mo/W ligand in DMSORs has indelibly shaped the diversification of these enzymes through deep time. Ubiquitous in Archaea and Bacteria, mononuclear molybdoenzymes of the dimethyl sulfoxide reductase (DMSOR) family are believed to have been core components of the first anaerobic respiratory chains, and thus present at life's origins 1-4. Reactions catalyzed by these enzymes are integral components of the carbon, nitrogen, and sulfur biogeochemical cycles, as well as the biogeochemical cycles of arsenic and selenium 5 , and likely antimony 6,7. The family, which has been defined by the presence of a mononuclear molybdopterin or tungstopterin bis(pyranopterin guanine dinucleotide) (Mo/W-bisPGD) co-factor 5 , was named after DMSO reductases, the first members of the family to be well-characterized 8-12. As more representatives of the family were discovered and characterized, many were found to be heterotrimeric complexes, consisting of the catalytic subunit (the Mo/W-bisPGD-harboring subunit), an electron transfer subunit with as many as four [Fe-S] clusters, and a membrane anchoring subunit that tethers the complex to the membrane and transfers electrons to or from the membrane quinone pool. Thus, members of the family have also been referred to as Complex Iron-Sulfur Molybdoenzymes (CISMs) 13. The catalytic subunit may additionally have a twin-arginine translocation motif for export to the periplasm, and a [4Fe-4S] or [3Fe-4S] iron-sulfur cluster 13,14. It has been noted, however, that these characteristics are not uniform across the family, as there are numerous examples where one or more of the associated subunits are missing, or the catalytic subunits associate with different subunits altoget...