Structural variants (SVs) represent an important genetic resource for both natural and artificial selection. Here we present a chromosome-scale reference genome for domestic yak (Bos grunniens) that has longer contigs and scaffolds (N50 44.72Mb and 114.39 Mb, respectively) than reported for any other ruminant genome. We further obtained long-read resequencing data for 6 wild and 23 domestic yaks and constructed a genetic SV map of 37,220 SVs that covers the geographic range of the yaks. The majority of the SVs contains repetitive sequences and several are in or near genes. By comparing SVs in domestic and wild yaks, we identified genes that are predominantly related to the nervous system, behavior, immunity and reproduction and may have been targeted by artificial selection during yak domestication. These findings provide new insights in the domestication of animals living at high altitude and highlight the importance of SVs in animal domestication.

Genome size (also known as the C-value) refers to the total amount of DNA contained within one copy of a single complete genome; it is broadly constant within an organism (Greilhuber et al., 2005; Swift, 1950). More and more species' genome sizes have been assessed since early studies in the 1950s, covering more than 12,273

Speciation mechanisms remain controversial. Two speciation models occur in Israeli subterranean mole rats, genusSpalax: a regional speciation cline southward of four peripatric climatic chromosomal species and a local, geologic-edaphic, genic, and sympatric speciation. Here we highlight their genome evolution. The five species were separated into five genetic clusters by single nucleotide polymorphisms, copy number variations (CNVs), repeatome, and methylome in sympatry. The regional interspecific divergence correspond to Pleistocene climatic cycles. Climate warmings caused chromosomal speciation. Triple effective population size,Ne, declines match glacial cold cycles. Adaptive genes evolved under positive selection to underground stresses and to divergent climates, involving interspecies reproductive isolation. Genomic islands evolved mainly due to adaptive evolution involving ancient polymorphisms. Repeatome, including both CNV and LINE1 repetitive elements, separated the five species. Methylation in sympatry identified geologically chalk-basalt species that differentially affect thermoregulation, hypoxia, DNA repair, P53, and other pathways. Genome adaptive evolution highlights climatic and geologic-edaphic stress evolution and the two speciation models, peripatric and sympatric.

As the third largest family containing approximately 765 genera and over 19,500 species worldwide (Polhill, 1981), Leguminosae comprises essential resources for ecology, the economy, medicine, and agriculture (Allen & Allen, 1981;Duke, 2012). Forage legumes play an indispensable role in animal husbandry and are mostly used as cut fodder or grazed pasture because of their rich protein and mineral content, excellent palatability, and easy digestion (Dewhurst et al., 2009). More than 1500 species of legumes can be used as feed for livestock, and approximately 60 species have been developed and widely used as cultivated forages (Frame, 2019). Common forage legumes include alfalfa, white and red clover, wild pea, sweet clover, and others. Among them, alfalfa has

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