Goats (Capra hircus) are an important farm animal species. Copy number variation (CNV) represents a major source of genomic structural variation. We investigated the diversity of CNV distribution in goats using CaprineSNP50 genotyping data generated by the ADAPTmap Project. We identified 6286 putative CNVs in 1023 samples from 50 goat breeds using PennCNV. These CNVs were merged into 978 CNV regions, spanning ~262 Mb of total length and corresponding to ~8.96% of the goat genome. We then divided the samples into six subgroups per geographic distribution and constructed a comparative CNV map. Our results revealed a population differentiation in CNV across different geographical areas, including Western Asia, Eastern Mediterranean, Alpine & Northern Europe, Madagascar, Northwestern Africa, and Southeastern Africa groups. The results of a cluster heatmap analysis based on the CNV count per individual across different groups was generally consistent with the one generated from the SNP data, likely reflecting the population history of different goat breeds. We sought to determine the gene content of these CNV events and found several important CNVoverlapping genes (e.g. EDNRA, ADAMTS20, ASIP, KDM5B, ADAM8, DGAT1, CHRNB1, CLCN7, and EXOSC4), which are involved in local adaptations such as coat color, muscle development, metabolic processes, osteopetrosis, and embryonic development. Therefore, this research generated an extensive CNV map in the worldwide population of goat, which offers novel insight into the goat genome and its functional annotation.

The decrease in sequencing cost and increased sophistication of assembly algorithms for short-read platforms has resulted in a sharp increase in the number of species with genome assemblies. However, these assemblies are highly fragmented, with many gaps, ambiguities, and errors, impeding downstream applications. We demonstrate current state of the art for de novo assembly using the domestic goat (Capra hircus), based on long reads for contig formation, short reads for consensus validation, and scaffolding by optical and chromatin interaction mapping.These combined technologies produced the most contiguous de novo mammalian assembly to date, with chromosome-length scaffolds and only 663 gaps. Our assembly represents a >250-fold improvement in contiguity compared to the previously published C. hircus assembly, and better resolves repetitive structures longer than 1 kb, supporting the most complete repeat family and immune gene complex representation ever produced for a ruminant species.

We present high quality, phased genome assemblies representative of taurine and indicine cattle, subspecies that differ markedly in productivity-related traits and environmental adaptation. We report a new haplotype-aware scaffolding and polishing pipeline using contigs generated by the trio binning method to produce haplotype-resolved, chromosomelevel genome assemblies of Angus (taurine) and Brahman (indicine) cattle breeds. These assemblies were used to identify structural and copy number variants that differentiate the subspecies and we found variant detection was sensitive to the specific reference genome chosen. Six gene families with immune related functions are expanded in the indicine lineage. The very high quality of the assemblies from both sub-species enabled transcripts to be phased to detect allele-specific expression, and to study genome-wide selective sweeps. An indicus-specific extra copy of fatty acid desaturase is under positive selection and may contribute to indicine adaptation to heat and drought. MainAbout 10,000 years ago, cattle were domesticated from the aurochs which ranged across Eurasia and North Africa but are now extinct 1 . Modern day cattle belong to two subspecies, the humped zebu or indicine breeds (Bos taurus indicus) and the humpless taurine breeds (Bos taurus taurus), which arose from independent domestication events of genetically distinct aurochs populations 2 .During the last century, taurine breeds have been intensively selected for production traits, particularly milk and/or meat yield and quality, and generally have higher fertility than indicine breeds. European taurine breeds, such as Angus, have excellent carcass and meat quality, high fertility, and reach puberty early. These breeds have been imported by farmers around the world to improve or replace less-productive breeds. However, while European taurine animals are well adapted to temperate environments, they do not thrive and perform in hot, humid tropical environments with high disease and parasite burden.Indicine breeds originate from the Indus valley and later spread to Africa and across southeast Asia 3 . Between 1854 and 1926, the four indicine breeds, Ongole, Krishna, Gir and Gujarat, were imported into the United States and crossed with European taurine cattle to create the Brahman breed. Current US Brahman cattle retain ~10% of their genome of taurine origin 4 . Brahman have short, thick, glossy coat that reflects sunlight and loose skin that increases the body surface area exposed for cooling. While the Brahman are less productive and have lower fertility than taurine breeds, they have desirable traits, such as heat tolerance, and lower susceptibility to parasites such as ticks, and are disease and drought resistant 5 .We previously demonstrated a novel trio binning approach to assemble haplotypes of diploid individuals at the contig level. The quality of the contigs exceeded those of the best livestock reference genomes 6 . Here we present chromosome-level taurine (Angus) and indicine (Brahman) cattle ge...

49The male-specific part of the Y-chromosome is in mammalian and many other species the 50 longest haplotype that is inherited without recombination. By its paternal transmission it has a 51 small effective population size in species with dominant males. In several species, Y-52 chromosomal haplotypes are sensitive markers of population history and introgression. 53Previous studies have identified in domestic goats four major Y-chromosomal haplotypes 54 Y1A, Y1B, Y2A and Y2B with a marked geographic differentiation and several regional 55 variants. In this study we used published whole-genome sequences of 70 male goats from 16 56 modern breeds, 11 ancient-DNA samples and 29 samples from seven wild goat species. We 57 identified single-copy male-specific SNPs in four scaffolds, containing SRY, ZFY, DBY with 58 SSX3Y and UTY, and USP9Y with UMN2001, respectively. Phylogenetic analyses indicated 59 haplogroups corresponding to the haplotypes Y1B, Y2A and Y2B, respectively, but Y1A was 60 split into Y1AA and Y1AB. All haplogroups were detected in ancient DNA samples from 61 southeast Europe and, with the exception of Y1AB, in the bezoar goat, which is the wild 62 ancestor of the domestic goats. Combining these data with those of previous studies and with 63 genotypes obtained by Sanger sequencing or the KASP assay yielded haplogroup distributions 64 for 132 domestic breeds or populations. The phylogeographic differentiation indicated 65 paternal population bottlenecks on all three continents. This possibly occurred during the 66 Neolithic introductions of domestic goats to those continents with a particularly strong 67 influence in Europe along the Danubian route. This study illustrates the power of the Y-68 chromosomal haplotype for the reconstructing the history of mammalian species with a wide 69 geographic range. 70 71 223 2018-01-8708 "Application of NGS in assessment of genomic variability in ruminants" and 224 by the European Union (projects ECONOGENE QLK5-CT2001-02461. We are grateful to 225 Dr E. Cuppen (Utrecht Medical Centre) for access to the dideoxy sequencing facilities. 226 227Acknowldegements. 228This study has benefited from an interaction with Vargoats consortium 229

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