Abstract
BackgroundGoat, one of the first domesticated livestock, is a worldwide important species both culturally and economically. The current goat reference genome, known as ARS1, is reported as the first nonhuman genome assembly using 69× PacBio sequencing. However, ARS1 suffers from incomplete X chromosome and highly fragmented Y chromosome scaffolds.ResultsHere, we present a very high-quality de novo genome assembly, Saanen_v1, from a male Saanen dairy goat, with the first goat Y chromosome scaffold based on 117× PacBio long-read sequencing and 118× Hi-C data. Saanen_v1 displays a high level of completeness thanks to the presence of centromeric and telomeric repeats at the proximal and distal ends of two-thirds of the autosomes, and a much reduced number of gaps (169 vs. 773). The completeness and accuracy of the Saanen_v1 genome assembly are also evidenced by more assembled sequences on the chromosomes (2.63 Gb for Saanen_v1 vs. 2.58 Gb for ARS1), a slightly increased mapping ratio for transcriptomic data, and more genes anchored to chromosomes. The eight putative large assembly errors (1 to ~ 7 Mb each) found in ARS1 were amended, and for the first time, the substitution rate of this ruminant Y chromosome was estimated. Furthermore, sequence improvement in Saanen_v1, compared with ARS1, enables us to assign the likely correct positions for 4.4% of the single nucleotide polymorphism (SNP) probes in the widely used GoatSNP50 chip.ConclusionsThe updated goat genome assembly including both sex chromosomes (X and Y) and the autosomes with high-resolution quality will serve as a valuable resource for goat genetic research and applications.
Highlights
Goat, one of the first domesticated livestock, is a worldwide important species both culturally and economically
Considering that the Y chromosome is the most difficult part of the genome to sequence and assemble, to obtain more continuous assemblies of the sex chromosomes, we examined the continuity of the Y chromosome-linked scaffolds of the two versions
Since we mainly focused on single nucleotide polymorphism (SNP) positional improvement in the Saanen_v1 assembly, we found 13 probes that were uniquely mapped to ARS1, which were most likely due to the presence of ARS1-specific sequences that were not included in the list of SNP positional discrepancies
Summary
One of the first domesticated livestock, is a worldwide important species both culturally and economically. CHIR_1.0 represents the first application of the optical mapping technology to genome assembly scaffolding and has served as a valuable resource for gene mapping and marker-assisted breeding in goats. This assembly further enabled the design of the first 50K GoatSNP50 chip [3] which has been extensively used to study genetic diversity in domestic goats [4,5,6,7,8,9] and its effect on phenotypic variation [10,11,12].
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