Chromosome-Scale Genome Assemblies of Two Black Bengal Goat (Capra hircus) Individuals

Abstract The Black Bengal Goat (Capra hircus), a small-bodied, prolific breed native to West Bengal, India and neighboring Bangladesh, is valued for its meat quality, disease resistance, and adaptability to marginal environments, yet lacks a dedicated reference-quality genome assembly. Here we report chromosome-scale genome assemblies for two Black Bengal Goat individuals — 803M (male) and D863F (female) — generated from PacBio HiFi long-read sequencing (~ 30× coverage) using hifiasm followed by reference-guided scaffolding against the Capra hircus ARS1.2 assembly. The resulting assemblies span 2.86 Gb (803M) and 2.78 Gb (D863F), with scaffold N50 values of 88 Mb and 92 Mb (L50 = 13 and 12), reflecting near-chromosome-level contiguity, and genome-mode BUSCO completeness of 99.5% and 99.3% (cetartiodactyla_odb10), respectively. Protein-coding genes were annotated using RNA-seq-evidence-based BRAKER1, yielding 23,563 (803M) and 47,030 (D863F) gene models after filtering for assembly-boundary artifacts. Demographic history reconstructed via PSMC revealed a shared Pleistocene population bottleneck followed by partial recovery, consistent between both individuals. These assemblies — deposited under BioProject PRJNA1502507 — provide the first chromosome-scale reference genome resource for Black Bengal Goat, supporting future work in comparative genomics, marker-assisted selection, and conservation genetics of this economically important South Asian breed.