Comparative analysis of cattle (Bos taurus, 2n = 60) and river buffalo (Bubalus bubalis, 2n = 50) genome assemblies reveals two evolutionary conserved inversions and invalid centromere–telomere orientation of some autosomes

Abstract

This study investigates autosome evolution between river buffalo (Bubablus bubalis, BBU) and cattle (Bos taurus, BTA), two closely related species within the Bovidae family. Despite differences in chromosome numbers (2n = 60 in cattle and 2n = 50 in river buffalo), previous cytogenetic studies have shown high autosome similarity. However, standard banding techniques have limitations in detecting small-scale genomic rearrangements. Using molecular comparisons, this study identifies two previously undetected chromosomal inversions: a 30-Mb inversion on BBU7 (compared to BTA6) and a 4-Mb inversion on BBU14 (compared to BTA13). These findings were validated through bioinformatics analyses (genomic alignments and BLAST searches) and confirmed via fluorescence in situ hybridization technique. In addition, it has been shown that several river buffalo chromosomes are shown inverted in the genome assembly considered in this study (NDDB_SH_1). The study highlights that autosome evolution in Bovidae involves not only centric fusions but also cryptic intra-chromosomal rearrangements. These results contribute to a deeper understanding of genome evolution in closely related species and demonstrate the importance of high-resolution molecular techniques in uncovering hidden genomic changes.