Background The current bovine genomic reference sequence was assembled from a
Hereford cow. The resulting linear assembly lacks diversity because it does not contain allelic …

Background Autochthonous cattle breeds are an important source of genetic variation
because they might carry alleles that enable them to adapt to local environment and food …

Advantages of pangenomes over linear reference assemblies for genome research have
recently been established. However, potential effects of sequence platform and assembly …

Background Several models and algorithms have been proposed to build pangenomes
from multiple input assemblies, but their impact on variant representation, and consequently …

Many genomic analyses start by aligning sequencing reads to a linear reference genome.
However, linear reference genomes are imperfect, lacking millions of bases of unknown …

Background Genotyping of sequence variants typically involves, as a first step, the alignment
of sequencing reads to a linear reference genome. Because a linear reference genome …

Background Structural variations (SVs) in individual genomes are major determinants of
complex traits, including adaptability to environmental variables. The Mongolian and Hainan …

Background The key-ancestor approach has been frequently applied to prioritize individuals
for whole-genome sequencing based on their marginal genetic contribution to current …

Cattle are ideally suited to investigate the genetics of male reproduction, because semen
quality and fertility are recorded for all ejaculates of artificial insemination bulls. We analysed …

Background RNA interference (RNAi) related pathways provide defense against viruses
and transposable elements, and have been implicated in the suppression of meiotic drive …