Long read and preliminary pangenome analyses reveal breed-specific structural variations and novel sequences in...

Most SV studies in livestock rely on short-read sequencing, posing challenges in accurately characterizing large genomic variants due to their limited read length.

Our goal is to reveal structural variation and novel sequences specific to Holstein and Jersey cattle breeds using long-read and pan-genome analyses.

We sequenced 20 Holsteins and 8 Jersey cattle using PacBio HiFi to 20×, and integrated five read-based and one assembly-based SV caller to determine SVs.

We assembled the 28 genomes averaging 3.25 Gb with a contig N50 of 69.36 Mb and using the ARS-UCD1.2 reference, we acquired Holstein/Jersey SV catalogs with 74,068/54,689 events spanning 202/135 Mb (7.43 %/4.97 % of the genome). SVs were enriched in less conserved, non-coding, and non-regulatory regions. Comparing Holsteins with differing feed efficiency (FE), SVs unique to high FE were linked to energy metabolism and olfactory receptors, while those specific to low FE were associated with material transport. We constructed Holstein/Jersey pangenome graphs with 148,598/105,875 nodes and 208,891/147,990 edges, representing 47,028/37,137 biallelic and multi-allelic events, and 63.75/42.34 Mb of novel sequence. We observed SV count saturation with 20 Holsteins, while adding Jerseys significantly increased the SV count, highlighting breed-specific SV events.

Our long-read data and SV catalogs are valuable resources, revealing that the cattle genome is more complex than previously thought.