Duplications and Retrogenes Are Numerous and Widespread in Modern Canine Genomic Assemblies.

ABSTRACT: Recent years have seen a dramatic increase in the number of canine genome assemblies available. Duplications are an important source of evolutionary novelty and are also prone to misassembly. We explored the duplication content of nine canine genome assemblies using both genome self-alignment and read-depth approaches. We find that 8.58% of the genome is duplicated in the canFam4 assembly, derived from the German Shepherd Dog Mischka, including 90.15% of unplaced contigs. Highlighting the continued difficulty in properly assembling duplications, less than half of read-depth and assembly alignment duplications overlap, but the mCanLor1.2 Greenland wolf assembly shows greater concordance. Further study shows the presence of multiple segments that have alignments to four or more duplicate cop

SUBMITTER: Nguyen AK 

PROVIDER: S-EPMC11259980 | biostudies-literature | 2024 Jul

REPOSITORIES: biostudies-literature