Accurate Runs of Homozygosity Estimation From Low Coverage Genome Sequences in Non-Model Species.

ABSTRACT: Runs of homozygosity (ROH) are increasingly being analysed using whole genome sequences in non-model species as a measure of inbreeding and to assess demographic history, thus providing useful information for conservation. However, most studies have used Plink for ROH inference which performs poorly when sequencing depth is below 10×, often underestimating ROH. This can lead to erroneous status assessment and poor management decisions. We assessed the performance of ROHan, a program developed for ROH and heterozygosity estimation using lower coverage sequences that have so far only been optimised for human data. Using high coverage whole genomes from 22 caribou, a non-model species at risk presenting varying levels of inbreeding, we assessed the effects of sequencing depth (1-15×), the inp

SUBMITTER: Taylor RS 

PROVIDER: S-EPMC12673428 | biostudies-literature | 2026 Jan

REPOSITORIES: biostudies-literature