A population-level statistic for assessing Mendelian behavior of genotyping-by-sequencing data from highly duplicated genomes.

ABSTRACT:

Background

Given the economic and environmental importance of allopolyploids and other species with highly duplicated genomes, there is a need for methods to distinguish paralogs, i.e. duplicate sequences within a genome, from Mendelian loci, i.e. single copy sequences that pair at meiosis. The ratio of observed to expected heterozygosity is an effective tool for filtering loci but requires genotyping to be performed first at a high computational cost, whereas counting the number of sequence tags detected per genotype is computationally quick but very ineffective in inbred or polyploid populations. Therefore, new methods are needed for filtering paralogs.

Results

We introduce a novel statistic, H_ind/H_E, that uses the probability that two reads sampled f

SUBMITTER: Clark LV 

PROVIDER: S-EPMC8939213 | biostudies-literature | 2022 Mar

REPOSITORIES: biostudies-literature