Extensive sequence duplication in Arabidopsis revealed by pseudo-heterozygosity.

ABSTRACT:

Background

It is apparent that genomes harbor much structural variation that is largely undetected for technical reasons. Such variation can cause artifacts when short-read sequencing data are mapped to a reference genome. Spurious SNPs may result from mapping of reads to unrecognized duplicated regions. Calling SNP using the raw reads of the 1001 Arabidopsis Genomes Project we identified 3.3 million (44%) heterozygous SNPs. Given that Arabidopsis thaliana (A. thaliana) is highly selfing, and that extensively heterozygous individuals have been removed, we hypothesize that these SNPs reflected cryptic copy number variation.

Results

The heterozygosity we observe consists of particular SNPs being heterozygous across individuals in a manner that strongly suggests it reflects sha

SUBMITTER: Jaegle B 

PROVIDER: S-EPMC9999624 | biostudies-literature | 2023 Mar

REPOSITORIES: biostudies-literature