Long-read sequencing reveals Helitron-driven copy number variation of wax-related KCS genes in Populus trichocarpa
By
Michael R. Garvin
Summary
This study uses long-read sequencing to create telomere-to-telomere assemblies of chromosome 10 in Populus trichocarpa (black cottonwood), revealing complex adaptive variation in 3-ketoacyl-CoA-synthase (KCS) genes that drive wax cuticle diversity. The analysis of 78 long-read haplotypes identified more than twice as many KCS genes as previously reported with short-read assemblies, along with numerous non-synonymous substitutions. Random Forest models showed that alkene levels are best predicted by combinations of KCS copies rather than individual genes. Each KCS gene was linked to a Helitron transposon, and phylogenetic analysis suggests Helitrons are the evolutionary mechanism generating KCS tandem arrays. The research demonstrates that long-read sequencing is critical for interpreting complex genomic regions containing tandem copy number variants that are missed by short-read approaches.
Source
bskyLong-read sequencing reveals Helitron-driven copy number variation of wax-related KCS genes in Populus trichocarpadoi.orgKey quotes
· 5 pulledLong-read sequencing enables the development of telomere-to-telomere resources to detect cryptic variation, including CNVs, which are currently missed.
Our analysis of 78 long-read haplotypes from chromosome 10 identified more than twice as many KCS genes as previously reported, and numerous intragenic non-synonymous substitutions.
Alkene levels are best predicted by the combinations of KCS copies.
A phylogenetic analysis suggests Helitrons are the evolutionary mechanism for generating KCS tandem arrays.
Our results highlight that, given current challenges in annotation and assembly, detailed and focused long-read sequences are key to interpreting complex genomic regions that contain tandem copy number variants.
The model woody plant
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