Genome-wide comparison reveals large structural variants in cassava landraces
Michael Landi1,2, Anna Vittoria Carluccio3, Trushar Shah4
1Department of Animal Biosciences, Bioinformatics Section, Swedish University of Agricultural Sciences, Uppsala, Sweden. michael.landi@slu.se.
BMC Genomics
|April 11, 2025
Summary
This study identified a large structural variant in the TMEB117 cassava genome, revealing its variability across landraces. This region contains unique genes and transposable elements, impacting cassava genomic diversity.
Area of Science:
- Genomics
- Plant Science
- Molecular Biology
Background:
- Structural variants (SVs) are key drivers of genomic diversity and phenotypic variation in plants.
- Cassava (Manihot esculenta Crantz) genomic research has not previously characterized a large, highly repetitive 9.7 Mbp segment on chromosome 12 in the TMEB117 genotype.
Purpose of the Study:
- To investigate the presence and variability of a 9.7 Mbp structural variant on chromosome 12 in the TMEB117 cassava genotype.
- To explore the genomic significance and potential implications of this variant across diverse cassava landraces.
Main Methods:
- Validated the 9.7 Mbp segment in the TMEB117 genome assembly.
- Mapped short-read sequencing data from 16 cassava landraces to chromosome 12.
- Analyzed gene content and transposable element presence within the variant region.
Main Results:
- Confirmed the 9.7 Mbp segment in TMEB117, distinct from other assemblies.
- Observed significant read mapping variability across 16 landraces, indicating structural differences.
- Identified two deacetylase genes (HDA14, SRT2) and overrepresentation of the MUDR-Mutator transposable element within the insertion.
Conclusions:
- A large structural variant on chromosome 12 in TMEB117 cassava exhibits variability among genotypes.
- The variant region's enrichment with HDA14, SRT2 genes, and MUDR-Mutator elements suggests potential functional roles.
- Findings contribute to understanding the impact of structural variations on cassava genomic diversity.
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