Genome-wide comparison reveals large structural variants in cassava landraces

Michael Landi, Anna Vittoria Carluccio, Trushar Shah, Adnan Niazi, Livia Stavolone, Laurent Falquet, Andreas Gisel, Erik Bongcam-Rudloff

BMC Genomics; 2025 Apr 10; 26(1):362. doi: 10.1186/s12864-025-11523-y.

Abstract

Background: Structural variants (SVs) are critical for plant genomic diversity and phenotypic variation. This study investigates a large, 9.7 Mbp highly repetitive segment on chromosome 12 of TMEB117, a region not previously characterized in cassava (Manihot esculenta Crantz). We aim to explore its presence and variability across multiple cassava landraces, providing insights into its genomic significance and potential implications.

Results: We validated the presence of the 9.7 Mbp segment in the TMEB117 genome, distinguishing it from other published cassava genome assemblies. By mapping short-read sequencing data from 16 cassava landraces to TMEB117 chromosome 12, we observed variability in read mapping, suggesting that while all genotypes contain the insertion region, some exhibit missing segments or sequence differences. Further analysis revealed two unique genes associated with deacetylase activity, HDA14 and SRT2, within the insertion. Additionally, the MUDR-Mutator transposable element was significantly overrepresented in this region.

Conclusions: This study uncovers a large structural variant in the TMEB117 cassava genome, highlighting its variability among different genotypes. The enrichment of HDA14 and SRT2 genes and the MUDR-Mutator elements within the insertion suggests potential functional significance, though further research is needed to explore this. These findings provide important insights into the role of structural variations in shaping cassava genomic diversity.

See https://pubmed.ncbi.nlm.nih.gov/40211122/

Figure 1:

Chromosome lengths and pairwise comparison of chromosome 12 across cassava cultivars (a) Stacked bar plots display the chromosome lengths of TMEB117 (both haplotypes), TME204 (both haplotypes), TME7 (primary haplotype), and AM560-2 version 8 genome. The plot uncovers that TMEB117’s chromosome 12 exceeds 50 Mbp, exhibiting a considerable size difference compared to other cassava genome assemblies. (b, c) Pairwise synteny plots comparing chromosome 12 haplotypes (hap1 and hap2) of TMEB117 and TME204. (d) Comparison of TMEB117 chromosome 12 hap1 with the cassava reference genome AM560-2 (version 8). (e) Assembly of TMEB117 chromosome 12 using HiCanu (blue, primary haplotype), hifiasm (orange, hap1), and Flye (green, mosaic haplotype), (f) Zoomed in view of chromosome 12 from Landi et al., 2023, showing high repeat density and low gene density near the chromosome’s end.