CASSAVASTORE

Cassava (Manihot esculenta Crantz) is a vital staple crop, yet genomic resources for diverse ecotypes, particularly from key regions like Thailand, remain limited. To address this, we generated high-quality genome assemblies for nine Thai M. esculenta cultivars and one wild relative, Manihot glaziovii. High-contiguity assemblies were produced and comprehensively annotated for repeats, genes, and functions using multiple evidence sources including transcriptome data where available. Phylogenetic analysis placed the nine Thai cultivars as a distinct clade relative to established African and South American reference genomes, with M. glaziovii positioned as a close relative to M. esculenta. Comparative genomics revealed high macrosynteny across all ten genomes. Detailed pairwise analysis against a reference genome confirmed overall collinearity but identified numerous intra-specific structural variants (inversions, duplications) and supported a large chromosome 4/15 translocation specific to the HighlandRough cultivar (~16 Mbp affected). Considerably greater structural and sequence divergence was observed between M. glaziovii and M. esculenta. Analysis of gene family evolution identified 100 rapidly evolving families, characterized by significant expansions early in Manihot divergence and within the M. glaziovii lineage, alongside a notable contraction event on the branch leading to the reference ancestor. Functional enrichment analysis of these rapidly evolving families highlighted processes related to photosynthesis, phytohormone action, gene expression regulation, nutrient acquisition, and environmental stress/pathogen response, while core housekeeping functions like DNA replication and cell cycle control appeared more constrained regarding family size changes. These high-quality genome assemblies and comparative analyses provide a valuable resource for cassava breeding, functional genomics, and understanding the evolution of cassava in Thailand.