Comprehensive analysis of 385 chloroplast genomes unveils phylogenetic relationships and evolutionary history in cassava.

BACKGROUND: Cassava (Manihot esculenta Crantz) is a crucial staple food crop, yet our understanding of its chloroplast (cp.) genome has been limited due to the extensive diversity among cultivars. This lack of clarity has significantly impeded our comprehension of cp. genome evolution and genetic relationships within cassava germplasm. RESULTS: A total of 385 complete chloroplast (cp.) genomes of cassava cultivars were newly assembled. Comprehensive comparative analysis and phylogenetic trees were conducted. The cp. genomes varied in size from 160,702 to 161,564 bp, with GC content ranging from 35.87 to 35.97%. The cp. genomes exhibited a typical quadripartite structure, consisting of a large single-copy (LSC) region (88,633 − 89,406 bp), a small single-copy (SSC) region (18,132 − 18,255 bp), and two inverted repeat (IRa/IRb) regions (26,931 − 26,995 bp). Notably, the rps19 gene located in the IRa region was pseudogenic in all cultivars, while the ycf1 gene was pseudogenic in only three cultivars. Among the remaining 382 plastomes, 131 genes (111 unique) were encoded, including 85 protein-coding genes, 38 tRNA genes, and eight rRNA genes. Phylogenetic analysis classified the 385 cultivars into four distinct clades, designated as Clade 1 to Clade 4. Additionally, 48 distinct haplotypes were grouped into four clusters that corresponded with the four clades. The cassava plastomes showed high overall similarity. Codon usage was nearly identical across plastomes. We identified three hypervariable regions, including rrn16S-trnI-GAU, ycf1, and rps4-trnF-GAA, that could distinctly separate the 385 accessions into four clades, aligning precisely with Clade 1 to Clade 4. A total of 31,045 simple sequence repeats (SSRs) and 30,105 dispersed repeats were identified. Notably, the four distinct clades were also distinguishable based on SSR types, which could serve as potential molecular markers. CONCLUSIONS: Our study provided a thorough analysis of chloroplast genome features spanning a diverse array of cassava germplasm, significantly advancing our understanding of chloroplast genome evolution in this crucial crop. Phylogenetic relationships among 385 cassava cultivars were also elucidated. These profound insights are highly valuable for advancing genetic improvement strategies and guiding breeding endeavors aimed at enhancing cassava crops.