The mitochondrial genome of pequi tree (Caryocar brasiliense Cambess.): genome structure, gene transfers, and evolutionary insights within Malpighiales

Abstract

The complete mitochondrial genome of Caryocar brasiliense (Caryocaraceae), an ecologically and economically important species native to the Brazilian savannas, was assembled and annotated. Using a hybrid assembly approach combining Oxford Nanopore and Illumina sequencing data, we assembled a 533,641 bp bipartite mitogenome organized into two circular chromosomes. A high density of dispersed repeats and simple sequence repeats (SSRs) was detected, along with extensive DNA transfers from the chloroplast and nuclear genomes (MTPTs and NUMTs). The variation of mitogenome size is positively correlated with the number of dispersed repeats (R² = 0.88). Genome annotation revealed 74 protein-coding genes, including sequences derived from both mitochondrial and chloroplast origins, as well as 376 predicted RNA editing sites, particularly concentrated in energy metabolism genes such as ccm and nad gene family. Comparative analysis across ten Malpighiales species identified conserved core mitochondrial genes and revealed topological differences between mitochondrial and plastid phylogenies. These findings offer new insights into the structural and evolutionary dynamics of angiosperm mitochondrial genomes and provide a foundational resource for future genetic, evolutionary, and conservation studies in C. brasiliense and related taxa.