The complete sequence and comparative analysis of avocado mitochondrial genomes

• Published in: Tree genetics & genomes Vol. 21; no. 5; p. 25
• Main Authors: Liu, Yanyu, Zhang, Di, Huang, Jiepeng, Zhu, Wen, Yang, Shiting, Song, Yu
• Format: Journal Article
• Language: English
• Published: Berlin/Heidelberg Springer Berlin Heidelberg 01.10.2025; Springer Nature B.V
• Subjects: Bats; Biomedical and Life Sciences; Biotechnology; Botanical gardens; Comparative analysis; Datasets; Deoxyribonucleic acid; DNA; Domestication; Forestry; Fragments; Gene clusters; Genes; Genetic testing; Genomes; Genomic analysis; Interspecific hybridization; Life Sciences; Mitochondria; Nucleotide sequence; Original Article; Phylogenetics; Plant Breeding/Biotechnology; Plant Genetics and Genomics; RpoB protein; Simple sequence repeats; Transfer RNA; Tree Biology; Mexico; China; Mitogenome; Lauraceae; Phylogenomic analyses
• ISSN: 1614-2942; 1614-2950
• DOI: 10.1007/s11295-025-01702-z

In this study, we successfully assembled an 851,448 bp complete avocado mitochondrial genome and five other incomplete avocado mitogenome sequences, with length ranging from 794,676 to 851,356 bp. The six mitogenomes contain 1,198–1,344 dispersed repeats, 38–42 tandem repeats, and 267–286 simple sequence repeats. These repetitive sequences can play critical roles in driving structural variants, and frequent rearrangement events have indeed been identified between the mitogenomes of Persea americana and Caryodaphnopsis henryi  or  Hernandia nymphaeifolia . Nine conserved gene clusters were also detected among these three mitogenomes. Then, we identified 35 homologous DNA fragments between the complete mitogenome and plastome, and 1,664 homologous DNA fragments between the mitogenome and nuclear genome, suggesting that horizontal sequence transfer occurred frequently between the mitogenome and plastome or nuclear genome in avocado. Besides, comparative genomic analysis indicated that there are 16–743 mutation events including 11–707 substitutions and 5–36 Indels among the six avocado mitogenomes. Significant differences were found in codon usage of the protein-coding genes (PCGs) between the mitogenome and plastome of avocado, and positive selections were detected in the plastid rpoB , rpoC2 , and ycf1 genes. Finally, phylogenetic analyses based on the mitochondrial PCGs dataset, whole plastome dataset, and nuclear ribosomal cistron dataset (nrDNA) divided the six avocado accessions into three, three, and five groups, indicating that introgression or incomplete lineage sorting could exist in avocado domestication.