Complete mitogenome analysis of Alnus hirsuta reveals abundant dispersed repeats and their roles in evolutionary dynamics

Alnus hirsuta (Betulaceae), a pivotal pioneer species native to East Asia, displays prominent tolerance to cold and waterlogging. While the chloroplast genome of A. hirsuta has been sequenced, its mitochondrial genome remains uncharacterized, significantly constraining our comprehension of mitochondrial genome evolution in Betulaceae. In this study, we sequenced, assembled, and comprehensively annotated the complete mitochondrial genome of A. hirsuta using PacBio HiFi sequencing, aiming to provide novel insights into mitochondrial genome evolution in Betulaceae. The mitochondrial genome of A. hirsuta was assembled as a 150,583 bp circular molecule and a 613,799 bp linear molecule, totaling 764,382 bp, with a GC content of 44.43%. Genome annotation identified 80 mitochondrial genes, including 36 protein‑coding genes, 39 tRNA genes, 3 rRNA genes, and 2 pseudogenes ( rpl16 and rps14 ). The codon usage of these 33 protein‑coding genes exhibited a pronounced A/T (U) bias. Meanwhile, repetitive element analysis revealed 282 simple sequence repeats, 146 tandem repeats, and 6952 dispersed repeats in the mitochondrial genome. In total, 35 homologous fragments were identified between the mitochondrial and chloroplast genomes of A. hirsuta . Additionally, a total of 504 RNA editing sites were predicted, among which C-to-U conversions represented the major form. Selection pressure analysis revealed that the mitochondrial genome of A. hirsuta exhibits strong purifying selection. Phylogenetic analysis based on 18 shared mitochondrial protein‑coding genes from representative Fagales species showed that A. hirsuta clustered within the genus Alnus , a relationship further supported by collinearity analysis. This study represents the first complete mitochondrial genome of A. hirsuta , characterizing its structural features, distribution of repetitive elements, and phylogenetic position. These findings provide valuable molecular resources for elucidating mitochondrial genome evolution in Betulaceae and establish a foundation for molecular breeding and germplasm conservation of Alnus species.