Phylogenomic insights from the complete chloroplast genome of Alnus hirsuta (Betulaceae): Genome structure and lineage relationships within the genus Alnus

The genus Alnus (Betulaceae) comprises approximately 29–35 species that are typically distributed across the temperate Northern Hemisphere, playing key ecological roles through symbiotic nitrogen fixation with Frankia. Although chloroplast genomes have been increasingly utilized to resolve phylogenetic relationships with the genus Alnus, no plastome-level study has focused on A. hirsuta, a widespread Northeast Asian alder of both ecological and economic importance. Here, we aimed to sequence and assemble the complete chloroplast genome of A. hirsuta using Illumina NovaSeq data and conducted comparative plastome analyses using 19 congeners. The plastome of A. hirsuta was 160,879 bp in length and exhibited the typical quadripartite structure, with 112 annotated genes and a GC content of 36.4%. Comparative analyses revealed a highly conserved genomic architecture across the genus Alnus, with only minor lineage-specific variations at the boundary between inverted repeat and small single-copy (SSC) regions. A sliding-window analysis identified divergence hotspots predominantly located in large single-copy/SSC intergenic spacers, particularly cemA–petA, rpl32–trnL, psaC–ndhE, and ycf2, which may serve as informative markers for phylogenetic inference and species delimitation within the genus. Phylogenomic reconstruction based on 76 protein-coding genes strongly supported the monophyly of Alnus, with the subg. Alnobetula forming a distinct lineage. Notably, A. hirsuta was resolved as a sister to A. formosana and closely related to A. fauriei, thereby clarifying previously ambiguous relationships within the subg. Alnus. Our findings provide new genomic resources and phylogenetic insights into the diversification of Alnus, contributing to both evolutionary studies and practical applications such as species identification and conservation.