Plastome evolution and phylogenomic insights from representative taxa across all nine subfamilies of Malvaceae

Malvaceae Juss. comprises nine subfamilies and approximately 4,225 species, many of which are ecologically significant and several of which are cultivated for their high economic value. However, the backbone phylogeny of the family remains poorly resolved, and comprehensive structural variations across the entire family's plastomes are not comprehensively investigated. We newly sequenced 45 Malvaceae samples and integrated them with 85 plastomes from GenBank for phylogenetic analyses. After excluding two outgroups and four plastomes containing gaps, 124 Malvaceae plastomes were used for comparative structural analyses. The newly assembled plastomes exhibit a typical quadripartite structure, with length ranging from 158,346 to 163,741 bp and encoding 129-132 genes. We identified five distinct types of boundaries between inverted repeat regions (IRs) and single-copy (SC) regions. Furthermore, six coding genes (e.g., matK, ndhF) and 14 non-coding regions (e.g., trnH-psbA) were identified as highly variable, providing potential DNA markers for species delimitation. Analyses of simple sequence repeats (SSRs) and long repeats revealed unique repeat patterns in Durio Adans., while codon usage bias analysis revealed a strong A/T preference across this family. Selection pressure analysis detected positive selection (dN/dS > 1) in the rpl23 gene, suggesting its potential role in adaptive evolution. Phylogenomic analyses reconstructed a highly supported backbone topology, resolving Malvaceae into two major clades: Byttneriina and Malvadendrina. Within Malvadendrina, Helicteroideae was the earliest-diverging lineage, and Tilioideae was strongly supported as sister to Dombeyoideae. Additionally, Hibiscus L. and Sida L. were confirmed to be non-monophyletic. This study clarifies the major phylogenetic relationships within Malvaceae using a densely sampled plastome dataset and provides novel insights into the structural features and evolution of Malvaceae plastomes.