Insight into the Phylogenetic Relationships and Evolutionary History of Indocalamus (Bambusoideae) Through Comparative Analyses of Plastomes

Indocalamus Nakai, a genus within the tribe Arundinarieae, has significant horticultural and economic value. However, its classification has long been challenging, and due to limited sampling, both intra- and intergeneric phylogenetic relationships, as well as its evolutionary history, remain unclear. In this study, extensive field surveys and comprehensive sample collection were conducted to address these challenges. A total of 31 complete plastomes of Indocalamus species were assembled. All plastomes exhibit a typical quadripartite structure, ranging in length from 139,555 bp to 139,791 bp, and contain 137 genes, including 90 protein-coding genes, 39 tRNA genes, and 8 rRNA genes. Phylogenetic analyses indicate that Indocalamus is polyphyletic and divided into three distinct clades (IV, V, and X). Based on integrated phylogenomic and morphological evidence, we propose a revised classification of Indocalamus into three major sections. Fossil-calibrated divergence estimates reveal that the major clades of Indocalamus are not monophyletic, highlighting a complex reticulate evolutionary history exemplifying the widespread rapid radiation observed in temperate woody bamboos. The intensification of the East Asian monsoon is likely to have played a key role in driving the rapid radiation of these lineages. Additionally, several clade-specific DNA barcodes (trnT-trnE, petN-trnC, petA-psbJ, and petD-rpoA) were identified, which will enhance the identification of Indocalamus and its closely related genera. This study, through extensive sampling and integration of morphological and molecular phylogenetic evidence, provides a preliminary delimitation of the genus Indocalamus, elucidates its complex evolutionary history, and lays a solid foundation for future systematic research and horticultural applications.