Chloroplast genome analysis of Dendrocalamus × mutatus and its implications for bamboo classification

Abstract Background The bamboo species Dendrocalamus × mutatus T.P.Yi & B.X.Li (D. mutatus) holds great economic and ecological importance in China. Although previously D. mutatus was presumed to be a hybrid of Bambusa grandis and Bambusa pervariabilis, its taxonomic status has remained uncertain. Therefore, we combined plastomes and nuclear SSR datasets, in addition to morphological data, to refine our understanding of the taxonomic status of D. mutatus. Results The chloroplast genome of D. mutatus exhibits a typical quadripartite structure, comprising a large single-copy region (LSC), a small single-copy region (SSC), and two inverted repeat regions (IRa and IRb), containing a total length of 139,432 bp. Comparative genomic analyses revealed extremely high similarity between D. mutatus and D. yunnanicus, differing by only two single-nucleotide polymorphisms (SNPs). In contrast, a greater divergence was observed when compared with D. sikkimensis (six SNPs and one four-base insertion). Phylogenetic reconstruction using the Maximum Likelihood and Bayesian Inference method based on chloroplast genomes strongly supported the close relationship between D. mutatus and D. yunnanicus, while distinctly separating them from the previously proposed parent species Bambusa grandis and Bambusa pervariabilis. Morphological comparisons further confirmed the similarity between D. mutatus and D. yunnanicus, particularly with respect to the absence of conspicuous culm sheath auricles and oral setae, as well as the lack of fimbriate hairs on the ligule. Nuclear SSR marker analyses also showed identical predominant allele at the SSR 23 and 24 loci between D. mutatus and D. yunnanicus. Collectively, the comprehensive integration of chloroplast genome data, nuclear SSR evidence, and morphological observations supports the conclusion that D. mutatus is a synonym of D. yunnanicus rather than a hybrid of Bambusa grandis and Bambusa pervariabilis. Conclusions This research provides a comprehensive understanding of the chloroplast genome of D. mutatus, providing valuable insights that enhance the taxonomic resolution and conservation strategies for bamboo species.