Chloroplast Genome Variation and Phylogenetic Analyses of Seven Dwarf Ornamental Bamboo Species

Abstract

Dwarf ornamental bamboos are a class of low shrub plants with minor interspecific morphological differences and are difficult to distinguish by traditional classification. In order to identify this type of bamboo species at the molecular level, we sequenced the genomes of the chloroplasts in seven species of dwarf ornamental bamboo: Pleioblastus argenteostriatus (Regel) Nakai, Pleioblastus fortunei (Van Houtte) Nakai, Pleioblastus pygmaeus (Miq.) Nakai, Pleioblastus pygmaeus ‘Disticha’, Sasaella glabra (Nakai) Koidz., Sasaella glabra ‘Albostriata’ and Sasaella kongosanensis ‘Aureostriatus’ using high-throughput sequencing. The quadripartite structure of the chloroplast genomes is typical, with sizes ranging from 139,031 bp (P. argenteostriatus) to 139,759 bp (S. kongosanensis ‘Aureostriatus’). The genomes contain 116 genes, including four rRNA genes, 30 tRNA genes and 82 protein-coding genes. Four hotspots, including ndhI-ndhA, trnC-rpoB, petB and ccsA, and a total of 46 simple sequence repeats (SSRs) were identified as potential variable markers for species delimitation and population structure analysis. The phylogenetic analyses of chloroplast genomes of seven dwarf ornamental bamboos indicates that these bamboo species can be classified into three categories: Sasaella I, Pleioblastus II and Pleioblastus III. Except S. kongosanensis ‘Aureostriatus’, the other six species were distributed into two branches, indicating that both S.glabra and S. glabra ‘Albostriata’ belong to Pleioblastus Nakai genus. There are four mutations on the chloroplast genomes of S. glabra and S. glabra ‘Albostriata’, suggesting that the mutations may contribute to their obvious different leaf morphologies. Our study reveals the chloroplast structural variations and their phylogenetic relationship and mutation dynamics in seven dwarf ornamental bamboos and also facilitates studies on population genetics, taxonomy and interspecific identification in dwarf bamboo plants.