The complete chloroplast genome of Dendrocalamus liboensis Hsueh & D. Z. Li 1985 and its phylogenetic analysis

Abstract Dendrocalamus liboensis Hsueh & D. Z. Li 1985 is a unique member of the Bambusoideae subfamily found in Guizhou, China. The species has both economic importance and ornamental value. This study represents the first report of the sequencing and assembly of the complete chloroplast genome of D. liboensis. The total length of the genome was 139,483 bp, with a conventional quadripartite framework consisting of a large single-copy (LSC) region (83,001 bp in length), a small single-copy (SSC) region (12,896 bp in length), and two inverted repeats (IR) regions (both 21,793 bp in length). Overall, the D. liboensis chloroplast genome contained 128 functional genes, including 83 protein-coding genes, 37 tRNAs, and 8 rRNAs. Phylogenetic analysis showed that D. liboensis closely resembled D. sapidus, with both found on a strongly supported branch of the phylogenetic tree.


Introduction
First described in 1985, Dendrocalamus liboensis Hsueh & D. Z. Li is a member of the Dendrocalamus genus that is structurally similar to D. tsiangii but with larger rods.D. liboensis is only found in Libo County in Guizhou, China, where it is endemic and grows primarily in habitats at altitudes of about 650 m.In common with species such as Chimonobambusa lactistriata, Indocalamus hirsutissimus, and Ampelocalamus scandens, D. liboensis is increasingly threatened by deteriorating natural environmental conditions and a reduction in the size of the wild population (Zhong et al. 2021;Hu et al. 2022;Wu et al. 2022).Bamboo shoots serve as a wild vegetable consumed by local populations and are also used as ornamental garden plants, while bamboo culm is also valued as a building material (Du et al. 2009;Deng and Wang 2006).
Dendrocalamus is a member of the subgenus Bambusa within the Poaceae family.Li and Hsueh (1988) classification divides the genus Dendrocalamus into two subgenera and five groups, whereas the Forest Code (FOC) divides it into three subgenera and seven groups.Recent systematics studies have shown that Dendrocalamus is closely related to Bambusa and Gigantochloa, which together form the BDG complex (Yang et al. 2008).To date, there has been no analysis of the complete chloroplast genome of D. liboensis.Thus, to contribute to the preservation of this species and explore its genetic resources by furthering research efforts, we sequenced, assembled, and analyzed the full D. liboensis chloroplast genome.The present report provides a comprehensive description of the D. liboensis chloroplast genome and its phylogenetic relationships with other Dendrocalamus species.

Materials and methods
Fresh leaves of D. liboensis (Figure 1) were harvested from specimens found in Libo County, Guizhou, China, in April 2022 (25 � 26 0 23.24 00 N, 107 � 55 0 0.26 00 E, altitude: 628 m).The leaves were placed in silica gel and specimens were deposited at the Natural Museum of Guizhou University (contact person: Guang-Qian Gou; email: ggqian106@163.com)under the voucher number GB264.Total DNA was extracted from the leaves using a modified CTAB method (Doyle and Doyle 1987), and the quality and quantity of the DNA was assessed using 1% agarose gel electrophoresis and spectrophotometry (Nanodrop, Thermo Fisher, Waltham, MA, USA), respectively.
The DNA samples were sent to BMK-Beijing (China) for library construction and sequencing on an Illumina HiSeq 2500 instrument (Illumina, San Diego, CA).After quality control, 4.24 Gb of clean data were obtained and assembled into circular contigs with GetOrganelle v.1.7.5 (Jin et al. 2020) and annotated through Plastid Genome Annotator (PGA) (Qu  et al. 2019), using Dendrocalamus brandisii (MK679786) as the reference (Liu et al. 2020).Genious 9.0.2 was used for the manual correction of the annotated sequencing data (Kearse et al. 2012).The map of the chloroplast genome was drawn using OGDRAW v1.3.1.Mapping raw reads into the chloroplast genome sequence to generated the coverage plot by matplotlib v.3.7.0 (https://matplotlib.org/) (Supplementary Figure 1).The cis-splicing genes and trans-splicing genes were processed using CPGview (Liu et al. 2023).The completed D. liboensis chloroplast genome was uploaded to GenBank (accession number OR083041).
Phylogenetic relationships between D. liboensis and other Dendrocalamus species were explored by downloading 18 complete Dendrocalamus chloroplast genome sequences from the NCBI database, as well as the chloroplast genomes of Bambusa emeiensis and Bambusa multiplex as outgroups.The sequences were aligned using MAFFT (Katoh and Standley 2013), and the optimal model for phylogenetic tree construction was selected with IQtree (Nguyen et al. 2015).

Discussion and conclusion
Compared with nuclear and mitochondrial genomes, chloroplast genomes are highly conserved and play an important role in phylogeny and species evolution studies (Du et al. 2017).With the development of high-throughput sequencing technology, chloroplast genome sequences are widely used as super barcodes in species identification and other studies (Li et al. 2021).In this study, the complete chloroplast genome of the economically important and ornamentally valuable species D. liboensis was sequenced for the first time and formally submitted to genome repositories.The chloroplast genome structure of D. liboensis shows a typical tetrad structure, including the LSC region, SSC region and IR region.The D. liboensis chloroplast genome was found to be similar in length and composition to those of other Dendrocalamus species (Pei et al. 2022).The geographical distribution of D. liboensis and D. sapidus is similar, both occurring in southern Guizhou.In addition, these two species have similar morphological characters, including bamboo stems, branches and leaves.The close relationship between the two species is consistent with the results of phylogenetic analyses using chloroplast genome construction.The result enriches the genomic data for the genus Dendrocalamus, which will contribute to phylogenetic and evolutionary studies in future.

Figure 2 .
Figure 2. Map of the D. liboensis chloroplast genome(GenBank: OR083041).This map was drawn using the OGDRAW.Genes inside the circle are transcribed clockwise, and those on the outside are transcribed counter-clockwise.Genes with related functions are shown in the same color.The darker gray in the inner circle corresponds to DNA G þ C content, while the lighter gray corresponds to A þ T content.LSC: large single-copy; SSC: small single-copy; IR: inverted repeat.