The complete plastid gentome of Dendrocalamus yunnanicus (Poaceae, Bambuseae)

Abstract

Dendrocalamus is an economically important woody bamboo genus. In this study, the complete chloroplast genome of D. yunnanicus was determined from Illumina HiSeq pair-end sequencing data. The genome was 139,432 bp in length, including a large single-copy region (LSC) of 82,964 bp and a small single-copy region (SSC) of 12,878 bp, and two inverted repeat regions (IR) of 21,795 bp. There were 132 genes predicted, containing 85 protein-coding genes, 8 ribosomal RNA genes, and 39 transfer RNA genes.

Keywords:

• Chinese bamboo
• Dendrocalamus
• phylogeny
• plastid genome

Dendrocalamus Nees (Poaceae; Bambusoideae; Bambuseae), an economically important woody bamboo genus described in 1835 based on D. strictus (Roxb.) Nees., consists of approximately 52 species collectively distributed in the tropical and subtropical regions of Asia (Ohrnberger 1999; Li and Stapleton 2006). The challenges of limitation between Dendrocalamus and Bambusa remain in their flowers being rare. In this study, we first reported the complete chloroplast genome of D. yunnanicus.

The total genomic DNA was extracted from fresh leaves issue of D. yunnanicus using a modified CTAB method (Doyle and Doyle 1987). The sample was acquired from Cangshan district, Fujian, China (26°38′N, 119°27′E), and the voucher specimen was deposited at the Herbarium of Fujian Agriculture and Forestry University (specimen code HTY005). After DNA extraction, library constructing, sequencing, and data filtering were performed on an Illumina Hiseq 2500 platform, generating ∼20 Gb of sequence data. The chloroplast genome was assembled with the program NOVOPlasty (Dierckxsens et al. 2017) with the complete chloroplast genome of its close relative D. latiflorus (GenBank accession NC_013088) as the reference. The assembled chloroplast genome was annotated using Plann (Huang and Cronk 2015), and the annotation was corrected using Geneious (Kearse et al. 2012). The annotation map of the new chloroplast genome was drawn using OGDRAW (Lohse et al. 2013).

The complete D. yunnanicus (GenBank accession MN782326) plastid genome is a quadripartite structure with the length of 139,432 bp, contains a large single-copy region (LSC) of 82,964 bp, a small single-copy (SSC) region of 12,878 bp, and two inverted repeat (IR) regions of 21,795 bp. The new sequences possess total 132 genes, including 85 protein-coding genes, 8 rRNA genes, and 39 tRNA genes. The overall GC content of the chloroplast genome was 38.92%, while the corresponding values of the LSC, SSC, and IR regions are 37.03%, 33.19%, and 44.21%, respectively.

To investigate the phylogenetic position of D. yunnanicus, 20 representative species of Bambuseae were downloaded from the NCBI GenBank database for phylogenetic analysis. The sequences were aligned using MAFFT v7.307(Katoh and Standley 2013), and phylogenetic tree was constructed by RAxML (Stamatakis 2014). The ML tree showed that D. yunnanicus is sister to D. latiflorus with strong support (Figure 1).

Figure 1. The maximum-likelihood (ML) tree based on the 21 plastid genomes of Bambuseae. Numbers near the nodes mean bootstrap support value.

Disclosure statement

No potential conflict of interest was reported by the author(s).

Additional information

Funding

This work was supported by the Central Fiscal Forestry Science and Technology Extension Project [2013 No. 7], the Science and Technology Major Projects of Fujian Province [2013NZ0001], the Regional Development Project of Fujian Province [2015 No.3015], Research Development Fund of Fujian Agriculture and Forestry University [KF2015085] and [CXZX2017119], Program for Scientific and Technological Innovation Team for Universities of Fujian Province [2018 No.49].