Complete plastid genome of Dendrocalamus brandisii (Poaceae, Bambusoideae)

Abstract

Dendrocalamus brandisii is high bamboo with branches several, dominant branches well developed. In this study, the complete plastid genome of D. brandisii was assembled and annotated. The total plastid genome was 139,423 bp in length, consisting a large single-copy region (LSC) of 82,956 bp, a small single-copy region (SSC) of 12,879 bp, and a pair of inverted repeats (IR) regions of 21,794 bp. The complete chloroplast genome contains 132 genes, including 39 transfer RNA (tRNA) genes, 8 ribosomal RNA (rRNA) genes and 85 protein-coding genes. The phylogenetic analysis suggested that D. brandisii sister to D. latiflorus.

Keywords:

• Dendrocalamus
• bamboo
• phylogeny
• plastid genome

Woody bamboos (Poaceae: Bambusoideae) comprise ca. 80 genera including more than 1200 species, which are mainly distributed in the subtropical and tropical regions of Asia, America and Africa (Li et al. 2006; Yi et al. 2008). Dendrocalamus is a woody bamboo genus placed in the subtribe Bambusinae and tribe Bambuseae (Ohrnberger 1999). Species of the mentioned genera are characterized by their sympodial rhizomes and large-sized, dense clumps and it contains over 50 species, naturally distributed in tropical and subtropical regions of the Old World (Pattanaik and Hall 2011).

Fresh Leaf sample of D. brandisii was acquired from Cangshan district, Fuzhou city, Fujian Province of China (26°38′N, 119°27′E), and the voucher specimen deposited at the Herbarium of Fujian Agriculture and Forestry University (specimen code HTY004). The total genomic DNA was extracted from fresh leaves using a modified Cetyltrimethylammonium Ammonium Bromide (CTAB) method (Doyle and Doyle 1987) and sequenced by the BGISEQ-500 platform. The samples were collected from clean reads were used to assemble the complete chloroplast genome by the GetOrganelle pipe-line (Jin et al. 2018), with the chloroplast genome of Dendrocalamus latiflorus (GenBank accession NC_013088) as the reference sequences. The assembled chloroplast genome was annotated using the Geneious R11.15 (Kearse et al. 2012).

The complete plastid genome sequence of D. brandisii (GenBank accession MN782325) was 139,423 bp in length, consisting of a large single-copy region (LSC) of 82,956 bp, a small single-copy region (SSC) of 12,879 bp, and a pair of inverted repeats (IR) regions of 21,794 bp. The GC content of the chloroplast genome was 38.91%. Complete plastid genome contains 132 genes, including 39 transfer RNA (tRNA) genes, 8 ribosomal RNA (rRNA) genes and 85 protein-coding genes. To confirm the phylogenetic position of D. brandisii, a phylogenetic analysis was performed based on 20 representative plastid genome sequences. All sequences were aligned with the HomBlock pipeline (Bi et al. 2018), and the phylogenetic tree constructed by RAxML (Stamatakis 2014). The ML tree showed that D. brandisii 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].