Abstract
Dendrocalamopsis vario-striata is one of the most economical and ornamental significant bamboo. It has the characteristics of annual flowering but no death. Here, we report on the first complete chloroplast (cp) genome of D. vario-striata. Its full-length of 139,458 bp, include large single-copy (LSC) region of 83,279 bp, small single-copy (SSC) region of 12,143bp, a pair of invert repeats (IR) regions of 22,018bp. Plastid genome contains 264 genes, 170 protein-coding genes, 78 tRNA genes, and 16 rRNA genes. The maximum likelihood phylogenetic analysis shows that D. vario-striata was sister to all other species of Bambusoideae.
Keywords: Dendrocalamopsis vario-striata, plastid genome, phylogeny, bamboo
Dendrocalamopsis vario-striata is a cluster of bamboos within the family of Gramineae, which is distributed in a large area along the southeast coast and is widely in Fujian and Zhejiang Provinces in China (Wang et al. 2012). Dendrocalamopsis vario-striata is fast growing with high material quality, and the bamboo shoots have a delicious taste and high nutritional value, therefore it has high economic value. The special biological characteristics of the bamboo allow it to be planted in sandbank and other harsh environments to improve soil and prevent soil erosion (Zhang and Zheng 2008). Although some studies have reported the growth habits and cultivation techniques of D. vario-striata. (Zheng and Chen 2004; Jin and Wang 1996) There is a lack of research on its chloroplast genome. The complete chloroplast genomic data will be useful for population and phylogenetic studies of D. vario-striata.
The plant material of D. vario-striata was collected from Fujian province, China (Fujian Agriculture and Forestry university, Fuzhou: 119°23′23.93″E, 26°07′54.75″N), and dried into silica gel immediately. The voucher specimen is kept at the Herbarium of College of Forestry, Fujian Agriculture and Forestry University (specimen code FAFU0819). DNA extraction from fresh leaf tissue, with 500 bp randomly interrupted by the Covaris ultrasonic breaker for library construction. The constructed library was sequenced PE150 by Illumina Hiseq Xten platform, approximately 2GB data generated. Illumina data were filtered by script in the cluster (default parameter:-L 5, -p 0.5, -N 0.1). Complete plastid genome of D. vario-striata (GeneBank accession: KX852398) as reference, plastid genome of D. vario-striata was assembled by GetOrganelle pipe-line (https://github.com/Kinggerm/GetOrganelle), it can get the plastid-like reads, and the reads were viewed and edited by Bandage (Wick et al. 2015). Assembled choroplast genome annotation base on comparison with D. vario-striata by Geneious v 11.1.5 (Biomatters Ltd., Auckland, New Zealand) (Kearse et al. 2012). The annotation result was drawn with the online tool OGDRAW (http://ogdraw.mpimp-golm.mpg.de/) (Lohse et al. 2013).
The complete plastid genome sequence of D. vario-striata (GenBank accession: MN038143) was 139,458 bp in length, with a large single-copy (LSC) region of 83,279 bp, a small single-copy (SSC) region of 12,143 bp, and a pair of inverted repeats (IR) regions of 22,018 bp. Complete chloroplastid genome contains 264 genes, there were 170 protein-coding genes, 78 tRNA genes, and 16 rRNA genes. In order to reveal the phylogenetic position of D. vario-striata with other members of Dendrocalamopsis, a phylogenetic analysis was performed based on 19 complete chloroplast genomes of Bambusoideae, and two taxa (Connorochloa tenuis, Amphicarpum muhlenbergianum) as outgroups. They all downloaded from NCBI GenBank. The sequences were aligned by MAFFT v7.307 (Katoh and Standley 2013), and phylogenetic tree constructed by RAxML (Stamatakis 2014).
The maximum likelihood phylogenetic analysis shows that D. vario-striata was sister to the all other species of Bambusoideae.
Disclosure statement
No potential conflict of interest was reported by the authors.
Figure 1.
Phylogenetic analysis of 20 species of Bambusoideae and two taxa Connorochloa tenuis, Amphicarpum muhlenbergianum) as an outgroup based on plastid genome sequences by RAxML, bootstrap support value near the branch.
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