A complete chloroplast genome of bamboo cultivar Phyllostachys edulis f. bicolor (Poaceae: Bambusoideae)

Abstract

Phyllostachys edulis f. bicolor, a beautiful ornamental bamboo species, is a new variant of P. edulis, with yellow stems and green grooves between nodes. In this study, we assembled and annotated the complete chloroplast (cp) genome of this variety for the first time. The complete cp genome size of P. edulis f. bicolor was 139,678 bp in length and a total of 130 unique genes were annotated, including 85 protein-coding genes, 37 tRNA encoding genes, and eight rRNA encoding genes. Phylogenetic analysis results provided evidence that P. edulis f. bicolor was closely related to P. edulis ‘heterocycla’. This study contributes to better understanding of intraspecific type evolution of P. edulis.

Keywords:

• Chloroplast genome
• Phyllostachys edulis f. bicolor
• phylogenetic
• Phyllostachys edulis f. heterocycla

Introduction

Phyllostachys edulis f. bicolor (Phyllostachys edulis (Carr.) H. de Lehaie f. bicolor (Nakai) G. H. Lai 2012) is a new variant of Phyllostachys showing color variation, and considered an excellent ornamental plant (Chen 2013). In contrast to the archetype, its bamboo culm is mainly yellow, but the longitudinal groove on the side of the internode branches is green, with a few thin green longitudinal stripes outside the groove. Some leaves are green with yellowish thin longitudinal stripes, and the colors of the bamboo sheath, culm sheath, and patches are lighter. The varieties are mainly distributed in south of the Huaihe River and north of Nanling (Lai 2012; Bu and Zhang 2015; Zeng et al. 2018). In this study, using high-throughput sequencing technology, a complete chloroplast (cp) genome of P. edulis f. bicolor was obtained for the first time to provide a reference for understanding the evolution of intraspecific types of P. edulis.

Materials

Samples were collected from an experimental bamboo forest (Figure 1) at Nanjing Forestry University (118.817139° E, 32.078625° N). Voucher specimens of P. edulis f. bicolor (collector: Qirong Guo, [email protected], voucher number NJFU-G2017P11) were deposited in the laboratory of the herbarium at the Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University.

Figure 1. Phyllostachys edulis f. bicolor. The main performance is that the bamboo culm is yellow, and the groove part is green; some leaves have yellow and green stripes. The photos of P. edulis f. bicolor were taken by the authors in Anji county, Zhejiang Province, China.

Methods

Genomic DNA was extracted using a Qiagen Plant Genomic DNA Prep Kit (Sangon Biotech, Shanghai, China), sequenced on the Illumina Hiseq 2500 platform, and deposited to NCBI under the record number SRR18455992. Data quality control was performed using fastp (Chen et al. 2018), and Novoplasty (v4.0) was used to assemble high-quality paired data into a complete cp genome. Genome annotation was performed using GeSeq (Tillich et al. 2017). Alignment was performed using the P. edulis cp genome sequence combined with manual manipulation, using Geneious R8 (Biomatters Ltd, Auckland, New Zealand) for correction. tRNA genes were further validated using the tRNAscan-SE online web server (Schattner et al. 2005). A gene map of the annotated P. edulis f. bicolor cp genome was drawn online using CPGview (Liu et al. 2023), and the annotated P. edulis f. bicolor cp genome sequence was submitted to NCBI (accession number: OM084949). To confirm the phylogenetic position of P. edulis f. bicolor, we obtained 11 published Phyllostachys varieties cp genomes from NCBI, and four Phyllostachys varieties cp genomes from the China National GeneBank DataBase (CNGBdb). The phylogeny was inferred using the maximum-likelihood (ML) method. MAFFT software was used for sequence alignment (Katoh and Standley 2013), and the phylogenetic tree was constructed using IQ-TREE (Minh et al. 2020). The best-fitting model was selected by ModelFinder (Kalyaanamoorthy et al. 2017) and implemented in IQ-TREE.

Results

Analysis of chloroplast genome characteristics

The full length of the P. edulis f. bicolor cp genome (Figure 2) of 139,678 bp is comprised of a large single-copy region (LSC, 83,212 bp), small single-copy region (SSC with 12,870 bp), and two inverted repeat regions (IR with 21,798 bp). The GC content of the total genome was 38.9%, and the GC content of the LSC, SSC, and IR regions was 37.0%, 33.2%, and 44.2%, respectively. There were 130 unique genes, including 85 protein-coding genes, 37 tRNA encoding genes, and eight rRNA encoding genes. According to their function, all annotated genes were divided into four main categories: genes related to photosynthesis (n = 45), genes related to self-replication (n = 75), genes encoding other proteins (n = 5), and genes of unknown function (n = 5), with 19 of them (ndhB, rps7, rps15, rps19, rpl2, rpl23, ycf2, trnA-UGC, trnH-GUG, trnI-CAU, trnI-GAU, trnL-CAA, trnN-GUU, trnR-ACG, trnV-GAC, rrn4.5, rrn5, rrn16, and rrn23) being double-copy genes.

Figure 2. Schematic map of overall features of the chloroplast genome of Phyllostachys edulis f. bicolor.

The map contains six circles. From the center going outward, the first circle shows the forward and reverse repeats connected with red and green arcs, respectively. The second circle and the third circle show tandem repeats and microsatellite sequences marked with short strips, respectively. The fourth circle indicates the position of LSC, SSC, IRA, and IRB, and the fifth circle indicates the GC content. The genes outside the sixth circle are transcribed counterclockwise, while the genes inside are transcribed clockwise. The genes were colored based on their functional categories.

Phylogenetic analysis of Phyllostachys edulis f. bicolor

The phylogenetic relationships of some P. edulis varieties are described using phylogenetic analysis. P. edulis ‘heterocycla’, P. edulis f. bicolor, P. edulis ‘pachyloen’, P. edulis curviculmis, and P. angusta formed a small branch, with P. edulis. P. edulis and P. angusta each gathered into one branch, P. edulis f. bicolor and P. edulis ‘heterocycla’ clustered together, and P. edulis curviculmis and P. angusta forming another cluster. This indicated that they were closely related to each other and had notable collinearity in the evolution of intraspecific types of Phyllostachys (Figure 3).

Figure 3. Phylogenetic relationships between Phyllostachys edulis f. bicolor and some other species of Phyllostachys Varieties. Bootstrap support values are given at the nodes.

The phylogenetic tree is constructed by the ML method. The sequences used for tree construction are as follows: P. edulis f. luteosulcata (SRP132620). P. prominens (SRP132620). P. kwangsiensis (SRP132620). P. edulis f. ventricose (SRP132620). P. reticulata (MN537808; Huang et al. 2019). P. glauca (MT657329; Cao et al. 2020). P. sulphurea (KJ722540; Gao and Gao 2016). P. nigra ‘henonis’ (HQ154129). P. edulis (HQ337796). P. edulis ‘heterocycla’ (KY038820; Dan et al. 2017). P. edulis f. bicolor (OM084949). P. edulis ‘pachyloen’ (MN537809; Huang et al. 2019). P. edulis curviculmis (MW007169; Gao et al. 2021). P. angusta (MW027348; Yu et al. 2021). P. edulis f. tubiformis (MW874473; Liu et al. 2022). Dendrocalamus farinosus (OM177223; Pei et al. 2022).

Discussion and conclusions

China’s Phyllostachys resources are rich; there are several varieties with significant phenotypic genetic difference among them (Zhang et al. 2007). In this study, we successfully assembled the complete cp genome of Phyllostachys edulis f. bicolor for the first time and selected the complete cp genome data of 15 other Phyllostachys varieties for phylogenetic analysis. The results showed that P. edulis f. bicolor was closely related to P. edulis ‘heterocycla’. The findings were consistent with those of previous studies on P. edulis curviculmis (Gao et al. 2021), where P. edulis f. bicolor formed a small branch with P. edulis curviculmis and P. edulis ‘pachyloen’, all of which are members of the Phyllostachys genus. Moreover, the cp genome size and structure of P. edulis f. bicolor and P. edulis curviculmis were the same, which further indicated the genetic relationship between the two. Elucidation of the complete cp genome of P. edulis f. bicolor provides important data for the phylogeny of Phyllostachys varieties that will help us in better understanding of the evolution of intraspecific types of Phyllostachys.

Author contributions

Qirong Guo contributed to the study concept and design; Bo Hu and Rou Wan collected the samples and performed the experiments; Wenxuan Jing analyzed and interpreted the data; all authors read and approved the final manuscript; and that all authors agree to be accountable for all aspects of the work.

Ethics statement

We confirmed that all the research meets ethical guidelines and adheres to the legal requirements of the study country. This study did not involve any ethical issues, so no ethics committee or relevant permissions were required.

Disclosure statement

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

Data availability statement

The genome sequence data that support the findings of this study are openly available in GenBank of NCBI at https://www.ncbi.nlm.nih.gov, under the accession number OM084949. The associated BioProject, SRA, and Bio-Sample numbers are PRJNA818118, SRR18455992, and SAMN26816507, respectively.

Additional information

Funding

This work was kindly supported by research projects of the National Natural Science Foundation of China [Grant No. 31971648], and the Talent Introduction Project of Nanjing Forestry University [Grant No. GXL2018001].