Skip to main content
NCBI home page
Mitochondrial DNA. Part B, Resources logoLink to Mitochondrial DNA. Part B, Resources
. 2022 Mar 15;7(3):492–494. doi: 10.1080/23802359.2022.2049986

The complete chloroplast genome of Chimonobambusa utilis (Keng) P. C. Keng, known as ‘the king of bamboo shoots’

Liangjun Xiao 1, Tao Wu 1, Yongjian Liao 1, Tian Xu 1,✉
PMCID: PMC8928828  PMID: 35311203

Abstract

The whole chloroplast (cp) genome sequence of Chimonobambusa utilis (Keng) P. C. Keng has been characterized using Illumina pair-end sequencing. The complete cp genome (GenBank accession: OK040769) was 139,540 bp in length, containing a large single copy region (LSC) of 83,133 bp and a small single copy region (SSC) of 12,811 bp, which were separated by a pair of 21,798 bp inverted repeat regions (IRs). The genome contained 133 genes (114 unique), including 86 protein-coding genes (81 unique), 39 tRNA genes (29 unique), and eight rRNA genes (four unique). The overall GC content of C. utilis cp genome is 38.88%. Phylogenetic analysis of 32 cp genomes within the supertribe Bambusatae suggests that C. utilis is closely related to C. quadrangularis.

Keywords: Poaceae, Chimonobambusa utilis, phylogeny, chloroplast genome

Chimonobambusa utilis (Keng) P. C. Keng 1948 is a kind of tall bamboo with a stalk as high as 10 m and diameter of 2–4 cm. It is an endemic bamboo species in Southwest China, mainly distributed in an altitude range of 1000–2100 m in Sichuan, Guizhou, Yunnan provinces and Chongqing municipality, with abundant natural resources and large preservation area (Li and Chris 2006; Ding et al. 2011). This bamboo is a rich source of nutrients, natural bioactive compounds and antioxidants. The young shoots of C. utilis are formed in September, and end in November, lasting for 60–70 days. They are famous all over the world for their unique fresh, fragrant, tender, and crisp quality, and are known as ‘the king of bamboo shoots’ (Ren et al. 2021). It is also a good raw material for papermaking and bamboo weaving. The genus Chimonobambusa includes about 37 species (Li and Chris 2006), but NCBI database currently only records a few chloroplast (cp) genome data from six species of this genus. The cp genome sequence of C. sichuanensis has been used to determine evolutionary relationships and to clarify the classification status of the species (Zhao et al. 2021). In this study, we report and characterize the complete cp genome of C. utilis, which will provide genomic data for further research.

Fresh and healthy leaves of a single plant of C. utilis were collected from Jinfo Mountain, Nanshan District, Chongqing municipality, China (N 29°1′11″, E 107°10′37″, altitude: 2080 m). The voucher specimen (Wu20210049) was deposited in the Herbarium of Yunnan Academy of Forestry and Grassland, Kunming, China (http://www.ynlky.org.cn/, Wu Tao, ynafwt@126.com). C. utilis in current research did not belong to the endangered or protected species. The experimental materials were collected complying with relevant institutional guidelines and national legislation. The samples were collected without causing harm to the plant habitat or the bamboos themselves. The total genomic DNA was isolated using DNAsecure Plant Kit (Beijing Tiangen Biotech Company, Beijing, China). The concentration and integrity of the DNA were analyzed by Invitrogen Qubit Fluorometers (Thermo Fisher Scientific, Waltham, MA) and agarose gel electrophoresis. A shotgun library with an insert size of 150 bp was prepared and sequenced using the Illumina Hiseq 2500 (Illumina, San Diego, CA). Approximately, 2.1 Gb raw data of 150 bp paired-end reads were obtained. The raw reads were filtered to obtain high-quality clean reads by using NGS QC Toolkit_v2.3.3 with default parameters (Patel and Jain 2012). Plastomes were de novo assembled by GetOrganelle (Jin et al. 2020). The genome sequence was annotated using the published C. hejiangensis cp genomes (NC053872) as references, then adjusted and confirmed with Geneious Prime 2020.0.5 (Kearse et al. 2012). The annotated genomic sequence was then deposited into GenBank with the accession number OK040769. The complete cp genome sequences of 32 species from the four tribes, Bambuseae, Dendrocalameae, Melocanneae, and Shibataeeae in supertribe Bambusatae were aligned using MAFFT (Katoh and Standley 2013), and a maximum-likelihood (ML) tree was established based on whole cp genome sequences using the RAxML8 (Stamatakis 2014) with GTR GAMMA I nucleotide model and 1000 bootstrap replicates, in order to ascertain the phylogenetic status of C. utilis.

The complete cp genome of C. utilis is 139,540 bp in length, containing a pair of inverted repeats (IRs) of 21,798 bp, a small single copy (SSC) of 12,811 bp, and a large single copy (LSC) of 83,133 bp. The overall GC content of the cp genome is 38.88%, the ones of the LSC, SSC, and IR were 36.95%, 33.22%, and 44.22%, respectively. A total of 133 genes (114 unique ones) in the cp genome were annotated, including 86 protein-coding genes (81 unique), 39 tRNA genes (29 unique), and eight rRNA genes (four unique). ML phylogenetic analysis revealed that C. utilis is closely related to C. quadrangularis (Figure 1). The newly characterized complete cp genome of C. utilis will provide essential resources for further study on the evolution and genetic diversity.

Figure 1.

Figure 1.

Open in a new tab

Maximum-likelihood phylogenetic analysis of 32 bamboo species from the four tribes, Bambuseae, Dendrocalameae, Melocanneae, and Shibataeeae in supertribe Bambusatae based on the complete chloroplast genome sequences. Bootstrap percentages are indicated for each branch.

Authors contributions

Conception and design, L.X. and T.X.; analysis and interpretation of the data, T.W. and Y.L.; writing and revising the manuscript, L.X., T.W., Y.L., and T.X.; supervision and funding acquisition, T.X. All authors approved the final manuscript and agreed to be accountable for all aspects of the work.

Acknowledgements

Ethics statement: The plant material of this study is a kind of bamboo, Chimonobambusa utilis, which is not a threatened or endangered species. The collection of plant material was carried out in accordance with guidelines provided by our institution, Yunnan Academy of Forestry and Grassland. The authors of this manuscript are willing to undertake relevant ethical responsibilities.

Funding Statement

This work was financially supported by the Yunan Demonstration and Promotion Fund for Forestry and Grass Science & Technology [[2020]TS07].

Disclosure statement

No potential conflict of interest was reported by the authors.

Data availability statement

The complete chloroplast genome generated for this study has been deposited in GenBank with accession number OK040769, which is openly available in GenBank of NCBI at website (https://www.ncbi.nlm.nih.gov/). All high-throughput sequencing data files are available from the GenBank Sequence Read Archive (SRA) accession number: SRR15725928. The associated BioProject and BioSample numbers are PRJNA760964 and SAMN21240067, respectively.

References

  1. Ding B, Yin JQ, Liu SN, Yang C, Yuan Z, Kong WX.. 2011. Research progress of Chimonobambusa utilis and its development and utilization. Guizhou Agric Sci. 39(10):175–178. [Google Scholar]
  2. Jin J-J, Yu W-B, Yang J-B, Song Y, dePamphilis CW, Yi T-S, Li D-Z.. 2020. GetOrganelle: a fast and versatile toolkit for accurate de novo assembly of organelle genomes. Genome Biol. 21(1):241. [DOI] [PMC free article] [PubMed] [Google Scholar]
  3. Katoh K, Standley DM.. 2013. MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol Biol Evol. 30(4):772–780. [DOI] [PMC free article] [PubMed] [Google Scholar]
  4. Kearse M, Moir R, Wilson A, Stones-Havas S, Cheung M, Sturrock S, Buxton S, Cooper A, Markowitz S, Duran C, et al. 2012. Geneious basic: an integrated and extendable desktop software platform for the organization and analysis of sequence data. Bioinformatics. 28(12):1647–1649. [DOI] [PMC free article] [PubMed] [Google Scholar]
  5. Li DZ, Chris S.. 2006. Chimonobambusa. In: Shouliang C, Dezhu L, Guanghua Z, editors. Flora of China, vol. 22: Poaceae. Beijing; St Louis: Science Press; Missouri Botanical Garden Press; p. 152–161. [Google Scholar]
  6. Patel RK, Jain M.. 2012. NGS QC toolkit: a toolkit for quality control of next generation sequencing data. PLoS One. 7(2):e30619. [DOI] [PMC free article] [PubMed] [Google Scholar]
  7. Ren C, Jia Y, Lou Y, Qiao S, Xu W, Qin L.. 2021. Analysis of nutritional and functional components of bamboo shoots in Chimonobambusa utilis, Guizhou. Food Ferment Ind. 47(10):214–221. [Google Scholar]
  8. Stamatakis A. 2014. RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics. 30(9):1312–1313. [DOI] [PMC free article] [PubMed] [Google Scholar]
  9. Zhao W, Cao B, Yang G, Zhang W, Yu F.. 2021. Complete chloroplast genome sequence and phylogenetic analysis of Chimonobambusa sichuanensis (Bambusoideae). Mitochondrial DNA B Resour. 6(3):824–825. [DOI] [PMC free article] [PubMed] [Google Scholar]

Associated Data

This section collects any data citations, data availability statements, or supplementary materials included in this article.

Data Availability Statement

The complete chloroplast genome generated for this study has been deposited in GenBank with accession number OK040769, which is openly available in GenBank of NCBI at website (https://www.ncbi.nlm.nih.gov/). All high-throughput sequencing data files are available from the GenBank Sequence Read Archive (SRA) accession number: SRR15725928. The associated BioProject and BioSample numbers are PRJNA760964 and SAMN21240067, respectively.

Articles from Mitochondrial DNA. Part B, Resources are provided here courtesy of Taylor & Francis

RESOURCES