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Article

Complete Chloroplast Genome Features of Dendrocalamusfarinosus and Its Comparison and Evolutionary Analysis with Other Bambusoideae Species

by
Jialong Pei
1,
Yong Wang
2,
Juan Zhuo
1,
Huibin Gao
2,
Naresh Vasupalli
1,
Dan Hou
1 and
Xinchun Lin
1,*
1
State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, 666 Wusu Street, Hangzhou 311300, China
2
Yibin Forestry and Bamboo Industry Research Institute, Yibin 644599, China
*
Author to whom correspondence should be addressed.
Genes 2022, 13(9), 1519; https://doi.org/10.3390/genes13091519
Submission received: 28 July 2022 / Revised: 16 August 2022 / Accepted: 22 August 2022 / Published: 24 August 2022
(This article belongs to the Section Plant Genetics and Genomics)
Browse Figures
Versions Notes

Abstract

:
Dendrocalamus farinosus is one of the essential bamboo species mainly used for food and timber in the southwestern region of China. In this study, the complete chloroplast (cp) genome of D. farinosus is sequenced, assembled, and the phylogenetic relationship analyzed. The cp genome has a circular and quadripartite structure, has a total length of 139,499 bp and contains 132 genes: 89 protein-coding genes, eight rRNAs and 35 tRNAs. The repeat analyses showed that three types of repeats (palindromic, forward and reverse) are present in the genome. A total of 51 simple sequence repeats are identified in the cp genome. The comparative analysis between different species belonging to Dendrocalamus revealed that although the cp genomes are conserved, many differences exist between the genomes. The analysis shows that the non-coding regions were more divergent than the coding regions, and the inverted repeat regions are more conserved than the single-copy regions. Moreover, these results also indicate that rpoC2 may be used to distinguish between different bamboo species. Phylogenetic analysis results supported that D. farinosus was closely related to D. latiflorus. Furthermore, these bamboo species’ geographical distribution and rhizome types indicate two evolutionary pathways: one is from the tropics to the alpine zone, and the other is from the tropics to the warm temperate zone. Our study will be helpful in the determination of the cp genome sequences of D. farinosus, and provides new molecular data to understand the Bambusoideae evolution.

Graphical Abstract

1. Introduction

Bambusoideae is one of the largest subfamilies in the grass family (Poaceae), including 75 genera and 1680 species, which are widely distributed in tropical, subtropical and warm temperate zones [1,2]. Bamboo has a high economic value and is widely used in building materials, in making paper, furniture and musical instruments, and as food, etc. [3]. The traditional bamboo species identification is mainly based on morphological characteristics, such as bamboo shoots and flowers [4]. However, the identification and classification of bamboo has always been a complex problem because many species contain similar morphological characteristics and the flowering interval of most Bambusoideae species is very long. For example, Phyllostachys edulis is reported to have a flowering interval of 67 years, Ph. bambusoides, 120 years, and Melocanna baccifera, 48 years [5]. Therefore, it is difficult to classify Bambusoideae species by morphological characteristics.
Bambusa, Dendrocalamus and Gigantochloa are morphologically similar genera in Bambusoideae. Bambusa has more than 100 species, and nearly 80 species are found in southern and southwestern China [1]. Dendrocalamus contains 66 species, mainly distributed in tropical and subtropical Asia. Among them, 30 species are found in southwestern China [1,6]. In addition, out of 30 species of Gigantochloa, seven are in China. The classification of bamboo species of Bambusa, Dendrocalamus, and Gigantochloa has long been controversial. In particular, Gigantochloa and Dendrocalamus can only be distinguished by their filaments [1]. These characteristics make it challenging to differentiate these two genera. In recent years, researchers have continuously provided evidence to prove a difference between them, evidence which is used to classify bamboo species. The flora of China (http://www.iplant.cn/foc/AboutFoc, accessed on 11 January 2022) distinguished the three genera from the size of culm sheath blades and auricles, the length of culm internodes and the branchlets and the morphological characteristics of caryopsis [1]. However, the flowering interval of Bambusoideae is long, and caryopsis acquisition is difficult. Therefore, we need an effective method to assist in the classification of Bambusoideae species.
The chloroplast (cp) is regarded as the energy source for the evolution of life [7]. Photosynthesis is one of the most important chemical reactions and provides essential energy for most living things on earth [8]. The cp has an independent semi-autonomous extranuclear genome [9]. The cp genome is the crucial genetic material of plants, encoding 100–200 essential genes which encode proteins involved in photosynthesis and other chloroplast functions [10]. Moreover, the cp genomes are ideal tools for studying evolutionary relationships between species because cp genomes are very conserved, and their heredity is independent of the nucleus [11,12]. With the development of high-throughput sequencing technology, every year, numerous plant cp genomes have been sequenced [1]. Therefore, cp genomes have been widely used in plant classification and evolution [9]. Wu et al. (2009) sequenced the cp genomes of D. latiflorus and Bambusa oldhamii, and believed that cp genomes could be used to provide auxiliary information for the identification and evolution of bamboo species [13]. Many researchers have tried to use the cp genome to assist in bamboo species classification and believe that using the cp genome can provide valuable information in the classification of bamboo [14,15,16].
D. farinosus belongs to Dendrocalamus, which is mainly distributed in southwest China [17]. Compared with other species of Dendrocalamus, D. farinosus is resistant to cold and drought [18]. The bamboo shoots of D. farinosus have a high nutritive content, and D. farinosus is a high-quality material used for weaving and papermaking. With the continuous expansion of bamboo resources and the scale of development, further study of the cp genome will improve our understanding of this species, as well as assist in future breeding experiments. In this study, the complete cp genome of D. farinosus was assembled, and the features of this cp genome were fully elucidated. Moreover, 34 cp genomes of Bambusoideae were downloaded from GenBank and used to analyze the genealogical relationships and evolutionary history, which may allow us to better understand the identity of D. farinosus and the taxonomy of Bambusoideae. Moreover, this work gives us new information on the evolution and origin of Bambusoideae.

2. Results and Discussion

2.1. Characteristics of the D. farinosus cp Genome

In the current study, 3665 Mb of whole-genome raw data were developed from D. farinosus. After quality trimming, the data were reduced to 3128 Mb, with an average read length of 150 bp. Furthermore, we generated the complete cp genome by mapping the quality reads to the reference cp genome B. emeiensis (HQ337797), and 14.65% of the reads were mapped. The complete plastome sequence of D. farinosus has a circular and quadripartite structure, with a total length of 139,499 bp (GeneBankid: OM177223). The plastome has four distinct regions: a small single copy (SSC), a large single copy (LSC) and a pair of inverted repeats (IRa and IRb) (Figure 1). The gene coding region is 64,924 bp, constituting 46.54% of the genome. The length of the SSC, LSC, IRa and IRb regions were 12,879 bp (9.23%), 83,030 bp (59.52%), 21,795 bp (15.62%) and 21,795 bp (15.62%), respectively. Furthermore, the GC contents of the SSC, LSC, IRa and IRb regions were 33.2%, 37%, 44.3% and 44.3%, respectively (Table S1). The results are similar to those found in D. sinicus, Ph. heteroclada, Ph. nidularia and Thyrsostachys siamensis. The cp genomes of all five species were composed of SSC, LSC and IR regions, and the proportions of those regions in the cp genomes for all five species, were similar [19,20,21,22].
The complete cp genome of D. farinosus contains a total of 132 genes. Among the 132 genes are 89 protein-coding genes, eight rRNAs, and 35 tRNAs (Table 1). Furthermore, out of these 132 genes, 90 genes are present in the single-copy regions, 42 in the inverted repeat region, and the ndhH gene is present partly in both the SSC and IRa regions. In addition, the inverted repeat region contains 19 protein-coding genes, eight rRNAs and 20 tRNAs. In addition, the LSC includes 60 protein-coding genes and 23 tRNAs, while the SSC contains nine protein-coding genes and one tRNA. Hecht et al. (2017) identified that besides the canonical start codon (ATG), translation initiation with the non-canonical start codons might contribute to peptide synthesis [23]. The D. farinosus cp genome contains 14 genes with non-canonical start codons (Table S2). Among the 14 genes, eight genes are located in the LSC region, and six are located in the IR region. Furthermore, out of these 132 genes, 13 genes contain exons and introns. Among the 13 genes, 12 genes contain two exons and one intron. In addition, the pafI gene has three exons and two introns. Moreover, among these 13 genes, seven are distributed in the LSC, five genes occur in both the IRs and one in the SSC (Table 2). The longest intron of trnK-UUU is 2505 bp, while the shortest intron of rps12 is 537 bp. Most of the genes in the cp genome are protein-coding genes. This result is present in Bambusoideae, such as D. sinicus, Ph. heteroclada, Ph. nidularia, T. siamensis, etc., and also in other species such as Abutilon fruticosum and Catha edulis [19,20,21,22,24,25]. The trnK-UUU gene also has the longest intron in the cp genome of other species (A. fruticosum and C. edulis) [24,25].
Codon usage is believed to play a crucial role in the cp genome [26]. Codon usage is a factor shaping the evolution of cp genomes, and it varies across different species [27]. In this study, we analyzed the codon usage bias and relative synonymous codon usage (RSCU) based on the nucleotide sequence of protein-codon genes 64,924 bp, which encoded 21,023 amino acids (Table S3). The most popular type was leucine (10.85%), followed by isoleucine (8.18%) and serine (7.47%), whereas the least popular was cysteine (1.14%). The RSCU values of 30 codons were >1, and most of these codons ended with A/T (U), while for 29 codons, the values were <1, and most of them ended with G/C (Figure 2). Only two amino acids, tryptophan and methionine, showed no biased usage (RSCU = 1), which agrees with the analysis of cp genomes from other species [26,28,29].

2.2. Repeat Analyses

2.2.1. Long Repeats

The D. farinosus cp genome contains three kinds of long repeats (palindromic, forward and reverse) (Table S4). The analysis showed 14 palindromic repeats, 29 forward repeats and six reverse repeats. The longest repeat was 60 bp in length, and it was a forward-type repeat located in the LSC. While the two shortest repeats, a forward and a reverse repeat, both 19 bp in length, were located in the LSC. Most of the repeats were between 20–30 bp (85.71%) in length, with 10.2% of the repeats being longer than 30 bp, and 4.08% of the repeats being shorter than 20 bp. A total of thirty-six long repeats were present in the LSC, two repeats were present in the SSC, seven long repeats were detected in two different regions, and four repeats were present in the IR regions.

2.2.2. Simple Sequence Repeats (SSRs)

Simple sequence repeats (SSRs) are essential for genetic mapping, variety identification and molecular marker-assistant breeding. The D. farinosus cp genome contains forty-two SSRs, including seventeen mononucleotides (40.48%), four dinucleotides, three trinucleotides, nine tetranucleotides, and one pentanucleotide with a length of at least 10 bp (Table 3). In addition, the D. farinosus cp genome also contains eight compound SSRs (19.05%). All seventeen mononucleotides consisted of poly-A and poly-T. The AT/TA/TC types contributed to four dinucleotides, and the length of these SSRs was 10 bp. Three trinucleotide repeats were detected, namely AAT (12 bp), CAG (12 bp), and TTC (12 bp), which were located in the LSC. Moreover, the eight compound formations were also located in the LSC.

2.3. Comparative Analysis of Plastomes of Bambusoideae Species

To detect divergence in the cp genome of the six species of Dendrocalamus (D. farinosus, D. fugongensis, D. sinicus, D. membranaceus, D. latiflorus and D. strictus), a comparative analysis was conducted by aligning the cp genome sequences using D. farinosus as a reference genome (Figure 3). The results showed that the cp genomes of Dendrocalamus were conserved primarily. The most divergent gene among the six cp genomes is rpoC2. Furthermore, a lower level of variability was also observed in non-coding regions. Moreover, we also compared the divergence of six cp genomes belonging to five genera in Bambusoideae (D. farinosus, D. bambusoides, Yushania brevipaniculata, Ph. edulis, Fargesia edulis and B. flexuosa) (Figure 4). The analysis showed that the non-coding regions were more divergent than the coding regions, and the inverted repeat regions were more conserved than the single-copy regions. Again, the most divergent gene was rpoC2. In addition, a lower level of variability was also observed in the following genes: psbA, matK, psbD, rpoB, rpoC1, rps2, atpA, psaB, rps4, ndhK, atpB, rbcL, cemA, rpl22, ndhF, ccsA, ndhD and ndhH. The results suggest that these genes can be used as identification loci for different genera in Bambusoideae, and rpoC2 may be used to distinguish different bamboo species. Zhang et al. (2011) found that the genetic divergence is very low among the cp genomes of Bambusoideae, but the rpoC2 gene is an exception [30]. This result is consistent with our study.
The nonsynonymous (dN)/synonymous (dS) ratio was calculated for 19 genes that were observed to be divergent in the cp genomes of the Bambusoideae genera (Figure 5). The dN/dS of 13 genes (68.42%) were <1, suggesting that most of them were in negative selection. The dN/dS value of five genes, rbcL, matK, cemA, ccsA and rps4, were >1, indicating that they were in positive selection, and may provide an evolutionary advantage. Furthermore, the psbD gene does not contain any nonsynonymous changes in the plastome of the species used in this study.
The cp genome of plants is conserved in structure and size. In contrast, the expansion and contraction in the cp genomes also occur, and the size and location of the boundaries of single-copy regions and inverted repeat regions changed slightly. This is generally considered the driving force in plant cp genome variation [26]. The boundaries of the IR-LSC and the IR-SSC of six bamboo species (five genera) were compared and analyzed (Figure 6). The size of the six cp genomes ranged from 139,355 bp (B. flexuosa) to 139,678 bp (Ph. edulis). The gene, ndhH, existed simultaneously at the junction of the SSC-IRa (JSA) and the junction of the SSC-IRb (JSB) in the cp genome of D. farinosus, while it only appeared at the JSA in the other five cp genomes, and expanded to 187–197 bp in the IRa region. The gene, rps19, existed at both the junction of the LSC-IRa (JLA) and the junction of the LSC-IRb (JLB), and varying degrees of contraction and expansion occurs in the cp genomes of the six species. The rpl22 gene of D. farinosus, Ph. edulis and F. edulis contracted inward by 25 bp, 24 bp and 36 bp from the border, respectively. Kim et al. (2004) thought that the expansion and contraction in the cp genomes was probably mediated by the intramolecular recombination of two short direct repeat sequences which frequently occur within the genes located at the borders [31]. Therefore, the driving force for the expansion and contraction of the cp genome of D. farinosus may be greater than that of the other five cp genomes.

2.4. Phylogenetic Analysis

The cp genomes containing a large amount of genetic information are a good resource for inferring evolutionary and phylogenetic relationships [26,32,33,34]. Many bamboo species have a similar morphology, which makes them difficult to classify. In this study, the cp genomes of 34 Bambusoideae species (15 genera) were analyzed to understand the evolutionary relationship (Figure 7A). The results showed that these 34 species were classified into four clades, and Neomicrocalamus prainiias was an outgroup. D. farinosus was divided into the same clade as other members of Dendrocalamus. Members of Dendrocalamus, Bambusa, and Gigantochloa are in the same clade along with Neomicrocalamus yunnanensis. These results differed from the traditional classification method, while remaining consistent with recent studies [1,35]. Members of Phyllostachys are in a clade and members of Drepanostachyum are in a clade. The result is consistent with the classification according to morphology, indicating that the cp genome-assisted bamboo species classification may be able to solve the complex problem of bamboo classification. As increasing numbers of cp genomes of bamboo species are sequenced, it will be more advantageous to demonstrate that this method is feasible.
The evolutionary analysis of the cp genome may provide new information about the evolution and origin of bamboos. The evolution and origin of bamboo have long been controversial. The origin of bamboo is believed to be polycentric, with two major points of origin in Asia and South America. At the same time, Wen Taihui (1983) proposed that there is only one origin center for bamboo globally, and it is located in the Yunnan province of China [36]. In this study, out of 34 bamboo species, 33 were divided into four groups: high altitude region, warm temperate zone, Subtropics and tropics. These four groups overlap at the Sichuan and Yunnan provinces. At the same time, the 34th bamboo species used in this study, Neomicrocalamus prainii, is mainly distributed at the junction of four regions (Sichuan province, China, located in the subtropical region, altitude of 1000–3000 m) (Figure 7B). Furthermore, all 34 bamboo species used in this study were available in the Yunnan province, which we believe may be the origin of bamboo. The results are consistent with Wen [36]. The members of Drepanostachyum and Thamnocalamus are found mainly in the vicinity of the Himalayas, where the average height above sea level is 6000 m [37]. The Chimonocalamus longiusculus is primarily found in southeastern Tibet (average altitude: 4000 m) and southwestern Yunnan (average altitude: 2000 m) [37]. The members of Phyllostachys are found mainly in warm temperate zones and subtropical regions [37]. Nine species are distributed in the subtropical regions, and 16 are mainly distributed in the tropics [37].
The comparison of the rhizomes of the 34 species revealed that all of the species of high-altitude regions and the tropics have sympodial rhizomes, and all of the species of the Subtropics involved in the comparison have amphipodial rhizomes and monopodial rhizomes. Based on the geographical distribution and rhizome types of these bamboo species, we speculate that the evolution of all the species involved in the comparison in China may be divided into tropics to alpine and tropics to warm temperate zones. The rhizomes of bamboo species that evolve to a warm temperate zone transform from sympodial to amphipodial, and then from amphipodial to monopodial. This result is consistent with the prediction of bamboo phylogeny from morphology [38]. With the completion of sequencing and further analyses of the cp genomes of more bamboo species, new evidence for these hypotheses may be provided.

3. Materials and Methods

3.1. Plant Material and DNA Extraction

Young and healthy leaves of D. farinosus, was collected from Changning, Sichuan province (28°29’ N, 104°58’ E). The total DNA was extracted using a modified CTAB protocol [39]. The voucher specimens are available at the College of Forestry and Biotechnology, Zhejiang A&F University (Accession No. BR01).

3.2. Chloroplast Genome Assembly and Gene Annotation

The cp genome was sequenced using the Illumina NovaSeq PE150 platform (Novogene Bioinformatics Technology Co, Ltd. in Beijing, China). The complete cp genome was constructed using MITObim v1.3, and annotated using the online program, GeSeq [40]. Genes were annotated using CPGAVAS2 (Chloroplast Genome Annotation, Visualization, Analysis and GenBank Submission Tool) [41]. The circular cp genome maps were drawn using OGDRAW [42].

3.3. Repeat Analysis

The long repeat sequences of the D. farinosus cp genome were detected using REPuter [43] with default parameters. Simple sequence repeats (SSR) were detected using MISA [44] with the following settings: ten repeats for mono-types, five repeats for di-types, four repeats for tri-types, three repeats for tetra-types, three repeats for penta-types and three repeats for hexa-types.

3.4. Codon Bias Usage Analysis

CPGAVAS2 with default settings was used to analyze the codon bias usage of the protein-coding genes [24]. The relative synonymous codon usage (RSCU) was analyzed.

3.5. Comparison of Related cp Genomes

The mVISTA program was used to analyze sequence divergence between the D. farinosus cp genome and the cp genomes of nine related species [45]. IRscope (https://irscope.shinyapps.io/irapp/, accessed on 4 January 2022) was used to visualize the genes on the boundaries of the junction sites of the six cp genomes. MEGA 7.0 was used to estimate the dN/dS ratio to detect the genes under selection pressure [46].

3.6. Phylogenetic Analysis

The complete cp genomes of 34 Bambusoideae species were downloaded from GenBank (Table S5) and aligned using MAFFT v7 [47]. The evolutionary history was inferred using RAxML-NG with maximum likelihood, and the bootstrap consensus tree was inferred from 1000 replicates [48].

4. Conclusions

Our results identified the complete cp genome of D. farinosus and the evolutionary studies with other Bambusoideae species. Our study identified the basic structure and gene content of the cp genome of D. farinosus. Further, our analysis also determined that the rpoC2 gene might be used to distinguish between different bamboo species. Moreover, these bamboo species’ geographical distribution and rhizome types indicate two evolutionary pathways: the tropics to the alpine zone and the tropics to the warm temperate zone. This study provides the cp genome data for species identification and phylogenetic analysis of the Bambusoideae family.

Supplementary Materials

The following supporting information can be downloaded at: https://www.mdpi.com/article/10.3390/genes13091519/s1, Table S1: Base composition in the D. farinosus cp genome; Table S2: Genes with non-canonical start codons in the D. farinosus cp genome; Table S3: Summary of codon usage and amino acid patterns of the D. farinosus cp genome; Table S4: The long repeat sequences detected in the D. farinosus cp genome; Table S5: List of the cp genome of 34 Bambusoideae species used for phylogenetic analysis.

Author Contributions

Conceptualization, X.L. and Y.W.; methodology, J.P. and Y.W.; formal analysis, J.P. and J.Z.; investigation and resources, Y.W. and H.G.; writing—original draft preparation, J.P.; writing—review and editing, J.P., N.V., D.H. and X.L.; project administration, X.L. All authors have read and agreed to the published version of the manuscript.

Funding

This research was funded by Tissue culture system construction and molecular studies of excellent fiber production bamboo, grant number 2021YLZ005.

Institutional Review Board Statement

Not applicable.

Informed Consent Statement

Not applicable.

Data Availability Statement

The data which supports the findings of this study are openly available in GenBank of NCBI at https://www.ncbi.nlm.nih.gov, accessed on 20 January 2022, reference number (D. farinosus, OM177223).

Conflicts of Interest

The authors declare no conflict of interest.

References

  1. Liu, J.X.; Zhou, M.Y.; Yang, G.Q.; Zhang, Y.X.; Ma, P.F.; Guo, C.; Li, D.Z. ddRAD analyses reveal a credible phylogenetic relationship of the four main genera of Bambusa-Dendrocalamus-Gigantochloa complex (Poaceae: Bambusoideae). Mol. Phylogenet Evol. 2020, 146, 106758. [Google Scholar] [CrossRef] [PubMed]
  2. Santosh, S.; Lalit, M.B.; Poonam, S.; Naik, S.N. Bamboo shoot processing: Food quality and safety aspect (a review). Trends Food Sci. Technol. 2010, 21, 181–189. [Google Scholar] [CrossRef]
  3. Li, Y.; Xu, B.; Zhang, Q.; Jiang, S. Present situation and the countermeasure analysis of bamboo timber processing industry in China. J. For. Eng. 2016, 1, 2–7. [Google Scholar] [CrossRef]
  4. Lichtenthaler, H.K. Chlorophylls and carotenoids: Pigments of photosynthetic biomembranes. Meth. Enzymol. 1987, 148, 350–382. [Google Scholar] [CrossRef]
  5. Janzen, D.H. Why Bamboos Wait So Long to Flower. Annu. Rev. Ecol. Syst. 1976, 7, 347–391. [Google Scholar] [CrossRef]
  6. Yang, H.Q.; Xie, N.; Sun, M.S.; Xu, T.; Li, D.Z. Dendrocalamus atroviridis (Poaceae: Bambusoideae, Bambuseae), a new species from Southwest China. Phytotaxa 2016, 243, 170. [Google Scholar] [CrossRef]
  7. Neuhaus, H.E.; Emes, M.J. Nonphotosynthetic metabolism in plastids. Annu. Rev. Plant Physiol. Plant Mol. Biol. 2000, 51, 111–140. [Google Scholar] [CrossRef]
  8. Fan, S.J.; Guo, X.X. Advances in research and application of plant chloroplast genome. J. Shandong Normal Univ. (Nat. Sci.) 2022, 37, 22–31. [Google Scholar] [CrossRef]
  9. Li, Y.H.; Ren, Y.K.; Zhao, X.H.; Liu, J.; Han, B.; Wang, C.B.; Tang, Z.H. Research Progress on Chloroplast Genome of Major Gramineous Crops. Biotechnol. Bull. 2020, 36, 112–121. [Google Scholar] [CrossRef]
  10. Howe, C.J. Chloroplast Genome. In eLS; John Wiley & Sons, Ltd: Chichester, UK, 2012. [Google Scholar] [CrossRef]
  11. Wolfe, K.H.; Li, W.H.; Sharp, P.M. Rates of nucleotide substitution vary greatly among plant mitochondrial, chloroplast, and nuclear DNAs. Proc. Natl. Acad. Sci. USA 1987, 84, 9054–9058. [Google Scholar] [CrossRef]
  12. Jansen, R.K.; Cai, Z.Q.; Raubeson, L.A.; Daniell, H.; Depamphilis, C.W.; Mack, J.L.; Müller, K.F.; Bellian, M.G.; Haberle, R.C.; Hansen, A.K.; et al. Analysis of 81 genes from 64 plastid genomes resolves relationships in angiosperms and identifies genome-scale evolutionary patterns. Proc. Natl. Acad. Sci. USA 2007, 104, 19369–19374. [Google Scholar] [CrossRef] [PubMed]
  13. Wu, F.H.; Kan, D.P.; Lee, S.B.; Daniell, H.; Lee, Y.W.; Lin, C.C.; Lin, C.S. Complete nucleotide sequence of Dendrocalamus latiflorus and Bambusa oldhamii chloroplast genomes. Tree Physiol. 2009, 6, 847. [Google Scholar] [CrossRef] [PubMed]
  14. Burke, S.V.; Grennan, C.P.; Duvall, M.R. Plastome sequences of two New World bamboos—Arundinaria gigantea and Cryptochloa strictiflora (Poaceae)--extend phylogenomic understanding of Bambusoideae. Am. J. Bot. 2012, 99, 1951–1961. [Google Scholar] [CrossRef] [PubMed]
  15. Burke, S.V.; Clark, L.G.; Triplett, K.J.; Grennan, C.P.; Duvall, M.R. Biogeography and phylogenomics of New World Bambusoideae (Poaceae), revisited. Am. J. Bot. 2014, 101, 886–891. [Google Scholar] [CrossRef] [PubMed]
  16. Wysocki, W.P.; Clark, L.G.; Attigala, L.; Sanchez, E.R.; Duvall, M.R. Evolution of the bamboos (Bambusoideae; Poaceae): A full plastome phylogenomic analysis. BMC Evol. Biol. 2015, 15, 50. [Google Scholar] [CrossRef]
  17. Chen, P.; Zheng, R.H.; Wang, Y.; Hu, Y.B. Study on clonal selection of Dendrocalamus farinosus in south Sichuan. J. Sichuan For. Sci. Technol. 2021, 42, 109–113. [Google Scholar] [CrossRef]
  18. Fu, M.D.W. Research Progress in Overview of Bio-ecological Characteristics and Cultivation Technology for Dendrocalamus farinosus. World Bamboo Ratt. 2014, 12, 25–28. [Google Scholar] [CrossRef]
  19. Wang, Y.; Yuan, X.; Li, Y.; Zhang, J. The complete chloroplast genome sequence of Dendrocalamus sinicus. Mitochondrial DNA B Resour. 2019, 4, 2988–2989. [Google Scholar] [CrossRef]
  20. Tang, S.L.; Xie, J.H.; Cai, J.Z. The complete plastid genome of Thyrsostachys siamensis (Poaceae, Bambusoideae). Mitochondrial DNA B Resour. 2021, 6, 1781–1783. [Google Scholar] [CrossRef]
  21. Ya-Ping, H.; Jie, Z.; Zhao-Yan, Y.; Jia-Jia, L.; Ming-Ye, X.; Qi-Rong, G. The complete chloroplast genome of Phyllostachys heteroclada f. solida (Poaceae). Mitochondrial DNA B Resour. 2021, 6, 566–567. [Google Scholar] [CrossRef]
  22. Jie, Z.; Yaping, H.; Zhaoyan, Y.; Jiajia, L.; Mingye, X.; Qirong, G. The complete chloroplast genome of a solid type of Phyllostachys nidularia (Bambusoideae: Poaceae), a species endemic to China. Mitochondrial DNA B Resour. 2021, 6, 978–979. [Google Scholar] [CrossRef]
  23. Hecht, A.; Glasgow, J.; Jaschke, P.R.; Bawazer, L.A.; Munson, M.S.; Cochran, J.R.; Salit, M. Measurements of translation initiation from all 64 codons in E. coli. Nucleic Acids Res. 2017, 45, 3615–3626. [Google Scholar] [CrossRef] [PubMed]
  24. Alzahrani, D.A. Complete Chloroplast Genome of Abutilon fruticosum: Genome Structure, Comparative and Phylogenetic Analysis. Plants 2021, 10, 270. [Google Scholar] [CrossRef]
  25. Gu, C.; Tembrock, L.R.; Zheng, S.; Wu, Z. The Complete Chloroplast Genome of Catha edulis: A Comparative Analysis of Genome Features with Related Species. Int. J. Mol. Sci. 2018, 19, 525. [Google Scholar] [CrossRef] [PubMed]
  26. Zhu, B.; Qian, F.; Hou, Y.; Yang, W.; Cai, M.; Wu, X. Complete chloroplast genome features and phylogenetic analysis of Eruca sativa (Brassicaceae). PLoS ONE 2021, 16, e0248556. [Google Scholar] [CrossRef] [PubMed]
  27. Srivastava, D.; Shanker, A. Identification of Simple Sequence Repeats in Chloroplast Genomes of Magnoliids Through Bioinformatics Approach. Interdiscip Sci. 2016, 8, 327–336. [Google Scholar] [CrossRef]
  28. Du, X.; Zeng, T.; Feng, Q.; Hu, L.; Luo, X.; Weng, Q.; Zhu, B. The complete chloroplast genome sequence of yellow mustard (Sinapis alba L.) and its phylogenetic relationship to other Brassicaceae species. Gene 2020, 731, 144340. [Google Scholar] [CrossRef]
  29. Yan, C.; Du, J.; Gao, L.; Li, Y.; Hou, X. The complete chloroplast genome sequence of watercress (Nasturtium officinale R. Br.): Genome organization, adaptive evolution and phylogenetic relationships in Cardamineae. Gene 2019, 699, 24–36. [Google Scholar] [CrossRef]
  30. Zhang, Y.J.; Ma, P.F.; Li, D.Z. High-Throughput Sequencing of Six Bamboo Chloroplast Genomes: Phylogenetic Implications for Temperate Woody Bamboos (Poaceae: Bambusoideae). PLoS ONE 2011, 6, e20596. [Google Scholar] [CrossRef] [Green Version]
  31. Kim, K.J.; Lee, H.L. Complete Chloroplast Genome Sequences from Korean Ginseng (panax schinseng nees) and Comparative Analysis of Sequence Evolution among 17 Vascular Plants. DNA Res. 2004, 4, 247–261. [Google Scholar] [CrossRef]
  32. Tong, W.; Kim, T.S.; Park, Y.J. Rice Chloroplast Genome Variation Architecture and Phylogenetic Dissection in Diverse Oryza Species Assessed by Whole-Genome Resequencing. Rice 2016, 9, 57. [Google Scholar] [CrossRef] [PubMed]
  33. Du, Y.P.; Bi, Y.; Yang, F.P.; Zhang, M.F.; Chen, X.Q.; Xue, J.; Zhang, X.H. Complete chloroplast genome sequences of Lilium: Insights into evolutionary dynamics and phylogenetic analyses. Sci. Rep. 2017, 7, 5751. [Google Scholar] [CrossRef] [PubMed]
  34. Zheng, Y.; Hou, D.; Zhuo, J.; Zheng, R.; Wang, Y.; Li, B.; Lin, X. Complete chloroplast genome sequence of Bambusa rigida (Bambuseae). Mitochondrial DNA B Resour. 2020, 5, 2972–2973. [Google Scholar] [CrossRef] [PubMed]
  35. Goh, W.L.; Chandran, S.; Franklin, D.C.; Isagi, Y.; Koshy, K.C.; Sungkaew, S.; Wong, K.M. Multi-gene Region Phylogenetic Analyses Suggest Reticulate Evolution and a Clade of Australian Origin Among Paleotropical Woody Bamboos (poaceae: Bambusoideae: Bambuseae). Plant Syst. Evol. 2013, 299, 239–257. [Google Scholar] [CrossRef]
  36. Wen, T.H. Some ideas about the origin of bamboos. J. Bamboo Res. 1983, 2, 1–10. [Google Scholar]
  37. Wu, Z.Y. Flora of China; Science Press: Beijing, China, 2013. [Google Scholar]
  38. Hanjiao, G.; Cancan, Z.; Jinsong, W.; Xuewen, S.; Ruixue, X.; Bin, L.; Fusheng, C.; Wensheng, B. Variation in basic morphological and functional traits of Chinese bamboo. Biodivers. Sci. 2019, 27, 10. [Google Scholar] [CrossRef]
  39. Doyle, J. Dna Protocols for Plants. In Molecular Techniques in Taxonomy; Hewitt, G.M., Johnston, A.W.B., Young, J.P.W., Eds.; Springer: Berlin, Germany, 1991; Volume 57, pp. 283–293. [Google Scholar] [CrossRef]
  40. Tillich, M.; Lehwark, P.; Pellizzer, T.; Ulbricht-Jones, E.S.; Fischer, A.; Bock, R.; Greiner, S. GeSeq—Versatile and accurate annotation of organelle genomes. Nucleic Acids Res. 2017, 45, W6–W11. [Google Scholar] [CrossRef]
  41. Shi, L.; Chen, H.; Jiang, M.; Wang, L.; Wu, X.; Huang, L.; Liu, C. CPGAVAS2, an integrated plastome sequence annotator and analyzer. Nucleic Acids Res. 2019, 47, W65–W73. [Google Scholar] [CrossRef]
  42. Greiner, S.; Lehwark, P.; Bock, R. OrganellarGenomeDRAW (OGDRAW) version 1.3.1: Expanded toolkit for the graphical visualization of organellar genomes. Nucleic Acids Res. 2019, 47, W59–W64. [Google Scholar] [CrossRef] [Green Version]
  43. Kurtz, S.; Choudhuri, J.V.; Ohlebusch, E.; Schleiermacher, C.; Stoye, J.; Giegerich, R. REPuter: The manifold applications of repeat analysis on a genomic scale. Nucleic Acids Res. 2001, 29, 4633–4642. [Google Scholar] [CrossRef]
  44. Thiel, T.; Michalek, W.; Varshney, R.K.; Graner, A. Exploiting EST databases for the development and characterization of gene-derived SSR-markers in barley (Hordeum vulgare L.). Theor. Appl. Genet. 2003, 106, 411–422. [Google Scholar] [CrossRef] [PubMed]
  45. Frazer, K.A.; Pachter, L.; Poliakov, A.; Rubin, E.M.; Dubchak, I. VISTA: Computational tools for comparative genomics. Nucleic Acids Res. 2004, 32, W273–W279. [Google Scholar] [CrossRef] [PubMed]
  46. Li, H.; Hughes, A.L.; Bano, N.; McArdle, S.; Livingston, S.; Deubner, H.; Gretch, D.R. Genetic diversity of near genome-wide hepatitis C virus sequences during chronic infection: Evidence for protein structural conservation over time. PLoS ONE 2011, 6, e19562. [Google Scholar] [CrossRef] [PubMed]
  47. Katoh, K.; Rozewicki, J.; Yamada, K.D. MAFFT online service: Multiple sequence alignment, interactive sequence choice and visualization. Brief Bioinform. 2019, 20, 1160–1166. [Google Scholar] [CrossRef] [PubMed]
  48. Kozlov, A.M.; Darriba, D.; Flouri, T.; Morel, B.; Stamatakis, A. RAxML-NG: A fast, scalable and user-friendly tool for maximum likelihood phylogenetic inference. Bioinformatics 2019, 35, 4453–4455. [Google Scholar] [CrossRef] [Green Version]
Genes 13 01519 g001 550
Figure 1. The circle gene map of the D. farinosus cp genome. Genes on the outside and inside the map are transcribed clockwise and counterclockwise, respectively. Genes belonging to different functional groups are color-coded. The darker grey in the inner circle corresponds to GC content. The SSC region, LSC region, and inverted repeats (IRa and IRb) are indicated.
Figure 1. The circle gene map of the D. farinosus cp genome. Genes on the outside and inside the map are transcribed clockwise and counterclockwise, respectively. Genes belonging to different functional groups are color-coded. The darker grey in the inner circle corresponds to GC content. The SSC region, LSC region, and inverted repeats (IRa and IRb) are indicated.
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Genes 13 01519 g002 550
Figure 2. Codon content of 20 amino acids in all protein-coding genes of the D. farinosus cp genome.
Figure 2. Codon content of 20 amino acids in all protein-coding genes of the D. farinosus cp genome.
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Genes 13 01519 g003 550
Figure 3. Sequence alignment of the six cp genomes of Dendrocalamus by mVISTA, using D. farinosus as the reference. The six genomes of Dendrocalamus are D. farinosus, D. fugongensis, D. sinicus, D. membranaceus, D. latiflorus and D. strictus. The horizontal axis indicates the coordinates within the cp genome. Genome regions are color-coded as follows; genes are represented in blue; conserved non-coding sequences are represented in dark pink; forward and backward arrows represent the direction of the gene.
Figure 3. Sequence alignment of the six cp genomes of Dendrocalamus by mVISTA, using D. farinosus as the reference. The six genomes of Dendrocalamus are D. farinosus, D. fugongensis, D. sinicus, D. membranaceus, D. latiflorus and D. strictus. The horizontal axis indicates the coordinates within the cp genome. Genome regions are color-coded as follows; genes are represented in blue; conserved non-coding sequences are represented in dark pink; forward and backward arrows represent the direction of the gene.
Genes 13 01519 g003
Genes 13 01519 g004 550
Figure 4. Sequence alignment of the six cp genomes of Bambusoideae with mVISTA using D. farinosus as a reference. The six genomes of Bambusoideae are D. farinosus, D. bambusoides, Y. brevipaniculata, Ph. edulis, F. edulis and B. flexuosa. The horizontal axis indicates the coordinates within the cp genome. Genome regions are color-coded as follows; genes are represented in blue; conserved non-coding sequences are represented in dark pink; forward and backward arrows represent the direction of the gene.
Figure 4. Sequence alignment of the six cp genomes of Bambusoideae with mVISTA using D. farinosus as a reference. The six genomes of Bambusoideae are D. farinosus, D. bambusoides, Y. brevipaniculata, Ph. edulis, F. edulis and B. flexuosa. The horizontal axis indicates the coordinates within the cp genome. Genome regions are color-coded as follows; genes are represented in blue; conserved non-coding sequences are represented in dark pink; forward and backward arrows represent the direction of the gene.
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Genes 13 01519 g005 550
Figure 5. The nonsynonymous (dN)/synonymous (dS) ratio values of 19 genes from six Bambusoideae cp genomes (D. farinosus, Y. brevipaniculata, Ph. edulis, F. edulis, D. bambusoides and B. flexuosa).
Figure 5. The nonsynonymous (dN)/synonymous (dS) ratio values of 19 genes from six Bambusoideae cp genomes (D. farinosus, Y. brevipaniculata, Ph. edulis, F. edulis, D. bambusoides and B. flexuosa).
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Genes 13 01519 g006 550
Figure 6. Comparison of the borders of the SSC, LSC, IRa and IRb regions among six cp genomes of Bambusoideae. JLB: junction of the LSC and the IRb. JSB: junction of the SSC and the IRb. JSA: junction of the SSC and the IRa. JLA: junction of the LSC and the IRa.
Figure 6. Comparison of the borders of the SSC, LSC, IRa and IRb regions among six cp genomes of Bambusoideae. JLB: junction of the LSC and the IRb. JSB: junction of the SSC and the IRb. JSA: junction of the SSC and the IRa. JLA: junction of the LSC and the IRa.
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Genes 13 01519 g007 550
Figure 7. The maximum-likelihood tree based on the 19 cp genomes of Bambuseae and the distribution of the main geographical provenances in China. (A) The bootstrap value based on 1000 replicates is shown on each node. (B) Distribution of the main geographical provenances of 34 bamboo species in China. Red circle: the distribution of bamboos in high altitude regions; Yellow circle: the distribution of bamboos in the warm temperate zone; Green circle: the distribution of bamboos in the subtropics; Blue circle: the distribution of bamboos in the tropics.
Figure 7. The maximum-likelihood tree based on the 19 cp genomes of Bambuseae and the distribution of the main geographical provenances in China. (A) The bootstrap value based on 1000 replicates is shown on each node. (B) Distribution of the main geographical provenances of 34 bamboo species in China. Red circle: the distribution of bamboos in high altitude regions; Yellow circle: the distribution of bamboos in the warm temperate zone; Green circle: the distribution of bamboos in the subtropics; Blue circle: the distribution of bamboos in the tropics.
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Table
Table 1. Genes present in the cp genome of D. farinosus.
Table 1. Genes present in the cp genome of D. farinosus.
CategoryGroup of GenesName of Genes
Genes for photosynthesisSubunits of ATP synthaseatpA, atpB, atpE, atpF+, atpH, atpI
Subunits of NADH-dehydrogenasendhA +, ndhB +,a, ndhC, ndhD, ndhE, ndhF, ndhG, ndhH, ndhJ, ndhK
Subunits of cytochrome b/f complexpetA, petB +, petD+, petG, petL, petN
Subunits of photosystem IpsaA, psaB, psaC, psaI, psaJ
Subunits of photosystem IIpsbB, psbC, psbD, psbE, psbF, psbH, psbI, psbJ, psbK, psbL, psbM, psbT, psbZ
Subunit of rubiscorbcL
photosystem assembly/stability factorspafI ++, pafII, pbf1
Self replicationLarge subunit of ribosomerpl2+,a, rpl14, rpl16, rpl20, rpl22, rpl23 a, rpl32, rpl33, rpl36
Small subunit of ribosomerps2, rps3, rps4, rps7a, rps8, rps11, rps12++,a, rps12-fragment+, rps14, rps15a, rps16 +, rps18, rps19 a
DNA dependent RNA polymeraserpoA, rpoB, rpoC1+, rpoC2
tRNA GenestrnA-UGC+,a, trnC-GCA, trnD-GUC, trnE-UUC, trnF-GAA, trnfM-CAU, trnG-GCC, trnG-UCC +, trnH-GUGa, trnI-CAUa, trnI-GAU +,a, trnK-UUU +, trnL-CAA a, trnL-UAA +, trnL-UAG, trnM-CAU, trnN-GUU a, trnP-UGG, trnQ-UUG, trnR-ACGa, trnR-UCU, trnS-GCU, trnS-GGA, trnS-UGA, trnT-GGU, trnT-UGU, trnV-GAC a, trnV-UAC+, trnW-CCA, trnY-GUA
rRNA Genesrrn4.5a, rrn5a, rrn16 a, rrn23+,a
Other genesc-type cytochrom synthesis geneccsA
Envelop membrane proteincemA
ProteaseclpP1
Translational initiation factorinfA
MaturasematK
Component of TIC complexycf2, ycf15 a
Subunit acetyl-coA carboxylaseaccD
‘+’—Gene with one intron, ‘++’—gene with two introns and ‘a’—gene with copies.
Table
Table 2. The introns in the genes of the D. farinosus cp genome.
Table 2. The introns in the genes of the D. farinosus cp genome.
S. NoGeneLocationExon I (bp)Intron I (bp)Exon II (bp)Intron II (bp)Exon III (bp)
1rps16LSC36846222
2atpFLSC158837409
3pafILSC132732226724161
4rpl2IR405660432
5ndhBIR777712756
6rps12IR23253736
7ndhASSC5481026541
8trnK-UUULSC38250534
9trnG-UCCLSC2367348
10trnL-UAALSC3553950
11trnV-UACLSC3959637
12trnI-GAUIR4294635
13trnA-UGCIR3881135
Table
Table 3. Distribution of SSRs in the D. farinosus cp genome.
Table 3. Distribution of SSRs in the D. farinosus cp genome.
SSR TypeUnitLengthNumberPosition on Genome (bp)
P1A1047647–7656, 12,227–12,236, 31,304–31,313, 39,008–39,017
A11349,902–49,912, 107,247–107,257, 139,481–139,491
A12245,950–45,961, 46,921–46,932
A131110,286–110,298
T10438,212–38,221, 43,628–43,637, 67,161–67,170, 82,514–82,523
T11234,229–34,239, 79,557–79,567
T12151,765–51,776
P2AT10127,587–27,596
TA10287,344–87,353, 135,177–135,186
TC101117,486–117,495
p3AAT12126,292–26,303
CAG121684–695
TTC12167,459–67,470
P4AAAG12118,988–18,999
AACG121101,658–101,669
AATA121110,503–110,514
ATAC12117,899–17,910
GAAA12165,129–65,140
GTAG16153,971–53,986
TATT12150,161–50,172
TCCT12144,873–44,884
TCGT121120,860–120,871
p5TTTTA15131,515–31,529
C(A)10/(A)1150135,536–35,585
(T)10/(T)1028178,948–78,975
(T)10/(T)103218601–8632
(T)10/(A)13106148,475–48,580
(AGAA)3/(T)1139170,751–70,789
(TTTA)3/(A)1361174,099–74,159
(TCT)4/(T)1195182,955–83,049
(T)10/(AATA)3/(TATT)3143158,342–58,484
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Pei, J.; Wang, Y.; Zhuo, J.; Gao, H.; Vasupalli, N.; Hou, D.; Lin, X. Complete Chloroplast Genome Features of Dendrocalamusfarinosus and Its Comparison and Evolutionary Analysis with Other Bambusoideae Species. Genes 2022, 13, 1519. https://doi.org/10.3390/genes13091519

AMA Style

Pei J, Wang Y, Zhuo J, Gao H, Vasupalli N, Hou D, Lin X. Complete Chloroplast Genome Features of Dendrocalamusfarinosus and Its Comparison and Evolutionary Analysis with Other Bambusoideae Species. Genes. 2022; 13(9):1519. https://doi.org/10.3390/genes13091519

Chicago/Turabian Style

Pei, Jialong, Yong Wang, Juan Zhuo, Huibin Gao, Naresh Vasupalli, Dan Hou, and Xinchun Lin. 2022. "Complete Chloroplast Genome Features of Dendrocalamusfarinosus and Its Comparison and Evolutionary Analysis with Other Bambusoideae Species" Genes 13, no. 9: 1519. https://doi.org/10.3390/genes13091519

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