Skip to main content

Structure and features of the complete chloroplast genome of Melastoma dodecandrum

Abstract

Melastoma dodecandrum, the only creeping species in the Melastoma genus, serves as a medicinal herb in southeast China. It belongs to the huge family Melastomataceae, which contains over 5000 species worldwide. In this study, we used next-generation sequencing to determine the complete chloroplast genome sequences of M. dodecandrum, which is a circular molecule of 156,611 bp in length. After annotation, we identified 131 putative genes in total, comprised of 85 protein-coding genes, 38 transfer RNA genes and 8 ribosomal RNA genes. Genome structure, GC content, repeat sequences and codon usage were investigated to gain a comprehensive understanding of this genome. Furthermore, we conducted comparative genome analyses between the M. dodecandrum genome and that of four other Melastomataceae species. Additionally, a phylogenetic analysis was performed based on available chloroplast genomes of Melastomataceae species and several Myrtaceae species, revealing the taxonomic relationships between M. dodecandrum and related species. In conclusion, our study represents the first look into the complete chloroplast genome of M. dodecandrum, providing abundant information for further studies such as species identification, taxonomy and phylogenetic resolution of Melastomataceae species.

This is a preview of subscription content, access via your institution.

Fig. 1
Fig. 2
Fig. 3
Fig. 4
Fig. 5
Fig. 6

Abbreviations

cp:

Chloroplast

gDNA:

Genomic DNA

IR:

Inverted repeat

LSC:

Large single copy

ML:

Maximum likelihood

NCBI:

National Center for Biotechnology Information

NGS:

Next generation sequencing

NJ:

Neighbor-joining

SSC:

Small single copy

SSR:

Simple sequence repeats

References

  1. Allen JF (2015) Why chloroplasts and mitochondria retain their own genomes and genetic systems: colocation for redox regulation of gene expression. Proc Natl Acad Sci USA 112:10231–10238

    Article  CAS  PubMed  Google Scholar 

  2. Clegg MT, Gaut BS, Learn GH Jr, Morton BR (1994) Rates and patterns of chloroplast DNA evolution. Proc Natl Acad Sci USA 91:6795–6801

    Article  CAS  PubMed  Google Scholar 

  3. Daniell H, Lin CS, Yu M, Chang WJ (2016) Chloroplast genomes: diversity, evolution, and applications in genetic engineering. Genome Biol 17:134. https://doi.org/10.1186/s13059-016-1004-2

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  4. Dyall SD, Brown MT, Johnson PJ (2004) Ancient invasions: from endosymbionts to organelles. Science 304:253–257. https://doi.org/10.1126/science.1094884

    Article  CAS  PubMed  Google Scholar 

  5. Frazer KA, Pachter L, Poliakov A, Rubin EM, Dubchak I (2004) VISTA: computational tools for comparative genomics. Nucleic Acids Res 32:273–279. https://doi.org/10.1093/nar/gkh458

    Article  CAS  Google Scholar 

  6. Green BR (2011) Chloroplast genomes of photosynthetic eukaryotes. Plant J 66:34–44. https://doi.org/10.1111/j.1365-313X.2011.04541.x

    Article  CAS  PubMed  Google Scholar 

  7. Gu C, Tembrock LR, Johnson NG, Simmons MP, Wu Z (2016) The Complete Plastid Genome of Lagerstroemia fauriei and Loss of rpl2 Intron from Lagerstroemia (Lythraceae). PLoS ONE 11:e0150752. https://doi.org/10.1371/journal.pone.0150752

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  8. Hennequin C, Thierry A, Richard GF, Lecointre G, Nguyen HV, Gaillardin C, Dujon B (2001) Microsatellite typing as a new tool for identification of Saccharomyces cerevisiae strains. J Clin Microbiol 39:551–559. https://doi.org/10.1128/JCM.39.2.551-559.2001

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  9. Hoch B, Maier RM, Appel K, Igloi GL, Kossel H (1991) Editing of a chloroplast mRNA by creation of an initiation codon. Nature 353:178–180. https://doi.org/10.1038/353178a0

    Article  CAS  PubMed  Google Scholar 

  10. Huang H, Shi C, Liu Y, Mao SY, Gao LZ (2014) Thirteen Camellia chloroplast genome sequences determined by high-throughput sequencing: genome structure and phylogenetic relationships. BMC Evol Biol 14:151. https://doi.org/10.1186/1471-2148-14-151

    Article  PubMed  PubMed Central  Google Scholar 

  11. Ishii R, Saito K, Horie M, Shibano T, Kitanaka S, Amano F (1999) Inhibitory effects of hydrolyzable tannins from Melastoma dodecandrum Lour. on nitric oxide production by a murine macrophage-like cell line, RAW264.7, activated with lipopolysaccharide and interferon-gamma. Biol Pharm Bull 22:647–653

    Article  CAS  PubMed  Google Scholar 

  12. Jackman SD et al (2016) ABySS 20: resource-efficient assembly of large genomes using a Bloom filter. BioRxiv 27:768–777. https://doi.org/10.1101/068338

    Article  Google Scholar 

  13. Jarvis P, Lopez-Juez E (2013) Biogenesis and homeostasis of chloroplasts and other plastids. Nat Rev Mol Cell Biol 14:787–802. https://doi.org/10.1038/nrm3702

    Article  CAS  PubMed  Google Scholar 

  14. Katoh K, Misawa K, Kuma K, Miyata T (2002) MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform. Nucleic Acids Res 30:3059–3066

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  15. Kim KJ, Lee HL (2004) Complete chloroplast genome sequences from Korean ginseng (Panax schinseng Nees) and comparative analysis of sequence evolution among 17 vascular plants. DNA Res 11:247–261

    Article  CAS  PubMed  Google Scholar 

  16. Kumar S, Stecher G, Tamura K (2016) MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets. Mol Biol Evol 33:1870–1874. https://doi.org/10.1093/molbev/msw054

    Article  CAS  Google Scholar 

  17. Kuroda H, Suzuki H, Kusumegi T, Kusumegi T, Hirose T, Hirose T, Yukawa Y, Yukawa Y, Sugiura M (2007) Translation of psbC mRNAs starts from the downstream GUG, not the upstream AUG, and requires the extended Shine-Dalgarno sequence in tobacco chloroplasts. Plant Cell Physiol 48:1374–1378

    Article  CAS  PubMed  Google Scholar 

  18. Kurtz S, Choudhuri JV, Ohlebusch E, Schleiermacher C, Stoye J, Giegerich R (2001) REPuter: the manifold applications of repeat analysis on a genomic scale. Nucleic Acids Res 29:4633–4642

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  19. Liu T, Dai S, Wu W, Zhang R, Fan Q, Shi S, Zhou R (2013) Development and characterization of microsatellite markers for Melastoma dodecandrum (Melastomataceae). Appl Plant Sci. https://doi.org/10.3732/apps.1200294

    Article  PubMed  PubMed Central  Google Scholar 

  20. Liu Y, Nielsen M, Staerk D, Jager AK (2014) High-resolution bacterial growth inhibition profiling combined with HPLC-HRMS-SPE-NMR for identification of antibacterial constituents in Chinese plants used to treat snakebites. J Ethnopharmacol 155:1276–1283. https://doi.org/10.1016/j.jep.2014.07.019

    Article  CAS  PubMed  Google Scholar 

  21. Lohse M, Drechsel O, Kahlau S, Bock R (2013) OrganellarGenomeDRAW—a suite of tools for generating physical maps of plastid and mitochondrial genomes and visualizing expression data sets. Nucleic Acids Res 41:575–581. https://doi.org/10.1093/nar/gkt289

    Article  Google Scholar 

  22. Moore MJ, Dhingra A, Soltis PS, Shaw R, Farmerie WG, Folta KM, Soltis DE (2006) Rapid and accurate pyrosequencing of angiosperm plastid genomes. BMC Plant Biol 6:17. https://doi.org/10.1186/1471-2229-6-17

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  23. Morton BR (1998) Selection on the codon bias of chloroplast and cyanelle genes in different plant and algal lineages. J Mol Evol 46:449–459

    Article  CAS  PubMed  Google Scholar 

  24. Mower JP (2009) The PREP suite: predictive RNA editors for plant mitochondrial genes, chloroplast genes and user-defined alignments. Nucleic Acids Res 37:253–259. https://doi.org/10.1093/nar/gkp337

    Article  CAS  Google Scholar 

  25. Ng WL, Cai Y, Wu W, Zhou R (2018) The complete chloroplast genome sequence of Melastoma candidum (Melastomataceae). Mitochondrial DNA Part B 2:242–243. https://doi.org/10.1080/23802359.2017.1318680

    Article  Google Scholar 

  26. Nikiforova SV, Cavalieri D, Velasco R, Goremykin V (2013) Phylogenetic analysis of 47 chloroplast genomes clarifies the contribution of wild species to the domesticated apple maternal line. Mol Biol Evol 30:1751–1760. https://doi.org/10.1093/molbev/mst092

    Article  CAS  PubMed  Google Scholar 

  27. Ravi V, Khurana JP, Tyagi AK, Khurana P (2008) An update on chloroplast genomes. Plant Syst Evol 271:101–122. https://doi.org/10.1007/s00606-007-0608-0

    Article  CAS  Google Scholar 

  28. Reginato M, Neubig KM, Majure LC, Michelangeli FA (2016) The first complete plastid genomes of Melastomataceae are highly structurally conserved. Peer J 4:e2715. https://doi.org/10.7717/peerj.2715

    Article  CAS  PubMed  Google Scholar 

  29. Renner SS, Meyer K (2001) Melastomeae come full circle: biogeographic reconstruction and molecular clock dating. Evolution 55:1315–1324

    Article  CAS  PubMed  Google Scholar 

  30. Scharff LB, Bock R (2014) Synthetic biology in plastids. Plant J 78:783–798. https://doi.org/10.1111/tpj.12356

    Article  CAS  PubMed  Google Scholar 

  31. Sciences EboCfotCAo (1984) Flora of China, vol 53. Science Press, Beijing

    Google Scholar 

  32. Shen X et al (2017) Complete chloroplast genome sequence and phylogenetic analysis of the medicinal plant Artemisia annua. Molecules 22:1330. https://doi.org/10.3390/molecules22081330

    Article  CAS  PubMed Central  Google Scholar 

  33. Shi C, Liu Y, Huang H, Xia E-H, Zhang H-B, Gao L-Z (2013) Contradiction between plastid gene transcription and function due to complex posttranscriptional splicing: an exemplary study of ycf15 function and evolution in angiosperms. PLoS ONE 8:e59620. https://doi.org/10.1371/journal.pone.0059620

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  34. Smith DR, Keeling PJ (2015) Mitochondrial and plastid genome architecture: reoccurring themes, but significant differences at the extremes. Proc Natl Acad Sci USA 112:10177–101184. https://doi.org/10.1073/pnas.1422049112

    Article  CAS  PubMed  Google Scholar 

  35. Tillich M, Lehwark P, Pellizzer T, Ulbricht-Jones ES, Fischer A, Bock R, Greiner S (2017) GeSeq—versatile and accurate annotation of organelle genomes. Nucleic Acids Res 45:6–11. https://doi.org/10.1093/nar/gkx391

    Article  CAS  Google Scholar 

  36. Wang RJ, Cheng CL, Chang CC, Wu CL, Su TM, Chaw SM (2008) Dynamics and evolution of the inverted repeat-large single copy junctions in the chloroplast genomes of monocots. BMC Evol Biol 8:36. https://doi.org/10.1186/1471-2148-8-36

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  37. Wicke S, Schneeweiss GM, dePamphilis CW, Muller KF, Quandt D (2011) The evolution of the plastid chromosome in land plants: gene content, gene order, gene function. Plant Mol Biol 76:273–297. https://doi.org/10.1007/s11103-011-9762-4

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  38. Wu FH et al (2010) Complete chloroplast genome of Oncidium Gower Ramsey and evaluation of molecular markers for identification and breeding in Oncidiinae. BMC Plant Biol 10:68. https://doi.org/10.1186/1471-2229-10-68

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  39. Yang M et al (2010) The complete chloroplast genome sequence of date palm (Phoenix dactylifera L). PLoS ONE 5:e12762. https://doi.org/10.1371/journal.pone.0012762

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  40. Yang GX, Zhang RZ, Lou B, Cheng KJ, Xiong J, Hu JF (2014) Chemical constituents from Melastoma dodecandrum and their inhibitory activity on interleukin-8 production in HT-29 cells. Nat Prod Res 28:1383–1387. https://doi.org/10.1080/14786419.2014.903480

    Article  CAS  PubMed  Google Scholar 

  41. Zhao Y et al (2015) The complete chloroplast genome provides insight into the evolution and polymorphism of Panax ginseng. Front Plant Sci 5:696

    PubMed  PubMed Central  Google Scholar 

  42. Zou P et al (2017) Similar morphologies but different origins: hybrid status of two more semi-creeping taxa of Melastoma. Front Plant Sci 8:673. https://doi.org/10.3389/fpls.2017.00673

    Article  PubMed  PubMed Central  Google Scholar 

Download references

Author information

Affiliations

Authors

Corresponding authors

Correspondence to Jing Li or Ying Zhao.

Additional information

Publisher's Note

Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Electronic supplementary material

Rights and permissions

Reprints and Permissions

About this article

Verify currency and authenticity via CrossMark

Cite this article

Zheng, X., Ren, C., Huang, S. et al. Structure and features of the complete chloroplast genome of Melastoma dodecandrum. Physiol Mol Biol Plants 25, 1043–1054 (2019). https://doi.org/10.1007/s12298-019-00651-x

Download citation

Keywords

  • Chloroplast genome
  • Melastoma dodecandrum
  • Melastomataceae
  • Phylogenetic analysis
  • Next-generation sequencing