Hostname: page-component-848d4c4894-tn8tq Total loading time: 0 Render date: 2024-06-28T09:28:16.333Z Has data issue: false hasContentIssue false
  • English
  • Français

Characterization of the complete chloroplast genome of Vitex bicolor Willd. and its comparative analyses with other species belonging to the Vitex trifolia complex

Published online by Cambridge University Press:  29 June 2023

Renerio P. Gentallan Jr. Open the ORCID record for Renerio P. Gentallan Jr. [Opens in a new window] ,
Kristine Joyce O. Quiñones ,
Michael Cedric B. Bartolome ,
Roselle E. Madayag ,
Nestor C. Altoveros ,
Leah E. Endonela ,
Antonio G. Lalusin ,
Melquiades Emmanuel C. Reyes ,
Eureka Teresa M. Ocampo  and
Emmanuel Bonifacio S. Timog
...Show all authors
Renerio P. Gentallan Jr.*
Affiliation:
Institute of Crop Science, College of Agriculture and Food Science, University of the Philippines Los Baños, College, Laguna, Philippines
Kristine Joyce O. Quiñones
Affiliation:
Institute of Crop Science, College of Agriculture and Food Science, University of the Philippines Los Baños, College, Laguna, Philippines Department of Science and Technology, Science Education Institute, Taguig, Manila, Philippines
Michael Cedric B. Bartolome
Affiliation:
Institute of Crop Science, College of Agriculture and Food Science, University of the Philippines Los Baños, College, Laguna, Philippines
Roselle E. Madayag
Affiliation:
Institute of Crop Science, College of Agriculture and Food Science, University of the Philippines Los Baños, College, Laguna, Philippines
Nestor C. Altoveros
Affiliation:
Institute of Crop Science, College of Agriculture and Food Science, University of the Philippines Los Baños, College, Laguna, Philippines
Leah E. Endonela
Affiliation:
Institute of Crop Science, College of Agriculture and Food Science, University of the Philippines Los Baños, College, Laguna, Philippines
Antonio G. Lalusin
Affiliation:
Institute of Crop Science, College of Agriculture and Food Science, University of the Philippines Los Baños, College, Laguna, Philippines
Melquiades Emmanuel C. Reyes
Affiliation:
Institute of Crop Science, College of Agriculture and Food Science, University of the Philippines Los Baños, College, Laguna, Philippines
Eureka Teresa M. Ocampo
Affiliation:
Institute of Crop Science, College of Agriculture and Food Science, University of the Philippines Los Baños, College, Laguna, Philippines
Emmanuel Bonifacio S. Timog
Affiliation:
Institute of Crop Science, College of Agriculture and Food Science, University of the Philippines Los Baños, College, Laguna, Philippines Department of Forest Biological Sciences, College of Forestry and Natural Resources, University of the Philippines Los Baños, College, Laguna, Philippines
Teresita H. Borromeo
Affiliation:
Institute of Crop Science, College of Agriculture and Food Science, University of the Philippines Los Baños, College, Laguna, Philippines
*
Corresponding author: Renerio P. Gentallan Jr.; Email: rpgentallan@up.edu.ph
Get access Rights & Permissions [Opens in a new window]

Abstract

V. bicolor, V. trifolia s. str. and V. rotundifolia are part of a species complex that has recorded medicinal use in the Philippines. We assembled the first chloroplast genome of V. bicolor through next-generation sequencing and compared this to earlier established chloroplast genomes of V. trifolia s. str. and V. rotundifolia to provide additional insights into their genotypic differences. To ensure the continued utility of the research outputs in case of future taxonomic revisions, we characterized the morphology of PBN 2018-674, the reference germplasm utilized to generate the plastome. The complete chloroplast genome sequence of V. bicolor was 154,460 bp long with 131 coding genes comprising 87 mRNA genes, 36 tRNA genes and 8 rRNA genes. Using a separate accession from a different type locality, an identical chloroplast genome was equally established, indicating its conserved nature. When compared to V. trifolia s. str. and V. rotundifolia, slight variations were observed in genome features between these species; however, single nucleotide polymorphisms were exhibited in 13 protein-coding genes that often have a conserved nature. A phylogenetic analysis of the assembled genome, together with 12 other Lamiaceae species, exhibited high bootstrap support (>88%) within the species complex, and associated V. trifolia as the closest relative of V. bicolor. The identified variations in the plastomes can be utilized as markers that could distinguish the three closely related genotypes which can help the Philippine herbal industry provide a more stable source of quality herbal medicines.

Keywords

DNA barcodesmedicinal plantspecies complexVerbenaceaeViticoideae
Type
Research Article
Information
Plant Genetic Resources , Volume 21 , Issue 1 , February 2023 , pp. 19 - 27
Copyright
Copyright © The Author(s), 2023. Published by Cambridge University Press on behalf of National Institute of Agricultural Botany

Access options

Get access to the full version of this content by using one of the access options below. (Log in options will check for institutional or personal access. Content may require purchase if you do not have access.)

References

Amar, MH (2020) ycf1-ndhF genes, the most promising plastid genomic barcode, sheds light on phylogeny at low taxonomic levels in Prunus persica. Journal of Genetic Engineering and Biotechnology 18, 1–10.CrossRefGoogle ScholarPubMed
Amiryousefi, A, Hyvönen, J and Poczai, P (2018) IRscope: an online program to visualize the junction sites of chloroplast genomes. Bioinformatics (Oxford, England) 34, 3030–3031.Google ScholarPubMed
Beier, S, Thiel, T, Münch, T, Scholz, U and Mascher, M (2017) MISA-web: a web server for microsatellite prediction. Bioinformatics (Oxford, England) 33, 2583–2585.Google ScholarPubMed
Bramley, GL, Forest, F and de Kok, RP (2009) Troublesome tropical mints: re-examining generic limits of Vitex and relations (Lamiaceae) in South East Asia. Taxon 58, 500–510.CrossRefGoogle Scholar
Capareda, EP (2016) Vitex trifolia (PROSEA). (2016, March 11). PlantUse English. Retrieved 16:10, August 17, 2022 from https://uses.plantnet-project.org/e/index.php?title=Vitex_trifolia_(PROSEA)&oldid=215416.Google Scholar
Christin, PA, Salamin, N, Muasya, AM, Roalson, EH, Russier, F and Besnard, G (2008) Evolutionary switch and genetic convergence on rbcL following the evolution of C4 photosynthesis. Molecular Biology and Evolution 25, 2361–2368.CrossRefGoogle ScholarPubMed
de Kok, RP (2007) The genus Vitex L. (Lamiaceae) in New Guinea and the South Pacific Islands. Kew Bulletin 62, 587–603.Google Scholar
de Kok, R (2008) The genus Vitex (Labiatae) in the flora Malesiana region, excluding New Guinea. Kew Bulletin 63, 17–40.CrossRefGoogle Scholar
de Kok, RP and Sengun, S (2020) Vitex. In Bramley, GLC (ed.), Flora Malesiana Series I, Volume 23 (Lamiaceae). Singapore: Singapore Botanic Gardens, pp. 397–421.Google Scholar
Doyle, J and Doyle, JL (1987) A rapid DNA isolation procedure for small quantities of fresh leaf tissue. Phytochemical Bulletin 19, 11–15.Google Scholar
Ebert, D and Peakall, ROD (2009) Chloroplast simple sequence repeats (cpSSRs): technical resources and recommendations for expanding cpSSR discovery and applications to a wide array of plant species. Molecular Ecology Resources 9, 673–690.CrossRefGoogle Scholar
Frazer, KA, Pachter, L, Poliakov, A, Rubin, EM and Dubchak, I (2004) VISTA: computational tools for comparative genomics. Nucleic Acids Research 32, 273–279.CrossRefGoogle ScholarPubMed
Giang, VNL, Waminal, NE, Park, HS, Kim, NH, Jang, W, Lee, J and Yang, TJ (2020) Comprehensive comparative analysis of chloroplast genomes from seven Panax species and development of an authentication system based on species-unique single nucleotide polymorphism markers. Journal Ginseng Research 44, 135–144.Google Scholar
Greiner, S, Lehwark, P and Bock, R (2019) OrganellarGenomeDRAW (OGDRAW) version 1.3. 1: an expanded toolkit for the graphical visualization of organellar genomes. Nucleic Acids Research 47, 59–64.CrossRefGoogle Scholar
Hipolito, ACP (2012) Philippines towards a Science-Based Herbal Industry: Initiatives, Challenges, Solutions. DOST-PCHRD. Retrieved last October 18, 2022 from Available at http://pchrd.dost.gov.ph/index.php/events/2799-philippines-towards-a-science-based-herbal-industry-initiatives-challenges-solutions.Google Scholar
Jin, JJ, Yu, WB, Yang, JB, Song, Y, DePamphilis, CW, Yi, TS and Li, DZ (2020) GetOrganelle: a fast and versatile toolkit for accurate de novo assembly of organelle genomes. Genome Biology 21, 1–31.CrossRefGoogle ScholarPubMed
Katoh, K and Standley, DM (2013) MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Molecular Biology and Evolution 30, 772–780.CrossRefGoogle ScholarPubMed
Kim, K, Lee, SC, Lee, J, Lee, HO, Joh, HJ, Kim, NH and Yang, TJ (2015) Comprehensive survey of genetic diversity in chloroplast genomes and 45S nrDNAs within Panax ginseng species. PLoS One 10, e0117159.CrossRefGoogle ScholarPubMed
Kumar, S, Stecher, G, Li, M, Knyaz, C and Tamura, K (2018) MEGA X: molecular evolutionary genetics analysis across computing platforms. Molecular Biology and Evolution 35, 1547.CrossRefGoogle ScholarPubMed
Kurtz, S, Choudhuri, JV, Ohlebusch, E, Schleiermacher, C, Stoye, J and Giegerich, R (2001) REPuter: the manifold applications of repeat analysis on a genomic scale. Nucleic Acids Research 29, 4633–4642.CrossRefGoogle ScholarPubMed
Lam, HJ (1919) The Verbenaceæ of the Malayan Archipelago: Together with Those from the Malayan Peninsula, the Philippines, the Bismark-archipelago, and the Palau-, Marianne-and Caroline-islands… Groningen: M. de Waal.CrossRefGoogle Scholar
Li, B, Cantino, PD, Olmstead, RG, Bramley, GL, Xiang, CL, Ma, ZH, Tan, Y and Zhang, DX (2016) A large-scale chloroplast phylogeny of the Lamiaceae sheds new light on its subfamilial classification. Scientific Reports 6, 1–18.Google ScholarPubMed
Li, S, Duan, W, Zhao, J, Jing, Y, Feng, M, Kuang, B and Yang, X (2022) Comparative analysis of chloroplast genome in saccharum spp. and related members of ‘saccharum complex’. Internal Journal of Molecular Science 23, 7661.CrossRefGoogle ScholarPubMed
Linh, NN, Hang, PLB, Hue, HTT, Ha, NH, Hanh, HH and Ton, ND (2022) Species discrimination of novel chloroplast DNA barcodes and their application for identification of Panax (Aralioideae, Araliaceae). PhytoKeys 188, 1.CrossRefGoogle ScholarPubMed
Meena, AK, Niranjan, US, Rao, MM, Padhi, MM and Babu, R (2011) A review of the important chemical constituents and medicinal uses of Vitex genus. Asian Journal of Traditional Medicine 6, 54–60.Google Scholar
Moldenke, HN (1957) Wurdackia gen. nov. Botany of the Chimantá Massif. I. Gran Sabana, Venezuela. Annals of the Missouri Botanical Garden 9, 278–283.Google Scholar
Nei, M and Kumar, S (2000) Molecular Evolutionary Phylogenetics. New York, USA: Oxford University Press.CrossRefGoogle Scholar
Palmer, JD, Jansen, RK, Michaels, HJ, Chase, MW and Manhart, JR (1988) Chloroplast DNA variation and plant phylogeny. Annals of the Missouri Botanical Garden 1, 1180–1206.CrossRefGoogle Scholar
Pang, X, Liu, C, Shi, L, Liu, R, Liang, D, Cherny, SS and Li, H (2012) Utility of the trnH–psbA intergenic spacer region and its combinations as plant DNA barcodes: a meta-analysis. PLoS One 7, 48833.CrossRefGoogle ScholarPubMed
Park, YS, Park, JY, Kang, JH, Lee, WH and Yang, TJ (2021) Diversity and authentication of Rubus accessions revealed by complete plastid genome and rDNA sequences. Mitochondrial DNA Part B 6, 1454–1459.CrossRefGoogle ScholarPubMed
Philippine Pharmacopeia 1 [PPI] (2004) Philippine Pharmacopeia, 1. Bureau of Food and Drugs, Department of Health and Japan International Cooperation Agency. Manila: Himiko Arts and Concepts.Google Scholar
POWO (2022) Plants of the World Online. Facilitated by the Royal Botanic Gardens, Kew. Published on the Internet; http://www.plantsoftheworldonline.org/ Retrieved 25 February 2022.Google Scholar
Roy, S, Tyagi, A, Shukla, V, Kumar, A, Singh, UM, Chaudhary, LB, Datt, B, Bag, SK, Singh, PK, Nair, NK and Husain, T (2010) Universal plant DNA barcode loci may not work in complex groups: a case study with Indian Berberis species. PLoS One 5, 13674.CrossRefGoogle Scholar
Rozas, J, Ferrer-Mata, A, Sánchez-DelBarrio, JC, Guirao-Rico, S, Librado, P, Ramos-Onsins, SE and Sánchez-Gracia, A (2017) DnaSP 6: DNA sequence polymorphism analysis of large data sets. Molecular Biology and Evolution 34, 3299–3302.CrossRefGoogle ScholarPubMed
Santos, C and Pereira, F (2018) Identification of plant species using variable length chloroplast DNA sequences. Forensic Science International: Genetics 36, 1–12.CrossRefGoogle ScholarPubMed
Sen, L, Fares, MA, Liang, B, Gao, L, Wang, B, Wang, T and Su, YJ (2011) Molecular evolution of rbcL in three gymnosperm families: identifying adaptive and coevolutionary patterns. Biology Direct 6, 1–19.CrossRefGoogle ScholarPubMed
Shi, L, Chen, H, Jiang, M, Wang, L, Wu, X, Huang, L and Liu, C (2019) CPGAVAS2, an integrated plastome sequence annotator and analyzer. Nucleic Acids Research 47, 65–73.CrossRefGoogle ScholarPubMed
Song, Y, Zhao, W, Xu, J, Li, M and Zhang, Y (2022) Chloroplast genome evolution and species identification of Styrax (Styracaceae). BioMed Research International 2022, 5364094.CrossRefGoogle ScholarPubMed
Suzuki, JY, Matsumoto, TK, Keith, LM and Myers, RY (2014) The chloroplast psbK-psbI intergenic region, a potential genetic marker for broad sectional relationships in Anthurium. Hortscience 49, 1244–1252.CrossRefGoogle Scholar
Tillich, M, Lehwark, P, Pellizzer, T, Ulbricht-Jones, ES, Fischer, A, Bock, R and Greiner, S (2017) GeSeq–versatile and accurate annotation of organelle genomes. Nucleic Acids Research 45, 6–11.CrossRefGoogle ScholarPubMed
Wheeler, GL, Dorman, HE, Buchanan, A, Challagundla, L and Wallace, LE (2014) A review of the prevalence, utility, and caveats of using chloroplast simple sequence repeats for studies of plant biology. Applications in Plant Science 2, 1400059.CrossRefGoogle ScholarPubMed
Willdenow, KL (1809) Enumeratio Plantarum Horti Regii Botanici Berolinensis, Vol. 1. Berolini: In Taberna Libraria Scholae Realis.Google Scholar
Xu, J, Shen, X, Liao, B, Xu, J and Hou, D (2020) Comparing and phylogenetic analysis chloroplast genome of three Achyranthes species. Scientific Reports 10, 1–13.CrossRefGoogle ScholarPubMed
Zarsuelo, MAM, Zordilla, ZD and Anacio, DB (2018) Review of regulatory policies on and benefits of herbal medicine in the Philippines. Acta Medica Philippina 52, 473–479.CrossRefGoogle Scholar
Zhang, Z, Zhang, Y, Song, M, Guan, Y and Ma, X (2019) Species identification of Dracaena using the complete chloroplast genome as a super-barcode. Frontiers in Pharmacology 10, 1441.CrossRefGoogle ScholarPubMed
Zhao, F, Chen, YP, Salmaki, Y, Drew, BT, Wilson, TC, Scheen, AC, Celep, F, Bräuchler, C, Bendiksby, M, Wang, Q and Min, DZ (2021) An updated tribal classification of Lamiaceae based on plastome phylogenomics. BMC Biology 19, 1–27.CrossRefGoogle ScholarPubMed
Supplementary material: File

Gentallan et al. supplementary material
Download undefined(File)
File 45 KB