New distribution record and DNA barcoding of the steno-endemic plant Cordia diffusa (Boraginaceae)

Authors

  • M. Haritha Department of Botany, Avinashilingam Institute of Home Science and Higher Education for Women, Coimbatore, Tamil Nadu 641043, India. https://orcid.org/0000-0003-3367-8355
  • D. Leena Lavanya Department of Botany, Avinashilingam Institute of Home Science and Higher Education for Women, Coimbatore, Tamil Nadu 641043, India.
  • H. Abinaya Department of Botany, Avinashilingam Institute of Home Science and Higher Education for Women, Coimbatore, Tamil Nadu 641043, India.

DOI:

https://doi.org/10.11609/jott.9486.17.2.26547-26552

Keywords:

Boraginaceae, Endangered species, Kurumbapalayam, matk, chloroplast markers, psbA-tnH, rbcL, species identification

Abstract

The research marks the first documented occurrence of Cordia diffusa in Kurumbapalayam, a location where it had not been reported previously. In this study, genomic markers were also utilized to document the endemic plant species Cordia diffusa K.C.Jacob of the Boraginaceae family. This study employed chloroplast markers such as matK, rbcL, and the psbA-tnH region to determine their efficiency in identifying the species. For the first time, C. diffusa has been analyzed and documented using these genetic markers. Sequences obtained from three different primer sets for each marker were submitted to GenBank. This research highlights the first genetic documentation and identification of C. diffusa using chloroplast markers, contributing valuable genetic data to GenBank and advancing the understanding of this endangered species distribution.

Author Biographies

M. Haritha, Department of Botany, Avinashilingam Institute of Home Science and Higher Education for Women, Coimbatore, Tamil Nadu 641043, India.

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D. Leena Lavanya, Department of Botany, Avinashilingam Institute of Home Science and Higher Education for Women, Coimbatore, Tamil Nadu 641043, India.

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H. Abinaya, Department of Botany, Avinashilingam Institute of Home Science and Higher Education for Women, Coimbatore, Tamil Nadu 641043, India.

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References

Arumugam, S., K.S. Kumar, B. Karthik & V. Ravichandran (2019). Cordia diffusa K.C. Jacob, the Kovai Manjack (Boraginaceae): a highly threatened steno-endemic species from Coimbatore City, Tamil Nadu, India. Journal of Threatened Taxa 11(14): 14870–14875. https://doi.org/10.11609/jott.5292.11.14.14870-14875

Mehmood, F., I. Shahzadi, S. Waseem, B. Mirza, I. Ahmed & M.T. Waheed (2020). Chloroplast genome of Hibiscus rosa-sinensis (Malvaceae): Comparative analyses and identification of mutational hotspots. Genomics 112(1): 581–591. https://doi.org/10.1016/j.ygeno.2019.04.010

Altschul, S., T.L. Madden, A.A. Schäffer, J. Zhang, Z. Zhang, W. Miller & D.J. Lipman (1997). Gapped BLAST and PSI-BLAST: A new generation of protein database search programs. Nucleic Acids Research 25(17): 3389–3402. https://doi.org/10.1093/nar/25.17.3389

Amiryousefi, A., J. Hyvonen & P. Poczai (2018). The chloroplast genome sequence of bittersweet (Solanum dulcamara): Plastid genome structure evolution in Solanaceae. PLoS One 13(4): e0196069. https://doi.org/10.1371/journal.pone.0196069

Aubriot, X., P.P. Lowry, C. Cruaud, A. Couloux & T. Haevermans (2013). DNA barcoding in a biodiversity hot spot: potential value for the identification of Malagasy Euphorbia L. listed in CITES Appendices I and II. Molecular Ecology Resources 13(1): 57–65. https://doi.org/10.1111/1755-0998.12028 PMID: 23095939 17

Bentham, G. & J.D. Hooker (1876). Genera Plantarum, Vol. 1. Reeve, London, 57–102.

CBOL Plant Working Group, P.M. Hollingsworth, L.L. Forrest, J.L. Spouge, M. Hajibabaei, S. Ratnasingham, M. Van der Bank, M. Chase, W. Cowan, R.S. Erickson, D.L. Fazekas, A.J. Graham, S.W. James, K.E. Kim, K.J. Kress, W.J. Schneider, H. van AlphenStahl, J. Barrett, S.C.H. van den Berg & C. Little (2009). A DNA barcode for land plants. Proceeding of the National Academy of Science 106(31): 12794–12797. https://doi. org/10.1073/pnas.0905845106

Chandrabose, M. (1968). A New Species of Polygala from South India. Bulletin of the Botanical Survey of India 9(1–4): 288–290.

Chandrabose., M. & N.C. Nair (1988). Flora of Coimbatore. Bishen Singh Mahendra Pal Singh, Dehra Dun, 398 pp.

Chevenet, F., C. Brun, A.L. Bañuls, B. Jacq & R. Christen (2006). TreeDyn: Towards dynamic graphics and annotations for analyses of trees. BMC Bioinformatics 7: 439. https://doi.org/10.1186/1471-2105-7-439

China Plant BOL Group; D.Z. Li, L.M. Gao, H.T. Li, H. Wang, X.J. Ge, J.Q. Liu, Z.D. Chen, S.L. Zhou, S.L. Chen, J.B. Yang, C.X. Fu, C.X. Zeng, H.F. Yan, Y.J. Zhu, Y.S. Sun, S.Y. Chen, L. Zhao, K. Wang, T. Yang & G.W. Duan (2011). Comparative analysis of a large dataset indicates that internal transcribed spacer (ITS) should be incorporated into the core barcode for seed plants. Proceeding of the National Academy of Science 108(49): 19641–19646. https://doi.org/10.1073/pnas. 1104551108 PMID: 2210073

Daniel, P. & P. Umamaheshwari (2001). Flora of Gulf of Mannar Southern India. Botanical Survey of India, Calcutta, 688 pp.

De Candolle, A.P. (1845). Prodromus Systematis Naturalis Regni Vegetabilis, Vol. 9. Paris, 573 pp. https://doi.org/10.5962/bhl.title.286

Ebach, M.C. & C. Holrege (2005). DNA barcoding is no substitute for taxonomy. Nature 434(7034): 697–697. https://doi.org/10.1038/434697b

Engler, A. (1898). Syllabus der Pflanzenfamilien, second edition. Berlin: Gebrüder Borntraeger. https://archive.org/details/syllabusderpfla00eng

Hebert, P.D., S. Ratnasingham & J.R. De Waard (2003). Barcoding animal life: cytochrome c oxidase subunit 1 divergences among closely related species. Proceedings of the Royal Society of London. Series B: Biological Sciences 270: S96–S99. https://doi.org/10.1098/rsbl.2003.0025

Henry, A.N., K. Vivekananthan & N.C. Nair (1978). Rare and threatened flowering plants of South India. Journal of the Bombay Natural History Society 75(3): 684–697.

Hollingsworth, M.L., A. Clark, L.L. Forrest, J. Richardson, R.T. Pennington, D.G. Long & P.M. Hollingsworth (2009). Selecting barcoding loci for plants: evaluation of seven candidate loci with species‐level sampling in three divergent groups of land plants. Molecular Ecology Resources 9(2): 439–457. https://doi.org/10.1111/j.1755-0998.2008.02439.x

Hu, H.S., J.Y. Mao, X. Wang, Y. Liang, B. Jiang & D.Q. Zhang (2023). Plastid phylogenomics and species discrimination in the “Chinese” clade of Roscoea (Zingiberaceae). Plant Diversity 45: 523–534. https://doi.org/10.1016/j.pld.2023.03.012

Kress, W.J. & D.L. Erickson (2007). A two-locus global DNA barcode for land plants: the coding rbcL gene complements the non-coding trnH-psbA spacer region. PLOS one 2(6): e508. https://doi.org/10.1371/journal.pone.0000508

Kress, W.J., K.J. Wurdack, E.A. Zimmer, L.A. Weigt & D.H. Janzen (2005). Use of DNA barcodes to identify flowering plants. Proceedings of the National Academy of Sciences 102(23): 8369–8374. https://doi.org/10.1073/pnas.0503123102

Li, H.Q., J.Y. Chen, S. Wang & S.Z. Xiong (2012). Evaluation of six candidate DNA barcoding loci in Ficus (Moraceae) of China. Molecular Ecology Resources 12(5): 783–790. https://doi.org/10.1111/j.1755-0998.2012.03147.x

Luebert, F., L. Cecchi, M.W. Frohlich, M. Gottschling, C.M. Guilliams, K.E. Hasenstab-Lehman, H.H. Hilger, J.S. Miller, M. Mittelbach, M. Nazaire, M. Nepi, D. Nocentini, D. Ober, R.G. Olmstead, F. Selvi, M.G. Simpson, K. Sutory, B. Valdes, G.K. Walden & M. Weigend (2016). Familial classification of the Boraginales. Taxon 65(3): 502–522. https://doi.org/10.12705/653.5

Lv, S.Y., X.Y. Ye, Z.H. Li, P.F. Ma & D.Z. Li (2022). Testing complete plastomes and nuclear ribosomal DNA sequences for species identification in a taxonomically difficult bamboo genus. Fargesia. Plant Diversity 45: 147–155. https://doi.org/10.1016/j.pld.2022.04.002

Nayar, M.P. (1996). Hotspots of Endemic Plants of India, Nepal, and Bhutan. Tropical Botanic Garden and Research Institute, Thiruvananthapuram, 254 pp.

Pang, X., C. Liu, L. Shi, R. Liu, D. Liang, H. Li, S.S. Cherny & S. Chen (2012). Utility of the trnH–psbA intergenic spacer region and its combinations as plant DNA barcodes: a meta-analysis. PLOS One 7(11): e48833. https://doi. org/10.1371/journal.pone.0048833

Parveen, I., H.K. Singh, S. Raghuvanshi, U.C. Pradhan & S.B. Babbar (2012). DNA barcoding of endangered Indian Paphiopedilum species. Molecular Ecology Resources 12(1): 82–90. https://doi.org/10.1111/j.1755-0998

Pilger, R. & K. Krause (1915). Die Natürlichen Pflanzenfamilien, Ergänzungsheft 3. Leipzig: W. Engelmann.

Prabu, K., A. Rajasekaran, D. Bharathi & S. Ramalakshmi (2019). Anti-oxidant activity, phytochemical screening and HPLC profile of rare endemic Cordia diffusa. Journal of King Saud University - Science 31(4): 724–727. https://doi.org/10.1016/j.jksus.2018.04.025

Quattrocchi, U. (2012). CRC World Dictionary of Medicinal and Poisonous Plants: Common Names, Scientific Names, Eponyms, Synonyms, and Etymology. CRC Press. https://doi.org/10.1201/b16504

Ramamurthy, K. (1987). Boraginaceae. Flora of Tamil Nadu, India, 97 pp.

Rao, C.K., B.L. Geetha & S. Geetha (2003). Red list of threatened vascular plant species in India. Botanical Survey of India, Kolkata.

Saarela, J.M., P.C. Sokoloff, L.J. Gillespie, L.L. Consaul & R.D. Bull (2013). DNA barcoding the Canadian Arctic flora: core plastid barcodes (rbcL + matK) for 490 vascular plant species. PLOS One 8(10): e77982. https://doi.org/10.1371/journal.pone.0077982

Savolainen, V., R.S. Cowan, A.P. Vogler, G.K. Roderick & R. Lane (2005). Towards writing the encyclopedia of life: an introduction to DNA barcoding. Philosophical Transactions of the Royal Society B 360: 1805–1811. https://doi.org/10.1098/rstb.2005.1730

Shaw, J., E.B. Lickey, E.E. Schilling & R.L. Small (2007). Comparison of whole chloroplast genome sequences to choose noncoding regions for phylogenetic studies in angiosperms: the tortoise and the hare III. American Journal of Botany 94(3): 275–288. https://doi.org/10.3732/ajb.94.3.275

Singh, P., K. Karthikeyan, P. Lakshminarasimhan & S.S. Dash (2015). Endemic Vascular Plants of India. Botanical Survey of India, Kolkata, 339 pp.

Smith, M.A., J.J. Rodriguez, J.B. Whitfield, A.R. Deans, D.H. Janzen, W. Hallwachs & P.D. Hebert (2008). Extreme diversity of tropical parasitoid wasps exposed by iterative integration of natural history, DNA barcoding, morphology, and collections. Proceedings of the National Academy of Sciences 105(34): 12359–12364. https://doi.org/10.1073/pnas.0805319105

Su, T., Y.F. Geng, C.L. Xiang, F. Zhao, M. Wang, L. Gu & G.X. Hu (2022). Chloroplast genome of salvia sect. Drymosphace: comparative and phylogenetic analysis. Diversity 14: 324. https://doi.org/10.3390/d14050324

Xu, Y.L., H.H. Shen, X.Y. Du & L. Lu (2022). Plastome characteristics and species identification of Chinese medicinal wintergreens (Gaultheria, Ericaceae). Plant Diversity 44: 519–529. https://doi.org/10.1016/j.pld.2022.06.002

Yan, H.F., Y.J. Liu, X.F. Xie, C.Y. Zhang, C.M. Hu, G. Hao & X.J. Ge (2015). DNA barcoding evaluation and its taxonomic implications in the species-rich genus Primula L. in China. PLOS One 10(4): e0122903. https:// doi.org/10.1371/journal.pone.0122903

Yu, W.B., P.H. Huang, R.H. Ree, M.L. Liu, D.Z. Li & H. Wang (2011). DNA barcoding of Pedicularis L. (Orobanchaceae): evaluating four universal barcode loci in a large and hemiparasitic genus. Journal of Systematics and Evolution 49(5): 425–437. https://doi.org/10.1111/j.1759-6831.2011.00154.x 12

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Published

26-02-2025

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