Cover Image

Molecular phylogeny and evolution of tropical vegetal genus Coccinia (Cucurbitaceae) using chloroplast barcode markers and its implications for speciation patterns

Mala Parab, Payel De, Sunita Singh

Abstract


Evaluation of molecular phylogeny employing barcode markers for a population analysis has revealed the association between character evolution and diversification. The present research study endeavors to estimate the molecular phylogeny and evolution amongst 30 geographically distant land races of Coccinia grandis using chloroplast barcode markers. On the basis of sequences of ­C. grandis landraces and sister genera’s of Cucurbits; phylogeny and evolutionary distances were estimated using bootstrap method of UPGMA and ML with MEGA and DAMBE software. The rbcL appear to be evolving marginally amongst land races studied, while matK loci exhibited several parsimonically insignificant variations. The ycf5 locus resolved efficiently the phylogeny at both intraspecies and intergeneric levels. The values of Tajima’s relative rate test, Nei’s genetic distance and gamma distribution, within C. grandis accessions and among Cucurbits denoted plausibility of occurrences of random population expansion, slow ontogenic transitions and high consanguinity percentage among core barcode regions.The present study thus lays a platform for researchers working with vegetatively propagated plants to plan strategies for exchange of varieties, their maintenance, utilization and enhancement for further crop development and propagation.

Keywords


Coccinia grandis, character evolution, diversification, phylogeny, genetic distance

Full Text:

PDF

References


Anvarkhah S, Hosseini M, Mohassel M, Panah A, and Hashemi H. “Identification of three species of genus Allium using DNA barcoding.” Intl J Agri Crop Sci, 5.11 (2013): 1195-1203. http://ijagcs.com/wp-content/uploads/2013/05/1195-1203.pdf

Barthet M and Hilu K. “Expression of matk: functional and evolutionary implications.” A. J. Bot 4.(2007):1402-1412. http://www.amjbot.org/content/94/8/1402.long

Bisognin D. “Origin and evaluation of cultivated cucurbits.” Ciencia Rral. 32.5 (2002): 715-723. https://www.academia.edu/31754521/Origin_and_evolution_of_cultivated_cucurbits

Borsch T, Hilu KW, Quandt W, Wilde V, Neinhuis C, and Barthlott W. “Noncoding plastid trnT-trnF sequences reveal a well resolved phylogeny of basal angiosperms.” J Evol Biol. 16(2003): 558-576. https://www.ncbi.nlm.nih.gov/pubmed/14632220

Chase M, Soltis D, Olmstead R, Morgan D, Les D, Mishler B, Duvall M, Price R, et al. “Phylogenetics of seed plants: an analysis of nucleotide sequences from the plastid gene rbcL” Ann Missouri Bot Gard, 80(1993):528-580. http://loco.biosci.arizona.edu/PDG/pdfs/Chase1993.pdf

Chase MW and Fay MF. “Barcoding of plants and fungi.” Science, 325 (2009):682–683. http://science.sciencemag.org/content/325/5941/682

Chen S, Yao H, Han J, Liu C, Song J, Shi L, Zhu Y, Ma X, Gao et al. “Validation of the ITS2 region as a novel DNA barcode for identifying medicinal plant species.” PLoS ONE. 5 (2010). e8613. http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0008613

Davis C, Xi Z and Mathews S. “Plastid phylogenomics and green plant phylogeny.” BMC Biology. 12.11 (2014). http://www.biomedcentral.com/1741-7007/12/11

Deokate U and Khadabadi S. “Pharmacology and photochemistry of Coccinia indica.” Pharmacophore. 3.3 (2012): 179-185.

http://www.pharmacophorejournal.com/May-June2012-article3.pdf

Duminil J and Michele M. “Plant species delimitation: a comparison of morphological and molecular markers.” Plant Biosystematics. 143 (2009): 528-542.

http://ebe.ulb.ac.be/ebe/ Duminil_files/Duminil%20%26%20al.%202009%20PB.pdf

Gonzalez M, Baralato C, Moris S, Petronelli P, Reira B, Thebaund C and Chave J. “Identification of Amazonian trees with DNA barcodes.” PLoS ONE, 4 (2009): e7483.

http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0007483

Harlan JR. “Origins and processes of domestication. In: Chapman GP (ed) Grass evolution and domestication.” Cambridge University Press, Cambridge, (1992): 159–175.

http://pdf.usaid.gov/pdf_docs/pnacf852.pdf

Hollingsworth P, Graham S and Little D. “Choosing and using a plant DNA Barcode.” PLoS ONE. 6.5 (2011): e19254. doi:10.1371/journal.pone.0019254.

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC 3261039/ pdf/PhytoKeys-007-027.pdf

Holstein N and Renner S. “Coccinia intermedia – a new Cucurbitaceae species from West Africa.” Phytokeys. 7 (2011): 27-36.

https://phytokeys.pensoft.net/article/1396/download/pdf/

Kress W and Erickson D. “A two-locus global DNA barcode for land plants: The coding rbcL gene complements the non-coding trnH-psbA spacer region.” PLoS ONE, (2007). doi.10.1371/journal.pone.0000508.

Kun Luo Chen S, Chen K, Song J, Yao H, Ma X, Zhu Y, Pang X, Yu H, Li X and Liu, Z. “Assessment of candidate plant DNA barcodes using the Rutaceae family.” Science China, Life Sci. 53 6 (2010): 701-708.

http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0000508.

Lahaye R, Van der Bank M, Bogarin D, Warner J, Pupulin F, Gigot G, Maurin O, Duthoit S, Barraclough, T and Savolainen V. “DNA barcoding the floras of biodiversity hot spot.” PNAS, USA, 105 (2008): 2923-2928.

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2268561/

Liang H and Hilu K. “Application of the matK gene sequences to grass systematic.” Canadian J. Bot. 74 (1996): 125-134.

http://www.nrcresearchpress.com/doi/abs/10.1139/b96-017#.WXcNe1H-vIU

Mckey D, Elias M, Pujol B and Duputie A. “The evolutionary ecology of clonally propagated domesticated plants.” New Phytol. 186 (2010): 318–332. https://www.ncbi.nlm.nih.gov/pubmed/20202131

Min X and Hickey D. “DNA barcodes provide a quick preview of mitochondrial genome composition.” PLoS ONE. 2.3 (2007): e325. http://journals.plos.org/plosone/article?id=10.1371/journal. pone.0000325

Muniappan R, Reddy G, and Raman A. “Coccinia grandis (L.) Voigt. (Cucurbitaceae) Biological Control of Tropical Weeds used Arthropods. Cambridge University Press. (2009): 175-182.

http://assets.cambridge.org/97805218/77916/frontmatter/9780521877916_frontmatter.pdf

Nei M. “Genetic distance and molecular phylogeny.” Columbia University Press, New York (2000): 193-223. http://nsgl.gso.uri.edu/washu/washub87001/washub87001_part6.pdf

Payel D, Mala P, and Sunita S. “Inter genus variation analysis in few members of Cucurbitaceae using ISSR markers.” Biotechnology and Bioequipment. 29.5 (2015): 882-886.

DOI: 10.1080/13102818.2015.1052760.

Reddy U. “A phylogenetic analysis of the Cucurbitaceae: evidences from matk nucleotide sequences.” International Journal of Bioinformatics Research. 1.2 (2009): 47-53.

https://bioinfopublication.org/viewhtml.php?artid=BIA0001340

Reddy U. “Cladistic analysis of few members of Cucurbitaceae using rbcL nucleotide and amino acid sequences.” International Journal of Bioinformatics Research, 1.2 (2009): 58-64.

https://bioinfopublication.org/viewhtml.php?artid=BIA0001342

Shaina T and Beevy S. “Reproductive biology of Coccinia grandis (L) Voigt. a dioecious vegetatively propagated Cucurbit: evidence for facultative apomixes.” Int J Plant Reprod Biol. 7.1 (2015): 67-77. http://ijprb.com/vol%2007%20(1)/pdf%2007.pdf

Singh S and Parab M. “Fingerprinting intra-specific diversity among Coccinia grandis landraces.” Int. J. Recent Sci. Res. 6.3 (2015): 3025-3032.

http://www.recentscientific.com/sites/default/files/2063.pdf

Small R, Ryburn J, Cronn R, Seelanan T and Wendel J. “The tortoise and the hare: choosing between noncoding plastome and nuclear adh sequences for phylogenetic reconstruction in a recently diverged plant group.” Am. J. Bot. 85 (1998): 1301-1315.

https://www.ncbi.nlm.nih.gov/pubmed/21685016

Tajima F. “Statistical method for testing the neutral mutation hypothesis by DNA polymorphism.” Genetics. 123.3 (1989): 585- 595.

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1203831

Tamura K, Stecher G, Peterson D, Filipski A and Kimar S. “MEGA6: Molecular Evolutionary Genetics Analysis version 6.0.” Molecular Biology & Evolution. (2013). doi: 10.1093/molbev/mst197. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3840312

Tsuruya K, Suzuki M, Plader W, Sugita C and Sugita M. “Chloroplast transformation reveals that tobacco ycf5 is involved in photosynthesis.” Acta Physiol. Plant 28 (2006): 365- 371.

https://link.springer.com/article/10.1007%2Fs11738-006-0033-y

Vadivu R, Krithika A, Biplab C, Dedeepya P, Shoeb and Lakshmi K. “Evaluation of hepatoprotective activity of the fruits of Coccinia grandis Linn. Int. J. Health Res. 3 (2008): 163-168.

https://www.ajol.info/index.php/ijhr/article/view/55366

Wang Z, Brown J, Tang Z and Fang J. “Temperature dependence, spatial scale, and tree species diversity in eastern Asia and North America.” PNAS, USA. 106.32 (2009b): 13388-13392. http://www.pnas.org/content/106/32/13388.

Xia X. “DAMBE 5: A comprehensive software package for data analysis in molecular biology and evolution.” Mol. Biol. & Evol. 30 (2013): 1720-1728.

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3684854

Zhang, C, Pratap, A, Natarajan S, Pugalendhi L, Shinji, K, Sassa H, Senthil N and Koba1 T. “Evaluation of Morphological and Molecular Diversity among South Asian germplasms of Cucumis sativus and Cucumis melo.” ISRN Agronomy. (2012). doi: 105402/2012/134134.

https://www.hindawi.com/journals/isrn/2012/134134.




DOI: https://doi.org/10.21746/aps.2017.6.12.3

Bookmark and Share


Copyright (c) 2017 Annals of Plant Sciences

Creative Commons License
This work is licensed under a Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License.