An in silico approach for evaluation of rbcL and matK loci for DNA barcoding of Cucurbitaceae family
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Abstract. Ho VT, Nguyen MP. 2020. An in silico approach for evaluation of rbcL and matK loci for DNA barcoding of Cucurbitaceae family. Biodiversitas 21: 3879-3885. DNA barcodes have been used intensively to discriminate different species in Cucurbitaceae family. The main of this study is to evaluate the effectiveness of rbcL and matK loci for 16 species of Cucurbitaceae family by using in silico approach. For analysis, sequences were firstly retrieved from NCBI and then calculated for sequence parameters. Sequences were then aligned and constructed phylogenetic try and examined for species resolution ability. The obtained data show the variability of resolving capacity among species. rbcL region is suitable for distinguishing five species namely S. edule, M. cochinchinensis, L. aegyptiaca, C. melo, and C. pepo, whereas matK locus is more proper for different five species consisting of M. balsamina, M. cochinchinensis, M. charantia, S. edule, and C. sativus. The resolving power is improved sharply by analyzing the rbcL + matK combination with up to nine species consisting of C. lanatus, B. hispida, C. melo, C. sativus, C. pepo, C. agryrosperma, L. aegyptiaca, S. edule, and M. cochinchinensis. Therefore, the integration of rbcL and matK loci may improve the competence of assessing genetic relatedness at species level of members in Cucurbitaceae family. The obtained information could be important for choosing proper DNA barcode loci for phylogenetic study of this crop family.
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References
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Tegally A, Jaufeerally-Fakim Y, Dulloo ME. 2019. Molecular characterisation of Solanum melongena L. and the crop wild relatives, S. violaceum Ortega and S. torvum Sw., using phylogenetic/DNA barcoding markers. Genet resource crop evol. doi.org/10.1007/s10722-019-00827-0
Thitikornpong W, Palanuvej C, Ruangrungsi N. 2018. DNA barcoding for authentication of the endangered plants in genus Aquilaria. Thai J Pharm Sci 42(4): 214-220.
Vu TH, Huynh P, Tran HD, Le L. 2019. In Silico Study on Molecular Sequences for Identification of Paphiopedilum Species. Evol Bioinform 14:1-9.
Welbaum GE 2014. Vegetable Production and Practices. CABI publisher.
Burgess KS, Fazekas AJ, Kesanakurti PR, Graham SW, Husband BC, Newmaster SG, Percy DM, Hajibabaei M, Barrett SCH. 2011. Discriminating plant species in a local temperate flora using the rbcL+matK DNA barcode. Methods Ecol Evol 2: 333-340.
Fatima T, Srivastava A., Somashekar PV, Hanur VS, Rao MS. 2019. Development of DNA-based species identification and barcoding of three important timbers. Bull Natl Res Cent 43:76 https://doi.org/10.1186/s42269-019-0116-8
Gonzalez MA, Baraloto C, Engel J, Mori SA, Petronelli P, Riera B, Roger A, Thhebaud C, Chave J. 2009. Identification of Amazonian trees with DNA barcodes. PLos ONE 4, e7483.
CBOL Plant Working Group et al. 2009. A DNA barcode for land plants. PNAS 106: 12794-12797
Hebert PDN, Ratnasingham S, deWaard JR 2003. Barcoding animal life: cytochrome c oxidase subunit 1 divergences among closely related species. Proc Biol Sci 270(1):S96–9. doi:10.1098/rsbl.2003.0025
Huxley?Jones EL, Shaw JL, Fletcher C, Parnell J, Watts PC 2012. Use of DNA barcoding to reveal species composition of convenience seafood. Conserv Biol 26(2): 367–71. doi:10.1111/j.1523-1739.2011.01813.x
Hollingsworth ML, Clark AA, Forrest LL, Richardson J, Pennington RT, Long DG, Cowan R, Chase MW, Gaudeul M, Hollinsworth P. 2009. Selecting barcoding loci for plants: evaluation of seven candidate loci with species-level sampling in three divergent groups of land plants. Mol Ecol Resour 9: 439–457. doi: 10.1111/j.1755-0998.2008.02439.x
Kates HR, Soltis PS, Soltis DE. 2017. Evolutionary and domestication history of Cucurbita (Pumpkin and squash) species inferred from 44 nuclear loci. Mol Phylogenet Evol 111:98-109.
Kiewnick S, Holterman M, van den Elsen S, van Megen H, Frey JE, Helder J. 2014. Comparison of two short DNA barcoding loci (COI and COII) and two longer ribosomal DNA genes (SSU & LSU rRNA) for specimen identification among quarantine root-knot nematodes (Meloidogyne spp.) and their close relatives. Eur J Plant Pathol. 140(1):97–110
Knebelsberger T, Landi M, Neumann H, Kloppmann M, Sell AF, Campbell PD, et al. 2014. A reliable DNA barcode reference library for the identification of the North European shelf fish fauna. Mol Ecol Resour 14(5):1060–71. doi:10.1111/1755-0998.12238.
Kocyan A, Zhang LB, Schaefer H, Rener SS 2007. A multi-locus chloroplast phylogeny for the Cucurbitaceae and its implications for character evolution and classification. Mol Phylogenet Evol 44: 553–577
Kumar SJU, Rmakrish M, Seethapathy GS, Krishna V, Shaanker R, Ravikanth G. 2020. DNA barcoding of Momordica species and assessment of adulteration in Momordica herbal products, an anti-diabetic drug. Plant Gene 22: 100227 https://doi.org/10.1016/j.plgene.2020.100227
Li Y, Feng Y, Wang XY, Liuu B, Lv GH. 2014. Failure of DNA barcoding in discriminating Calligonum species. Nord J Bot 32: 511-517.
Li Q, Wu J, Wang Y, Lian X, Wu F, Zhou L, Huan Z, Zhu S. 2017. The phylogenetic analysis of Dalbergia (Fabaceae: Papilionaceae) based on different DNA barcodes. Holzforschung 71(12): 939-949. DOI 10.1515/hf-2017-0052
Lijtmaer DA, Kerr KC, Stoeckle MY, Tubaro PL. 2012. DNA barcoding birds: from field collection to data analysis. Methods Mol Biol. 858:127–52. doi:10.1007/978-1-61779-591-6_7
Liu J, Yan HF, Ge XJ. 2016. The Use of DNA Barcoding on Recently Diverged Species in the Genus Gentiana (Gentianaceae) in China. PLos One 11(4): e0153008.
JM, Sokoloff PC, Gillespie LJ, Consaul LL, Bull RD. 2013. DNA Barcoding the Canadian Arctic Flora: Core Plastid Barcodes (rbcL + matK) for 490 Vascular Plant Species. PLoS ONE 8(10): e77982. doi:10.1371/journal.pone.0077982
Sarhan S, Hamed F, Al-Youssef A. 2016. The rbcL gene sequence variation among and within Prunus species. J Agr Sci Tech 18: 1105-1115.
Sikdar S, Tiwari S, Thakur VV, Sapre S, 2018. An in silico approach for evaluation of rbcL and matK loci for DNA barcoding of Fabaceae family. Int J Chem Stud 6(6): 2446-2451.
Singh A, Drishti, Negi G, Mohanty A. 2016. In silico analysis of sequence variation in rbcL gene to asses phylogentic relations in Setaria species. International Conference on Innovative Research in Agriculture, Food Science, Forestry, Horticulture, Aquaculture, Animal Sciences, Biodiversity, Ecological Sciences and Climate Change: 16-18.
Suesatpanit T, Osathanunkul K, Madesis P, Osathanunkul M. 2017. Should DNA sequence be incorporated with other taxonomical data for routine identifying of plant species? BMC Complement Altern Med 17:437 DOI 10.1186/s12906-017-1937-3
Tamura K, Stecher G, Peterson D, Filipski A, Kumar S. 2013. MEGA6: Molecular evolutionary genetic analysis version 6. Mol Biol Evol 30(12): 2725-2729.
Tegally A, Jaufeerally-Fakim Y, Dulloo ME. 2019. Molecular characterisation of Solanum melongena L. and the crop wild relatives, S. violaceum Ortega and S. torvum Sw., using phylogenetic/DNA barcoding markers. Genet resource crop evol. doi.org/10.1007/s10722-019-00827-0
Thitikornpong W, Palanuvej C, Ruangrungsi N. 2018. DNA barcoding for authentication of the endangered plants in genus Aquilaria. Thai J Pharm Sci 42(4): 214-220.
Vu TH, Huynh P, Tran HD, Le L. 2019. In Silico Study on Molecular Sequences for Identification of Paphiopedilum Species. Evol Bioinform 14:1-9.
Welbaum GE 2014. Vegetable Production and Practices. CABI publisher.
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