An in silico approach for evaluation of rbcL and matK loci for DNA barcoding of Cucurbitaceae family

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 evaluat...

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Autores principales:	Viet The Ho, MINH PHUONG NGUYEN
Formato:	article
Lenguaje:	EN
Publicado:	MBI & UNS Solo 2020
Materias:	cucurbitaceae, dna barcode, matk, rbcl, Biology (General) QH301-705.5
Acceso en línea:	https://doaj.org/article/53808d44f73f447fa8e67000412b8eb9
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spelling	oai:doaj.org-article:53808d44f73f447fa8e67000412b8eb92021-11-22T12:17:57ZAn in silico approach for evaluation of rbcL and matK loci for DNA barcoding of Cucurbitaceae family1412-033X2085-472210.13057/biodiv/d210858https://doaj.org/article/53808d44f73f447fa8e67000412b8eb92020-08-01T00:00:00Zhttps://smujo.id/biodiv/article/view/6296https://doaj.org/toc/1412-033Xhttps://doaj.org/toc/2085-4722Abstract. 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.Viet The HoMINH PHUONG NGUYENMBI & UNS Soloarticlecucurbitaceae, dna barcode, matk, rbcl,Biology (General)QH301-705.5ENBiodiversitas, Vol 21, Iss 8 (2020)
institution	DOAJ
collection	DOAJ
language	EN
topic	cucurbitaceae, dna barcode, matk, rbcl, Biology (General) QH301-705.5
spellingShingle	cucurbitaceae, dna barcode, matk, rbcl, Biology (General) QH301-705.5 Viet The Ho MINH PHUONG NGUYEN An in silico approach for evaluation of rbcL and matK loci for DNA barcoding of Cucurbitaceae family
description	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.
format	article
author	Viet The Ho MINH PHUONG NGUYEN
author_facet	Viet The Ho MINH PHUONG NGUYEN
author_sort	Viet The Ho
title	An in silico approach for evaluation of rbcL and matK loci for DNA barcoding of Cucurbitaceae family
title_short	An in silico approach for evaluation of rbcL and matK loci for DNA barcoding of Cucurbitaceae family
title_full	An in silico approach for evaluation of rbcL and matK loci for DNA barcoding of Cucurbitaceae family
title_fullStr	An in silico approach for evaluation of rbcL and matK loci for DNA barcoding of Cucurbitaceae family
title_full_unstemmed	An in silico approach for evaluation of rbcL and matK loci for DNA barcoding of Cucurbitaceae family
title_sort	in silico approach for evaluation of rbcl and matk loci for dna barcoding of cucurbitaceae family
publisher	MBI & UNS Solo
publishDate	2020
url	https://doaj.org/article/53808d44f73f447fa8e67000412b8eb9
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An in silico approach for evaluation of rbcL and matK loci for DNA barcoding of Cucurbitaceae family

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