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DNA barcoding, phylogenetic analysis and secondary structure predictions of nepenthes ampullaria, nepenthes gracilis and nepenthes rafflesiana

Nepentheceae, the most prominent carnivorous family in the Caryophyllales order, comprises the Nepenthes genus, which has modified leaf trap characteristics. Although most Nepenthes species have unique morphologies, their vegetative stages are identical, making identification based on morphology dif...

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Main Authors: Nur Azreen Saidon, Alina Wagiran, Abdul Fatah A. Samad, Faezah Mohd Salleh, Farhan Mohamed, Jaeyres Jani, Alona C Linatoc
Format: Article
Language:English
English
Published: Multidisciplinary Digital Publishing Institute (MDPI) 2023
Subjects:
QH1-(199.5) General Including nature conservation, geographical distribution
SB1-1110 Plant culture
Online Access:https://eprints.ums.edu.my/id/eprint/42223/1/ABSTRACT.pdf
https://eprints.ums.edu.my/id/eprint/42223/2/FULL%20TEXT.pdf
https://eprints.ums.edu.my/id/eprint/42223/
https://doi.org/10.3390/genes14030697
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spelling my.ums.eprints.422232024-12-10T07:01:02Z https://eprints.ums.edu.my/id/eprint/42223/ DNA barcoding, phylogenetic analysis and secondary structure predictions of nepenthes ampullaria, nepenthes gracilis and nepenthes rafflesiana Nur Azreen Saidon Alina Wagiran Abdul Fatah A. Samad Faezah Mohd Salleh Farhan Mohamed Jaeyres Jani Alona C Linatoc QH1-(199.5) General Including nature conservation, geographical distribution SB1-1110 Plant culture Nepentheceae, the most prominent carnivorous family in the Caryophyllales order, comprises the Nepenthes genus, which has modified leaf trap characteristics. Although most Nepenthes species have unique morphologies, their vegetative stages are identical, making identification based on morphology difficult. DNA barcoding is seen as a potential tool for plant identification, with small DNA segments amplified for species identification. In this study, three barcode loci; ribulose bisphosphate carboxylase (rbcL), intergenic spacer 1 (ITS1) and intergenic spacer 2 (ITS2) and the usefulness of the ITS1 and ITS2 secondary structure for the molecular identification of Nepenthes species were investigated. An analysis of barcodes was conducted using BLASTn, pairwise genetic distance and diversity, followed by secondary structure prediction. The findings reveal that PCR and sequencing were both 100% successful. The present study showed the successful amplification of all targeted DNA barcodes at different sizes. Among the three barcodes, rbcL was the least efficient as a DNA barcode compared to ITS1 and ITS2. The ITS1 nucleotide analysis revealed that the ITS1 barcode had more variations compared to ITS2. The mean genetic distance (K2P) between them was higher for interspecies compared to intraspecies. The results showed that the DNA barcoding gap existed among Nepenthes species, and differences in the secondary structure distinguish the Nepenthes. The secondary structure generated in this study was found to successfully discriminate between the Nepenthes species, leading to enhanced resolutions. Multidisciplinary Digital Publishing Institute (MDPI) 2023 Article NonPeerReviewed text en https://eprints.ums.edu.my/id/eprint/42223/1/ABSTRACT.pdf text en https://eprints.ums.edu.my/id/eprint/42223/2/FULL%20TEXT.pdf Nur Azreen Saidon and Alina Wagiran and Abdul Fatah A. Samad and Faezah Mohd Salleh and Farhan Mohamed and Jaeyres Jani and Alona C Linatoc (2023) DNA barcoding, phylogenetic analysis and secondary structure predictions of nepenthes ampullaria, nepenthes gracilis and nepenthes rafflesiana. Genes, 14. pp. 1-14. https://doi.org/10.3390/genes14030697
institution Universiti Malaysia Sabah
building UMS Library
collection Institutional Repository
continent Asia
country Malaysia
content_provider Universiti Malaysia Sabah
content_source UMS Institutional Repository
url_provider http://eprints.ums.edu.my/
language English
English
topic QH1-(199.5) General Including nature conservation, geographical distribution
SB1-1110 Plant culture
spellingShingle QH1-(199.5) General Including nature conservation, geographical distribution
SB1-1110 Plant culture
Nur Azreen Saidon
Alina Wagiran
Abdul Fatah A. Samad
Faezah Mohd Salleh
Farhan Mohamed
Jaeyres Jani
Alona C Linatoc
DNA barcoding, phylogenetic analysis and secondary structure predictions of nepenthes ampullaria, nepenthes gracilis and nepenthes rafflesiana
description Nepentheceae, the most prominent carnivorous family in the Caryophyllales order, comprises the Nepenthes genus, which has modified leaf trap characteristics. Although most Nepenthes species have unique morphologies, their vegetative stages are identical, making identification based on morphology difficult. DNA barcoding is seen as a potential tool for plant identification, with small DNA segments amplified for species identification. In this study, three barcode loci; ribulose bisphosphate carboxylase (rbcL), intergenic spacer 1 (ITS1) and intergenic spacer 2 (ITS2) and the usefulness of the ITS1 and ITS2 secondary structure for the molecular identification of Nepenthes species were investigated. An analysis of barcodes was conducted using BLASTn, pairwise genetic distance and diversity, followed by secondary structure prediction. The findings reveal that PCR and sequencing were both 100% successful. The present study showed the successful amplification of all targeted DNA barcodes at different sizes. Among the three barcodes, rbcL was the least efficient as a DNA barcode compared to ITS1 and ITS2. The ITS1 nucleotide analysis revealed that the ITS1 barcode had more variations compared to ITS2. The mean genetic distance (K2P) between them was higher for interspecies compared to intraspecies. The results showed that the DNA barcoding gap existed among Nepenthes species, and differences in the secondary structure distinguish the Nepenthes. The secondary structure generated in this study was found to successfully discriminate between the Nepenthes species, leading to enhanced resolutions.
format Article
author Nur Azreen Saidon
Alina Wagiran
Abdul Fatah A. Samad
Faezah Mohd Salleh
Farhan Mohamed
Jaeyres Jani
Alona C Linatoc
author_facet Nur Azreen Saidon
Alina Wagiran
Abdul Fatah A. Samad
Faezah Mohd Salleh
Farhan Mohamed
Jaeyres Jani
Alona C Linatoc
author_sort Nur Azreen Saidon
title DNA barcoding, phylogenetic analysis and secondary structure predictions of nepenthes ampullaria, nepenthes gracilis and nepenthes rafflesiana
title_short DNA barcoding, phylogenetic analysis and secondary structure predictions of nepenthes ampullaria, nepenthes gracilis and nepenthes rafflesiana
title_full DNA barcoding, phylogenetic analysis and secondary structure predictions of nepenthes ampullaria, nepenthes gracilis and nepenthes rafflesiana
title_fullStr DNA barcoding, phylogenetic analysis and secondary structure predictions of nepenthes ampullaria, nepenthes gracilis and nepenthes rafflesiana
title_full_unstemmed DNA barcoding, phylogenetic analysis and secondary structure predictions of nepenthes ampullaria, nepenthes gracilis and nepenthes rafflesiana
title_sort dna barcoding, phylogenetic analysis and secondary structure predictions of nepenthes ampullaria, nepenthes gracilis and nepenthes rafflesiana
publisher Multidisciplinary Digital Publishing Institute (MDPI)
publishDate 2023
url https://eprints.ums.edu.my/id/eprint/42223/1/ABSTRACT.pdf
https://eprints.ums.edu.my/id/eprint/42223/2/FULL%20TEXT.pdf
https://eprints.ums.edu.my/id/eprint/42223/
https://doi.org/10.3390/genes14030697
_version_ 1818835192653021184
score 13.244413

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