Unraveling the plant diversity of the Amazonian <i>canga</i> through DNA barcoding

Vasconcelos, Santelmo; Nunes, Gisele; Dias, Mariana Costa; Lorena, Jamily; Oliveira, Renato R. M.; Lima, Talvâne G. L.; Pires, Eder S.; Valadares, Rafael Borges da Silva; Alves, Ronnie; Watanabe, Maurício Takashi Coutinho; Zappi, Daniela; Hiura, Alice Lima; Pastore, Mayara; Vasconcelos, Liziane Vilela; Mota, Nara F. O.; Viana, Pedro Lage; Gil, André S. B.; Simões, André Olmos; Imperatriz-Fonseca, Vera Lúcia; Harley, R. M.; Giulietti, Ana María; Oliveira, Guilherme

doi:10.1002/ece3.8057

Cited by 9 publications

(6 citation statements)

References 103 publications

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“…Although rbc L and atp F- atp H have been reported to have little variability in the past among candidate loci, they have been used in a number of studies. Also, combinations of loci composed of the above mentioned regions have been proposed by various groups as universal multilocus barcodes for plants [ 10 , 36 , 37 ]. Therefore, this work also performed an analysis of the combination of two and three loci, taking into account the fact that if a single locus did not provide a complete distinction between species, then the combination of several regions could provide an optimal barcode for the species studied.…”

Section: Discussionmentioning

confidence: 99%

Unlocking the Genetic Identity of Endangered Paphiopedilum Orchids: A DNA Barcoding Approach

Karbarz,

Szlachcikowska,

Zapał

et al. 2024

Genes

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Orchids of the genus Paphiopedilum, also called slippers, are among the most valued representatives of the Orchidaceae family due to their aesthetic qualities. Due to overexploitation, deforestation, and illegal trade in these plants, especially in the vegetative phase, Paphiopedilum requires special protection. This genus is listed in Appendix I of the Convention on International Trade in Endangered Species of Wild Fauna and Flora. Their precise identification is of great importance for the preservation of genetic resources and biodiversity of the orchid family (Orchidaceae). Therefore, the main objective of the study was to investigate the usefulness of the DNA barcoding technique for the identification of endangered orchids of the genus Paphiopedilum and to determine the effectiveness of five loci: matK, rbcL, ITS2, atpF-atpH and trnH-psbA as potential molecular markers for species of this genus. Among single locus barcodes, matK was the most effective at identifying species (64%). Furthermore, matK, ITS2, matK + rbcL, and matK + trnH-psbA barcodes can be successfully used as a complementary tool to identify Paphiopedilum orchids while supporting morphological data provided by taxonomists.

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Section: Discussionmentioning

confidence: 99%

Unlocking the Genetic Identity of Endangered Paphiopedilum Orchids: A DNA Barcoding Approach

Karbarz,

Szlachcikowska,

Zapał

et al. 2024

Genes

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“…Multiple alignments of retrieved rRNA sequence and the primers were done using BIOEDIT tool. (Cahyaningsih et al, 2022) (Qarni et al, 2022) (J. Chen et al, 2021) (Vasconcelos et al, 2021) (Frigerio et al, 2021) (LV et al, 2020 (Zhao et al, 2018) (Gong et al, 2018) (N. Yu et al, 2017) (Feng et al, 2016) (X. Yu et al, 2016 (Gu et al, 2013) (Tripathi et al, 2013) (Pang et al, 2012) (S. Chen et al, 2010) 2.…”

Section: Methodsmentioning

confidence: 99%

Identification and validation of ITS2-specific universal primers for DNA barcoding in plants

Bhat,

Hegde,

Kammar

et al. 2024

Preprint

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Accurate identification of plant species is fundamental for various purposes, including biodiversity conservation and effective utilization of plants. Molecular-based techniques, particularly DNA barcoding, have emerged as a rapid and accurate alternative to traditional taxonomic methods for plant species identification. DNA barcoding involves analysing specific DNA regions to classify and identify organisms. Among different barcode markers, internal transcribed spacer 2 (ITS2) has gained prominence due to its shorter length and ease of sequencing. In this study we present a comprehensive survey of the literature, identifying a universal set of primers for ITS2 and validating their universality through in silico and in vitro analyses. This manuscript provides valuable insights into establishing a standardized approach for DNA barcoding using ITS2, helping researchers select appropriate primers for accurate plant species identification and classification. Standardized universal primers alleviate the time-consuming primer selection process, promoting efficient and reliable DNA barcoding practices within the plant scientific community.

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“…DNA extractions were carried out following the automated protocol previously described [ 51 ], with approximately 20 mg of plant material collected in NaCl-saturated CTAB solution [ 52 ]. Afterwards, paired-end libraries were constructed from 50 ng of DNA.…”

Section: Methodsmentioning

confidence: 99%

New plastomes of eight Ipomoea species and four putative hybrids from Eastern Amazon

et al. 2022

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Ipomoea is a large pantropical genus globally distributed, which importance goes beyond the economic value as food resources or ornamental crops. This highly diverse genus has been the focus of a great number of studies, enriching the plant genomics knowledge, and challenging the plant evolution models. In the Carajás mountain range, located in Eastern Amazon, the savannah-like ferruginous ecosystem known as canga harbors highly specialized plant and animal populations, and Ipomoea is substantially representative in such restrictive habitat. Thus, to provide genetic data and insights into whole plastome phylogenetic relationships among key Ipomoea species from Eastern Amazon with little to none previously available data, we present the complete plastome sequences of twelve lineages of the genus, including the canga microendemic I. cavalcantei, the closely related I. marabaensis, and their putative hybrids. The twelve plastomes presented similar gene content as most publicly available Ipomoea plastomes, although the putative hybrids were correctly placed as closely related to the two parental species. The cavalcantei-marabaensis group was consistently grouped between phylogenetic methods. The closer relationship of the I. carnea plastome with the cavalcantei-marabaensis group, as well as the branch formed by I. quamoclit, I. asarifolia and I. maurandioides, were probably a consequence of insufficient taxonomic representativity, instead of true genetic closeness, reinforcing the importance of new plastome assemblies to resolve inconsistencies and boost statistical confidence, especially the case for South American clades of Ipomoea. The search for k-mers presenting high dispersion among the frequency distributions pointed to highly variable coding and intergenic regions, which may potentially contribute to the genetic diversity observed at species level. Our results contribute to the resolution of uncertain clades within Ipomoea and future phylogenomic studies, bringing unprecedented results to Ipomoea species with restricted distribution, such as I. cavalcantei.

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Unraveling the plant diversity of the Amazonian canga through DNA barcoding

Abstract: This is an open access article under the terms of the Creat ive Commo ns Attri bution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.

Cited by 9 publications

References 103 publications

Unlocking the Genetic Identity of Endangered Paphiopedilum Orchids: A DNA Barcoding Approach

Unlocking the Genetic Identity of Endangered Paphiopedilum Orchids: A DNA Barcoding Approach

Identification and validation of ITS2-specific universal primers for DNA barcoding in plants

New plastomes of eight Ipomoea species and four putative hybrids from Eastern Amazon

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