DNA barcoding in Atlantic Forest plants: what is the best marker for Sapotaceae species identification?

Cv, Vivas; Rc, Moraes; Alves‐Araújo, Anderson; Alves, Marccus; Mariano‐Neto, Eduardo; Berg, Cássio van den; Gaiotto, Fernanda Amato

doi:10.1590/s1415-47572014005000019

Cited by 17 publications

(22 citation statements)

References 41 publications

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“…Further, needed full sequences of ITS region for resolving the phylogenetic issue. According to Vivas et al (2014) for species discrimination, ITS region provided the best results, followed by matK, trnH-psbA, and rbcL. Furthermore, the combined analysis of two, three or four markers did not result in higher rates of discrimination than with ITS alone.…”

Section: Gonystylusmentioning

confidence: 90%

Molecular phylogeny of trees species in Tripa Peat Swamp Forest, Aceh, Indonesia inferred by 5.8S nuclear gen

et al. 2018

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Authors. 2018. Molecular phylogeny of trees species in Tripa Peat Swamp Forest, Aceh, Indonesia inferred by 5.8S nucleargen. Biodiversitas 19: 1186-1193. Tripa peat swamp forest is protected areas that have high biodiversity. Nevertheless, in some areas,the damage occurred due to conversions of land function to oil palm plantations. The impact of conversions of peat swamp forest to oilpalm plantations has led to biodiversity decreased. Hence, it is important to identify the remain tree species in Tripa peat swamp forest.This study aimed to determine of trees species diversity in Tripa peat swamp forest by using of 5.8S rRNA nuclear gene. Research wasconducted at Forest Genetics and Molecular Forestry Laboratory, Faculty of Forestry, IPB from September 2015 to August 2016.Molecular identification consisted of DNA extraction, PCR analysis, and sequencing. The data were analyzed using Bioedit, MEGA 6,BLAST, and ITS2 database. Molecular identification using ITS 1 and ITS 4 primer successfully amplified (the ITS region ITS1-5.8SITS2)of 16 trees species from 9 families. BLAST analysis results indicate the presence of 16 species has similar bases sequence withthe GeneBank DNA database. The plant species are Branckenridgea palustris (Ochnaceae), Gonystylus sp. (Thymelaeaceae),Tristaniopsis whiteana (Myrtaceae), Syzygium sp.1 (Myrtaceae), Macaranga triloba (Euphorbiaceae), Syzygium garciniifolium(Myrtaceae), Knema intermedia (Myristicaceae), Palaquium ridleyi (Sapotaceae), Palaquium sp. (Sapotaceae), Dyera lowii(Apocynaceae), Elaeocarpus petiolatus (Elaeocarpaceae), Ficus sp. (Moraceae), Syzygium leptostemon (Myrtaceae), Chilocarpussuaveolens (Apocynaceae), Alstonia pneumatophora (Apocynaceae), and Alstonia sp. (Apocynaceae). Phylogeny tree reconstructionusing the Neighbor-Joining Method (NJ) showed that 5.8S rRNA nuclear gene was successful as marker for 16 trees species from 9different families. In addition, the 5.8S also successful for resolving phylogenetic relationships at genus level i.e. Alstonia, Palaquium,Syzygium, Tristaniopsis, Macaranga, Elaeocarpus, and Ficus.

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Section: Gonystylusmentioning

confidence: 90%

Molecular phylogeny of trees species in Tripa Peat Swamp Forest, Aceh, Indonesia inferred by 5.8S nuclear gen

et al. 2018

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“…Barcoding has also been useful as a forensic tool to determine the origin of commercialized natural products, such as medicinal plants [ 40 , 41 ], teas [ 42 ], and foods [ 43 ]. Furthermore, the recent reports on the barcoding of commercially important species of trees [ 44 , 45 ], forests communities [ 46 , 47 , 48 ] and CITES-protected timber species [ 49 ] have emphasized the feasibility of employing this approach as a routine method for identifying species of economic interest.…”

Section: Introductionmentioning

confidence: 99%

ITS and trnH-psbA as Efficient DNA Barcodes to Identify Threatened Commercial Woody Angiosperms from Southern Brazilian Atlantic Rainforests

et al. 2015

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The Araucaria Forests in southern Brazil are part of the Atlantic Rainforest, a key hotspot for global biodiversity. This habitat has experienced extensive losses of vegetation cover due to commercial logging and the intense use of wood resources for construction and furniture manufacturing. The absence of precise taxonomic tools for identifying Araucaria Forest tree species motivated us to test the ability of DNA barcoding to distinguish species exploited for wood resources and its suitability for use as an alternative testing technique for the inspection of illegal timber shipments. We tested three cpDNA regions (matK, trnH-psbA, and rbcL) and nrITS according to criteria determined by The Consortium for the Barcode of Life (CBOL). The efficiency of each marker and selected marker combinations were evaluated for 30 commercially valuable woody species in multiple populations, with a special focus on Lauraceae species. Inter- and intraspecific distances, species discrimination rates, and ability to recover species-specific clusters were evaluated. Among the regions and different combinations, ITS was the most efficient for identifying species based on the ‘best close match’ test; similarly, the trnH-psbA + ITS combination also demonstrated satisfactory results. When combining trnH-psbA + ITS, Maximum Likelihood analysis demonstrated a more resolved topology for internal branches, with 91% of species-specific clusters. DNA barcoding was found to be a practical and rapid method for identifying major threatened woody angiosperms from Araucaria Forests such as Lauraceae species, presenting a high confidence for recognizing members of Ocotea. These molecular tools can assist in screening those botanical families that are most targeted by the timber industry in southern Brazil and detecting certain species protected by Brazilian legislation and could be a useful tool for monitoring wood exploitation.

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“…Unfortunately, many species from GenBank were represented by a unique sequence, not representing the intraspecific variation. In the second one, the tree-based method (NJ) was only considered successful by the specific monophyletic groups for species for at least two specimens sequenced, and that showed bootstrap values ≥70% (as used by Zhang, Fan, Zhu, Zhao, &Fu, 2013 andVivas et al, 2014). Cladograms were analyzed and edited with MEGA6 (Tamura et al, 2013).…”

Section: Plant Materials and Genetic Analysis Of Dna Barcode Candidatesmentioning

confidence: 99%

DNA barcode regions for differentiating Cattleya walkeriana and C. loddigesii

Rivera-Jiménez

Rossini

Tambarussi

et al. 2017

Acta Sci. Biol. Sci.

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ABSTRACT. Growers appreciate Cattleya walkeriana and C. loddigesii due to striking shape and rarity. Thus, this study aimed to evaluate the feasibility of DNA barcode regions, namely ITS1, ITS2 and rpoC1, to discriminate between C. walkeriana and C. loddigesii species. DNA barcode regions were successfully amplified using primers designed to amplify plants. We also included sequences from public databases in order to test if these regions were able to discriminate C. walkeriana and C. loddigesii from other Cattleya species. These regions, and their combinations, demonstrated that the ITS1+ITS2 had the highest average interspecific distance (11.1%), followed by rpoC1 (1.06%). For species discrimination, ITS1+ITS2 provided the best results. The combined data set of ITS1+ITS2+rpoC1 also discriminated both species, but did not result in higher rates of discrimination. These results indicate that ITS region is the best option for molecular identification of these two species and from some other species of this genus.Keywords: orchid improvement, genetic variation, species separation.Regiões de DNA barcode para diferenciar Cattleya walkeriana e C. loddigesii RESUMO. As espécies Cattleya walkeriana e C. loddigesii são apreciadas pelos colecionadores devido às suas impressionantes forma e raridade. Este estudo teve como objetivo avaliar a viabilidade das regiões DNA barcode, ou seja, ITS1, ITS2 e rpoC1, para discriminar as espécies C. walkeriana e C. loddigesii. Regiões DNA barcode foram amplificadas com êxito utilizando os iniciadores desenhados para plantas. Nós também incluímos sequências de bases públicas de dados, a fim de testar se estas regiões foram capazes de discriminar C. walkeriana e C. loddigesii de outras espécies de Cattleya. Estas regiões e suas combinações demonstraram que o ITS1 + ITS2 teve a maior distância média interespecífica (11,1%), seguido por rpoC1 (1,06%). Para a discriminação das espécies, ITS1 + ITS2 proporcionaram os melhores resultados. Os dados combinados dos ITS1 + ITS2 + rpoC1 também discriminaram ambas as espécies, mas não resultaram em maiores taxas de discriminação. Estes resultados indicam que a região ITS é a melhor opção para a identificação molecular destas duas espécies e a partir de algumas outras espécies deste gênero.Palavras-chave: melhoramento de orquídeas, variação genética, separação de espécies.

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DNA barcoding in Atlantic Forest plants: what is the best marker for Sapotaceae species identification?

Cited by 17 publications

References 41 publications

Molecular phylogeny of trees species in Tripa Peat Swamp Forest, Aceh, Indonesia inferred by 5.8S nuclear gen

Molecular phylogeny of trees species in Tripa Peat Swamp Forest, Aceh, Indonesia inferred by 5.8S nuclear gen

ITS and trnH-psbA as Efficient DNA Barcodes to Identify Threatened Commercial Woody Angiosperms from Southern Brazilian Atlantic Rainforests

<b>DNA barcode regions for differentiating <i>Cattleya walkeriana</i> and <i>C. loddigesii</i>

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