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

ABSTRACT: 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.

SUBMITTER: Bolson M

PROVIDER: S-EPMC4704546 | biostudies-literature | 2015

REPOSITORIES: biostudies-literature

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

Bolson Mônica M Smidt Eric de Camargo Ede C Brotto Marcelo Leandro ML Silva-Pereira Viviane V

PloS one 20151202 12

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 ...[more]

PMID: 26630282

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Project description:BACKGROUND:DNA barcoding technology, which uses a short piece of DNA sequence to identify species, has wide ranges of applications. Until today, a universal DNA barcode marker for plants remains elusive. The rbcL and matK regions have been proposed as the "core barcode" for plants and the ITS2 and psbA-trnH intergenic spacer (PTIGS) regions were later added as supplemental barcodes. The use of PTIGS region as a supplemental barcode has been limited by the lack of computational tools that can handle significant insertions and deletions in the PTIGS sequences. Here, we compared the most commonly used alignment-based and alignment-free methods and developed a web server to allow the biologists to carry out PTIGS-based DNA barcoding analyses. RESULTS:First, we compared several alignment-based methods such as BLAST and those calculating P distance and Edit distance, alignment-free methods Di-Nucleotide Frequency Profile (DNFP) and their combinations. We found that the DNFP and Edit-distance methods increased the identification success rate to ~80%, 20% higher than the most commonly used BLAST method. Second, the combined methods showed overall better success rate and performance. Last, we have developed a web server that allows (1) retrieving various sub-regions and the consensus sequences of PTIGS, (2) annotating novel PTIGS sequences, (3) determining species identity by PTIGS sequences using eight methods, and (4) examining identification efficiency and performance of the eight methods for various taxonomy groups. CONCLUSIONS:The Edit distance and the DNFP methods have the highest discrimination powers. Hybrid methods can be used to achieve significant improvement in performance. These methods can be extended to applications using the core barcodes and the other supplemental DNA barcode ITS2. To our knowledge, the web server developed here is the only one that allows species determination based on PTIGS sequences. The web server can be accessed at http://psba-trnh-plantidit.dnsalias.org.

Dataset Information

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

Publications

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

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