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DNA barcode trnH-psbA is a promising candidate for efficient identification of forage legumes and grasses.

ABSTRACT: OBJECTIVE:Grasslands are widespread ecosystems that fulfil many functions. Plant species richness (PSR) is known to have beneficial effects on such functions and monitoring PSR is crucial for tracking the effects of land use and agricultural management on these ecosystems. Unfortunately, traditional morphology-based methods are labor-intensive and cannot be adapted for high-throughput assessments. DNA barcoding could aid increasing the throughput of PSR assessments in grasslands. In this proof-of-concept work, we aimed at determining which of three plant DNA barcodes (rbcLa, matK and trnH-psbA) best discriminates 16 key grass and legume species common in temperate sub-alpine grasslands. RESULTS:Barcode trnH-psbA had a 100% correct assignment rate (CAR) in the five analyzed legumes, followed by rbcLa (93.3%) and matK (55.6%). Barcode trnH-psbA had a 100% CAR in the grasses Cynosurus cristatus, Dactylis glomerata and Trisetum flavescens. However, the closely related Festuca, Lolium and Poa species were not always correctly identified, which led to an overall CAR in grasses of 66.7%, 50.0% and 46.4% for trnH-psbA, matK and rbcLa, respectively. Barcode trnH-psbA is thus the most promising candidate for PSR assessments in permanent grasslands and could greatly support plant biodiversity monitoring on a larger scale.

SUBMITTER: Loera-Sanchez M

PROVIDER: S-EPMC6969398 | biostudies-literature | 2020 Jan

REPOSITORIES: biostudies-literature

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DNA barcode trnH-psbA is a promising candidate for efficient identification of forage legumes and grasses.

Loera-Sánchez Miguel M Studer Bruno B Kölliker Roland R

BMC research notes 20200117 1

<h4>Objective</h4>Grasslands are widespread ecosystems that fulfil many functions. Plant species richness (PSR) is known to have beneficial effects on such functions and monitoring PSR is crucial for tracking the effects of land use and agricultural management on these ecosystems. Unfortunately, traditional morphology-based methods are labor-intensive and cannot be adapted for high-throughput assessments. DNA barcoding could aid increasing the throughput of PSR assessments in grasslands. In this ...[more]

PMID: 31952556

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Project description:BackgroundDNA 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.ResultsFirst, 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.ConclusionsThe 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

DNA barcode trnH-psbA is a promising candidate for efficient identification of forage legumes and grasses.

Publications

DNA barcode trnH-psbA is a promising candidate for efficient identification of forage legumes and grasses.

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