Please use this identifier to cite or link to this item: https://hdl.handle.net/10216/120439
Author(s): Santos C.
Pereira F.
Title: Identification of plant species using variable length chloroplast DNA sequences
Publisher: Elsevier
Issue Date: 2018
Abstract: The correct identification of species in the highly divergent group of plants is crucial for several forensic investigations. Previous works had difficulties in the establishment of a rapid and robust method for the identification of plants. For instance, DNA barcoding requires the analysis of two or three different genomic regions to attain reasonable levels of discrimination. Therefore, new methods for the molecular identification of plants are clearly needed. Here we tested the utility of variable-length sequences in the chloroplast DNA (cpDNA) as a way to identify plant species. The SPInDel (Species Identification by Insertions/Deletions) approach targets hypervariable genomic regions that contain multiple insertions/deletions (indels) and length variability, which are found interspersed with highly conserved regions. The combination of fragment lengths defines a unique numeric profile for each species, allowing its identification. We analysed more than 44,000 sequences retrieved from public databases belonging to 206 different plant families. Four target regions were identified as suitable for the SPInDel concept: atpF-atpH, psbA-trnH, trnL CD and trnL GH. When considered alone, the discrimination power of each region was low, varying from 5.18% (trnL GH) to 42.54% (trnL CD). However, the discrimination power reached more than 90% when the length of some of these regions is combined. We also observed low diversity in intraspecific data sets for all target regions, suggesting they can be used for identification purposes. Our results demonstrate the utility of the SPInDel concept for the identification of plants. © 2018
Subject: chloroplast DNA
plant DNA
chloroplast DNA
Acer rubrum
Amaryllidaceae
Apiaceae
Araceae
Article
Boechera holboelli
Brassicaceae
Carapichea ipecacuanha
consensus sequence
DNA sequence
Ericaceae
Fabaceae
fig
indel mutation
Justicia adhatoda
Lepidium
Lepidium montanum
Melanthiaceae
Musa acuminata
nonhuman
nucleotide sequence
Onobrychis viciifolia
Phalaris
Phalaris arundinaceae
plant genome
plant identification
Poa annua
Poaceae
Populus balsamifera
Potentilla
Potentilla argentea
priority journal
Ranunculus
Ranunculus kuepferi
Rubiaceae
Saxifragaceae
sequence alignment
Silene
Silene latifolia
Solanum dulcamara
species identification
classification
genetic variation
genetics
plant
species difference
DNA, Chloroplast
Genetic Variation
Genome, Plant
INDEL Mutation
Plants
Sequence Analysis, DNA
Species Specificity
URI: https://hdl.handle.net/10216/120439
Source: Forensic Science International: Genetics, vol. 36, p. 1-12
Related Information: info:eu-repo/grantAgreement/FCT/5876/147268/PT
Document Type: Artigo em Revista Científica Internacional
Rights: restrictedAccess
Appears in Collections:CIIMAR - Artigo em Revista Científica Internacional

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