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https://hdl.handle.net/10216/120439
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DC Field | Value | Language |
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dc.creator | Santos C. | |
dc.creator | Pereira F. | |
dc.date.accessioned | 2019-05-31T16:15:47Z | - |
dc.date.available | 2019-05-31T16:15:47Z | - |
dc.date.issued | 2018 | |
dc.identifier.issn | 18724973 | |
dc.identifier.uri | https://hdl.handle.net/10216/120439 | - |
dc.description.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 | |
dc.description.sponsorship | CS is supported by the “Programa Ciências Sem Fronteiras” from the Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq) and Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES), Brasil . FP is supported by the Portuguese Foundation for Science and Technology (FCT) , ERDF and Programa Operacional Potencial Humano ( IF/01356/2012 ). CIIMAR was partially supported by the Strategic Funding UID/Multi/04423/2013 through national funds provided by FCT and ERDF in the framework of the programme PT2020. Appendix A | |
dc.language.iso | eng | |
dc.publisher | Elsevier | |
dc.relation | info:eu-repo/grantAgreement/FCT/5876/147268/PT | |
dc.relation.ispartof | Forensic Science International: Genetics, vol. 36, p. 1-12 | |
dc.rights | restrictedAccess | |
dc.subject | chloroplast DNA | |
dc.subject | plant DNA | |
dc.subject | chloroplast DNA | |
dc.subject | Acer rubrum | |
dc.subject | Amaryllidaceae | |
dc.subject | Apiaceae | |
dc.subject | Araceae | |
dc.subject | Article | |
dc.subject | Boechera holboelli | |
dc.subject | Brassicaceae | |
dc.subject | Carapichea ipecacuanha | |
dc.subject | consensus sequence | |
dc.subject | DNA sequence | |
dc.subject | Ericaceae | |
dc.subject | Fabaceae | |
dc.subject | fig | |
dc.subject | indel mutation | |
dc.subject | Justicia adhatoda | |
dc.subject | Lepidium | |
dc.subject | Lepidium montanum | |
dc.subject | Melanthiaceae | |
dc.subject | Musa acuminata | |
dc.subject | nonhuman | |
dc.subject | nucleotide sequence | |
dc.subject | Onobrychis viciifolia | |
dc.subject | Phalaris | |
dc.subject | Phalaris arundinaceae | |
dc.subject | plant genome | |
dc.subject | plant identification | |
dc.subject | Poa annua | |
dc.subject | Poaceae | |
dc.subject | Populus balsamifera | |
dc.subject | Potentilla | |
dc.subject | Potentilla argentea | |
dc.subject | priority journal | |
dc.subject | Ranunculus | |
dc.subject | Ranunculus kuepferi | |
dc.subject | Rubiaceae | |
dc.subject | Saxifragaceae | |
dc.subject | sequence alignment | |
dc.subject | Silene | |
dc.subject | Silene latifolia | |
dc.subject | Solanum dulcamara | |
dc.subject | species identification | |
dc.subject | classification | |
dc.subject | genetic variation | |
dc.subject | genetics | |
dc.subject | plant | |
dc.subject | species difference | |
dc.subject | DNA, Chloroplast | |
dc.subject | Genetic Variation | |
dc.subject | Genome, Plant | |
dc.subject | INDEL Mutation | |
dc.subject | Plants | |
dc.subject | Sequence Analysis, DNA | |
dc.subject | Species Specificity | |
dc.title | Identification of plant species using variable length chloroplast DNA sequences | |
dc.type | Artigo em Revista Científica Internacional | |
dc.contributor.uporto | CIIMAR - Centro Interdisciplinar de Investigação Marinha e Ambiental | |
dc.identifier.doi | 10.1016/j.fsigen.2018.05.009 | |
dc.relation.publisherversion | http://dx.doi.org/10.1016/j.fsigen.2018.05.009 | |
Appears in Collections: | CIIMAR - Artigo em Revista Científica Internacional |
Files in This Item:
File | Description | Size | Format | |
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Santos C_2018.pdf Restricted Access | 1.66 MB | Adobe PDF | Request a copy |
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