2010
DOI: 10.1111/j.1467-7652.2010.00558.x
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Chloroplast genome sequences from total DNA for plant identification

Abstract: SummaryChloroplast DNA sequence data are a versatile tool for plant identification or barcoding and establishing genetic relationships among plant species. Different chloroplast loci have been utilized for use at close and distant evolutionary distances in plants, and no single locus has been identified that can distinguish between all plant species. Advances in DNA sequencing technology are providing new cost-effective options for genome comparisons on a much larger scale. Universal PCR amplification of chlor… Show more

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Cited by 335 publications
(301 citation statements)
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“…As a consequence, NGS has allowed for the description of a rapidly increasing number of nuclear, mitochondrial and plastid genomes (Rounsley et al 2009;Deschamps and Campbell 2010) and is set to contribute to a deeper understanding of both phylogeny and evolution in many lineages. Among the three types of genomes, data of entire plastid genomes have been widely used to seek for markers for the purpose of DNA barcoding (Hollingsworth et al 2011;Nock et al 2011), to investigate population genetics, and in phylogeographic studies (Powell et al 1995;Provan et al 2001;Mariac et al 2014), as well as to efficiently address phylogenetic questions in both angiosperms (Jansen et al 2007;Moore et al 2011;Huang et al 2014) and gymnosperms (Parks et al 2009;Lin et al 2010;Yi et al 2015). Here, we use data from NGS, combined with data from traditional Sanger sequencing and morphology, with the primary aim of resolving the phylogeny and species delimitation among Chinese lianoid species of Gnetum L. (Gnetales).…”
Section: Introductionmentioning
confidence: 99%
“…As a consequence, NGS has allowed for the description of a rapidly increasing number of nuclear, mitochondrial and plastid genomes (Rounsley et al 2009;Deschamps and Campbell 2010) and is set to contribute to a deeper understanding of both phylogeny and evolution in many lineages. Among the three types of genomes, data of entire plastid genomes have been widely used to seek for markers for the purpose of DNA barcoding (Hollingsworth et al 2011;Nock et al 2011), to investigate population genetics, and in phylogeographic studies (Powell et al 1995;Provan et al 2001;Mariac et al 2014), as well as to efficiently address phylogenetic questions in both angiosperms (Jansen et al 2007;Moore et al 2011;Huang et al 2014) and gymnosperms (Parks et al 2009;Lin et al 2010;Yi et al 2015). Here, we use data from NGS, combined with data from traditional Sanger sequencing and morphology, with the primary aim of resolving the phylogeny and species delimitation among Chinese lianoid species of Gnetum L. (Gnetales).…”
Section: Introductionmentioning
confidence: 99%
“…cpDNA and mtDNA markers are considered ideal systems in phylogeny and population genetics because of their uniparental mode of inheritance and low mutation rate compared to the nuclear genome (Galtier et al, 2009;Nock et al, 2011). Dane and Liu (2007) reported that the nature of specific DNA polymorphisms detectable using PCR-RFLP is typically limited to restriction site changes and indel mutations.…”
Section: Discussionmentioning
confidence: 99%
“…In this study, the few polymorphisms detected (27.2%) were highest in the chloroplast genome (40%) followed by the mitochondrial genome (20%), while the nuclear genome had the lowest percentage of polymorphisms (9.8%). Chloroplasts contain both highly conserved genes fundamental to plant life and more variable regions that are informative over broad time scales (Nock et al, 2011). However, the mitochondrial genome evolves considerably more slowly at the nucleotide sequence level than the nuclear or chloroplast genomes, although the rate of rearrangements is extraordinarily faster in plant mtDNA than in cpDNA due to the presence of repeated regions, which are sources of recombination within and between mtDNA genomes.…”
Section: Discussionmentioning
confidence: 99%
“…The chloroplast has highly-conserved genes which are elementary to plants and are variable and informative regions over a long time scale. The use of cpDNA can also analyse the maternal source genome donor and has been applied successfully in the phylogenetic analysis of many taxa (Shaw et al, 2007;Sun, 2007;Nock et al, 2011).…”
Section: Introductionmentioning
confidence: 99%