Wood identification with PCR targeting noncoding chloroplast DNA

Tang, Xiaoshu; Zhao, Guangjie; Ping, Liyan

doi:10.1007/s11103-011-9837-2

Cited by 20 publications

(14 citation statements)

References 31 publications

Supporting

Mentioning

Contrasting

Unclassified

Order By: Relevance

“…The yield of DNA from barks/woody tissue is reported to be low (50 ng µL -1 ) (Asif and Cannon, 2005). The DNA isolated from the dried wood of Cunninghamia lanceolata could not be visualized in agarose gel due to partial degradation of the DNA extract (Rachmayanti et al, 2009;Tang et al, 2011;Jiao et al, 2012). Degradation may be due to the mechanical treatment employed for harvesting the bark or decomposition of wood by microorganisms.…”

Section: Discussionmentioning

confidence: 99%

Isolation and amplification of genomic DNA from barks of Cinnamomum spp.

Swetha¹,

Parvathy²,

Sheeja³

et al. 2014

Turk J Biol

View full text Add to dashboard Cite

IntroductionSpices are widely used as medicine and food flavorants. Although there are about 109 species listed as spices in the International Standards Organization (ISO) list, their uses are specific as each of these commodities have different uses in flavoring foods or in medicine. Cinnamomum aromaticum, C. zeylanincum syn. C. verum, C. burmanii, C. loureirii, and C. tamala are included in the ISO list. While barks of the first 4 species are used as food flavorant, in beverages and in medicine, it is the leaves of C. tamala that are economically important for flavoring food items.The genus Cinnamomum belongs to the family Lauraceae and consists of about 250 species of plants that are aromatic and flavoring (Leela, 2008). Their antiinflammatory, antidiabetic, and antioxidant activities have popularized the use of Cinnamomum in folk medicine (Lee et al., 2010). C. verum, a native of Sri Lanka, is known as true cinnamon. It is cultivated in Sri Lanka and India, and the bark of this species forms the most important traded Cinnamomum. The dried bark of C. verum is used as a spice in flavoring foods like biscuits, cakes, sweets, and pickles (Abeysinghe et al., 2009). However, of late, adulteration of this commodity with the hard, thick, and less aromatic bark of C. aromaticum (C. cassia, cassia cinnamon or Chinese cinnamon) has been reported, as this species bears close resemblance with the bark of true cinnamon, making fraudulent practices easy (Thomas and Duethi, 2001). This commodity has a bitter and burning flavor. A high amount of coumarin is also present in C. aromaticum, which is known to cause liver and kidney damage in rats, mice, and probably in humans (Lungarini et al., 2008). The dried bark of C. malabatrum, another Cinnamomum species, common in many tropical countries as wild growth and, on rare occasion, in homestead gardens in India and Sri Lanka, is also passed off as true cinnamon. Identification of true cinnamon from adulterant species based on physical traits is very difficult, and the situation is all the more difficult once the commodity loses its physical form (e.g., powder). Incidentally, powdered bark is more frequently used as food flavorant and in medicine.Molecular markers are useful in discriminating adulterants from the genuine products in cases where there is high physical resemblance between the entities, or in the instances of change of the physical form. The first step in any DNA-based discrimination technique is the isolation and amplification of DNA.

show abstract

Section: Discussionmentioning

confidence: 99%

Isolation and amplification of genomic DNA from barks of Cinnamomum spp.

Swetha¹,

Parvathy²,

Sheeja³

et al. 2014

Turk J Biol

View full text Add to dashboard Cite

show abstract

“…DNA barcodes are established tools for identifying herbal medicinal materials, in quality control, and in forensic science 10 , 19 , 20 . Additionally, a number of studies relying upon DNA barcoding have verified the utility and potential for wood species identification 11 , 12 , 21 – 23 .…”

Section: Introductionmentioning

confidence: 99%

DNA Barcode Authentication and Library Development for the Wood of Six Commercial Pterocarpus Species: the Critical Role of Xylarium Specimens

Jiao

Wiedenhoeft

et al. 2018

Sci Rep

View full text Add to dashboard Cite

DNA barcoding has been proposed as a useful tool for forensic wood identification and development of a reliable DNA reference library is an essential first step. Xylaria (wood collections) are potentially enormous data repositories if DNA information could be extracted from wood specimens. In this study, 31 xylarium wood specimens and 8 leaf specimens of six important commercial species of Pterocarpus were selected to investigate the reliability of DNA barcodes for authentication at the species level and to determine the feasibility of building wood DNA barcode reference libraries from xylarium specimens. Four DNA barcodes (ITS2, matK, ndhF-rpl32 and rbcL) and their combination were tested to evaluate their discrimination ability for Pterocarpus species with both TaxonDNA and tree-based analytical methods. The results indicated that the combination barcode of matK + ndhF-rpl32 + ITS2 yielded the best discrimination for the Pterocarpus species studied. The mini-barcode ndhF-rpl32 (167–173 bps) performed well distinguishing P. santalinus from its wood anatomically inseparable species P. tinctorius. Results from this study verified not only the feasibility of building DNA barcode libraries using xylarium wood specimens, but the importance of using wood rather than leaves as the source tissue, when wood is the botanical material to be identified.

show abstract

“…According to the Plant Working Group of Consortium for the Barcode of Life, an ideal DNA barcode should have a highly universal primer pair, show high success rates of PCR amplification and sequencing (Bolson et al 2015), and provide maximal species discrimination at the species level (Hebert et al 2003;Kress et al 2005;Cowan et al 2006;Hollingsworth et al 2009). These guidelines implicitly assume high quality and quantity DNA, an assumption that is often violated when wood or wood products are the source of DNA, and only short DNA barcodes can reliably be amplified (Tang et al 2011;Jiao et al 2012Jiao et al , 2014Jiao et al , 2015Yu et al 2016).…”

Section: Introductionmentioning

confidence: 99%

DNA barcoding of vouchered xylarium wood specimens of nine endangered Dalbergia species

Jiao

Guo

et al. 2017

Planta

View full text Add to dashboard Cite

ITS2+ trnH - psbA was the best combination of DNA barcode to resolve the Dalbergia wood species studied. We demonstrate the feasibility of building a DNA barcode reference database using xylarium wood specimens. The increase in illegal logging and timber trade of CITES-listed tropical species necessitates the development of unambiguous identification methods at the species level. For these methods to be fully functional and deployable for law enforcement, they must work using wood or wood products. DNA barcoding of wood has been promoted as a promising tool for species identification; however, the main barrier to extensive application of DNA barcoding to wood is the lack of a comprehensive and reliable DNA reference library of barcodes from wood. In this study, xylarium wood specimens of nine Dalbergia species were selected from the Wood Collection of the Chinese Academy of Forestry and DNA was then extracted from them for further PCR amplification of eight potential DNA barcode sequences (ITS2, matK, trnL, trnH-psbA, trnV-trnM1, trnV-trnM2, trnC-petN, and trnS-trnG). The barcodes were tested singly and in combination for species-level discrimination ability by tree-based [neighbor-joining (NJ)] and distance-based (TaxonDNA) methods. We found that the discrimination ability of DNA barcodes in combination was higher than any single DNA marker among the Dalbergia species studied, with the best two-marker combination of ITS2+trnH-psbA analyzed with NJ trees performing the best (100% accuracy). These barcodes are relatively short regions (<350 bp) and amplification reactions were performed with high success (≥90%) using wood as the source material, a necessary factor to apply DNA barcoding to timber trade. The present results demonstrate the feasibility of using vouchered xylarium specimens to build DNA barcoding reference databases.

show abstract

Wood identification with PCR targeting noncoding chloroplast DNA

Cited by 20 publications

References 31 publications

Isolation and amplification of genomic DNA from barks of Cinnamomum spp.

Isolation and amplification of genomic DNA from barks of Cinnamomum spp.

DNA Barcode Authentication and Library Development for the Wood of Six Commercial Pterocarpus Species: the Critical Role of Xylarium Specimens

DNA barcoding of vouchered xylarium wood specimens of nine endangered Dalbergia species

Contact Info

Product

Resources

About