Wood identification of JapaneseCyclobalanopsis species (Fagaceae) based on DNA polymorphism of the intergenic spacer betweentrnT andtrnL 5′ exon

Ohyama, Motonari; K, Baba; Itoh, Takaò

doi:10.1007/bf00780554

Cited by 24 publications

(13 citation statements)

References 13 publications

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“…For the species-rich section Cyclobalanopsis in East Asia, little is known about evolution of chloroplast genome and phylogeny. So far, only the intergenic region of the chloroplast trn T- trn L was applied to distinguish six species of section Cyclobalanopsis distributed in Japan, and proved to have moderate efficiency ( Ohyama et al, 2001 ). Recent studies using cp DNA show that the species of section Cyclobalanopsis , e.g., Q. glauca ( Xu et al, 2015 ), Q. schottkyana ( Jiang et al, 2016 ), Q. arbutifolia ( Xu et al, 2016 ), and Q. kerrii ( Jiang et al, 2018 ), contain high variable regions to infer population history, but the resolution of cp DNA markers in discriminating section Cyclobalanopsis species is still unknown.…”

Section: Introductionmentioning

confidence: 99%

The Application and Limitation of Universal Chloroplast Markers in Discriminating East Asian Evergreen Oaks

et al. 2018

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The East Asian subtropics mostly occupied by evergreen broad-leaved forests (EBLFs), is one of the global diversity centers for evergreen oaks. Evergreen oaks are keystone canopy trees in EBLFs with important ecosystem function and crucial significance for regional biodiversity conservation. However, the species composition and diversity of Asian evergreen oaks are poorly understood. Here, we test whether the four chloroplast markers atpI-atpH, matK, psbA-trnH, and ycf1, can discriminate the two evergreen oak sections in Asia – Cyclobalanopsis and Ilex. Two hundred and seventy-two individuals representing 57 species were scanned and 17 species from other oaks sections were included for phylogenetic reconstruction. The genetic diversity of the Quercus sections was also compared. Overall, we found that universal chloroplast DNA (cpDNA) barcoding markers could resolve two clades in Quercus, i.e., subgenus Cerris (Old World Clade) and subgenus Quercus (New World Clade). The chloroplast markers distinguished the main sections, with few exceptions. Each cpDNA region showed no barcoding gap and none of them provided good resolution at the species level. The best species resolution (27.78%) was obtained when three or four markers were combined and analyzed using BLAST. The high conservation of the cpDNA and complicated evolutionary patterns, due to incomplete lineage sorting, interspecific hybridization and introgressions may hinder the ability of cpDNA markers to discriminate different species. When comparing diversification pattern across Quercus sections (Cyclobalanopsis, Ilex, Cerris, Quercus, and Protobalanus), we found that section Ilex was the most genetically diverse, and section Cyclobalanopsis was lower genetically diverse. This diversification pattern may have resulted from the interplay of the Eurasia Cenozoic tectonic movements, climate changes and different niches of their ancestral lineages.

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Section: Introductionmentioning

confidence: 99%

The Application and Limitation of Universal Chloroplast Markers in Discriminating East Asian Evergreen Oaks

et al. 2018

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“…The same sequence was selected for a primer named ccmp6 reverse in a previous study (Weising and Gardner 1999). The conservation of the trnL gene has also been well recognized (Taberlet et al 1991;Kajita et al 1998;Ohyama et al 2001), but none of the published primers were selected from the same location as ours. However, the conservation of two priming sites that we selected was not obvious: wp003forward annealed to a sequence within a large intron in the ycf3 gene, and wp005reverse annealed to a site locating in another intron of ycf3 in the tree species.…”

Section: Resultsmentioning

confidence: 99%

Wood identification with PCR targeting noncoding chloroplast DNA

2011

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Wood identification is extremely important in the modern forest industry. It also has significant applications in forensics, as well as in archeology and ecological research. In this study, five universal primer pairs amplifying chloroplast noncoding sequences of 300-1,200 bp were designed. Sequencing these amplicons in combination can lead to reliable identification of logs and wood products to cultivar, ecotype, or even the falling population. These primer pairs work on both gymnosperms and angiosperm trees. They also are potentially applicable to accurately identify shrubs and herbaceous species. In addition, a wood DNA purification method is proposed in which N-phenacylthiazolium bromide (PTB) is used to increase the quality and quantity of extracted DNA. This method was first validated using air-dried timber disks from three different tree species that were felled 4 years ago. The sapwood and outer heartwood provided the best locations for DNA extraction. The method was also successfully applied to extract DNA from the recalcitrant processed white oak wood, randomly selected staves of wine barrels. The single nucleotide polymorphism detected on the oak DNA sequences showed correlation to their geographical origins.

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“…Nucleotide substitution in the plastid genome provides the key base for wood identification at the species level. In Cyclobalanopsis, a subgenus of Quercus, nucleotide substitutions and insertion/deletion were detected at four positions in the 151 bp trnT-trnL fragment [7]. Between Q. rubra and Q. robur, there were five nucleotide insertions/deletions at the A/T-repeat region in the 290 bp trnD-trnT fragment [8].…”

Section: Pcr Amplifications and Sequencingmentioning

confidence: 99%

“…The genomic deoxyribonucleic acid (DNA) stored in wood includes the nucleotide sequences inherent in its species. Several studies have proved the effectiveness of DNA identification of wood materials that are difficult to distinguish based on anatomical features [7][8][9][10][11][12][13]. This method is also expected to function in identifying the woods used as the materials of historically valuable products and buildings.…”

Section: Introductionmentioning

confidence: 99%

Sequencing and quantifying plastid DNA fragments stored in sapwood and heartwood of Torreya nucifera

Watanabe

Abe

2017

J Wood Sci

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Wood identification of JapaneseCyclobalanopsis species (Fagaceae) based on DNA polymorphism of the intergenic spacer betweentrnT andtrnL 5′ exon

Cited by 24 publications

References 13 publications

The Application and Limitation of Universal Chloroplast Markers in Discriminating East Asian Evergreen Oaks

The Application and Limitation of Universal Chloroplast Markers in Discriminating East Asian Evergreen Oaks

Wood identification with PCR targeting noncoding chloroplast DNA

Sequencing and quantifying plastid DNA fragments stored in sapwood and heartwood of Torreya nucifera

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