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Application of deoxyribonucleic acid barcoding in Lauraceae plants.

Liu Z, Chen SL, Song JY, Zhang SJ, Chen KL - Pharmacogn Mag (2012)

Bottom Line: We tested the discrimination ability of psbA-trnH in 68 plant samples belonging to 42 species from 11 distinct genera and found that the rate of successful identification with the psbA-trnH was 82.4% at the species level.Using the BLAST1 method, the identification efficiency were 84.0% and 92.3% at the species and genus level, respectively.Therefore, psbA-trnH is confirmed as a useful marker for differentiating closely related species within Lauraceae.

View Article: PubMed Central - PubMed

Affiliation: Department of Pharmacy, The 309 Hospital of Chinese People's Liberation Army, Beijing.

ABSTRACT

Background: This study aims to determine the candidate markers that can be used as DNA barcode in the Lauraceae family.

Material and methods: Polymerase chain reaction amplification, sequencing efficiency, differential intra- and interspecific divergences, DNA barcoding gap, and identification efficiency were used to evaluate the four different DNA sequences of psbA-trnH, matK, rbcL, and ITS2. We tested the discrimination ability of psbA-trnH in 68 plant samples belonging to 42 species from 11 distinct genera and found that the rate of successful identification with the psbA-trnH was 82.4% at the species level. However, the correct identification of matK and rbcL were only 30.9% and 25.0%, respectively, using BLAST1. The PCR amplification efficiency of the ITS2 region was poor; thus, ITS2 was not included in subsequent experiments. To verify the capacity of the identification of psbA-trnH in more samples, 175 samples belonging to 117 species from the experimental data and from the GenBank database of the Lauraceae family were tested.

Results: Using the BLAST1 method, the identification efficiency were 84.0% and 92.3% at the species and genus level, respectively.

Conclusion: Therefore, psbA-trnH is confirmed as a useful marker for differentiating closely related species within Lauraceae.

No MeSH data available.


The interspecific divergence of the psbA-trnH region in Lauraceae
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Figure 2: The interspecific divergence of the psbA-trnH region in Lauraceae

Mentions: Ideally, barcoding involves separate distributions and without overlap between intra- and interspecific variations.[1016] Results of the present study showed that psbA-trnH have a faint gap, whereas matK and rbcL exhibited significant overlap without any gaps [Figures 1 and 2].


Application of deoxyribonucleic acid barcoding in Lauraceae plants.

Liu Z, Chen SL, Song JY, Zhang SJ, Chen KL - Pharmacogn Mag (2012)

The interspecific divergence of the psbA-trnH region in Lauraceae
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3307201&req=5

Figure 2: The interspecific divergence of the psbA-trnH region in Lauraceae
Mentions: Ideally, barcoding involves separate distributions and without overlap between intra- and interspecific variations.[1016] Results of the present study showed that psbA-trnH have a faint gap, whereas matK and rbcL exhibited significant overlap without any gaps [Figures 1 and 2].

Bottom Line: We tested the discrimination ability of psbA-trnH in 68 plant samples belonging to 42 species from 11 distinct genera and found that the rate of successful identification with the psbA-trnH was 82.4% at the species level.Using the BLAST1 method, the identification efficiency were 84.0% and 92.3% at the species and genus level, respectively.Therefore, psbA-trnH is confirmed as a useful marker for differentiating closely related species within Lauraceae.

View Article: PubMed Central - PubMed

Affiliation: Department of Pharmacy, The 309 Hospital of Chinese People's Liberation Army, Beijing.

ABSTRACT

Background: This study aims to determine the candidate markers that can be used as DNA barcode in the Lauraceae family.

Material and methods: Polymerase chain reaction amplification, sequencing efficiency, differential intra- and interspecific divergences, DNA barcoding gap, and identification efficiency were used to evaluate the four different DNA sequences of psbA-trnH, matK, rbcL, and ITS2. We tested the discrimination ability of psbA-trnH in 68 plant samples belonging to 42 species from 11 distinct genera and found that the rate of successful identification with the psbA-trnH was 82.4% at the species level. However, the correct identification of matK and rbcL were only 30.9% and 25.0%, respectively, using BLAST1. The PCR amplification efficiency of the ITS2 region was poor; thus, ITS2 was not included in subsequent experiments. To verify the capacity of the identification of psbA-trnH in more samples, 175 samples belonging to 117 species from the experimental data and from the GenBank database of the Lauraceae family were tested.

Results: Using the BLAST1 method, the identification efficiency were 84.0% and 92.3% at the species and genus level, respectively.

Conclusion: Therefore, psbA-trnH is confirmed as a useful marker for differentiating closely related species within Lauraceae.

No MeSH data available.