Study on the Extraction and Identification of DNA from Ten <i>Dalbergia</i> Species
Most <i>Dalbergia</i> species are economically valuable and have been over-exploited, which has raised concerns. The regulation and protection of this genus require accurate and rapid authentication and identification processes. To address the issue of high residual inhibitors in extract...
| Main Authors: | , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
MDPI AG
2023-11-01
|
| Series: | Forests |
| Subjects: | |
| Online Access: | https://www.mdpi.com/1999-4907/14/12/2318 |
| _version_ | 1797381026509488128 |
|---|---|
| author | Changtao Gan Haishan He Jian Qiu |
| author_facet | Changtao Gan Haishan He Jian Qiu |
| author_sort | Changtao Gan |
| collection | DOAJ |
| description | Most <i>Dalbergia</i> species are economically valuable and have been over-exploited, which has raised concerns. The regulation and protection of this genus require accurate and rapid authentication and identification processes. To address the issue of high residual inhibitors in extracted DNA from the <i>Dalbergia</i> xylem, an optimized DNA extraction experiment was performed on 10 species of <i>Dalbergia</i> wood stored for 1–5 years; in particular, no gene sequence for <i>D. tsoi</i> can be found in the NCBI database. Additionally, universal primers ITS2 were used for PCR amplification and sequencing to confirm the effectiveness of DNA extraction. The results revealed that rinsing the wood with 0.25 M ammonium acetate buffer produced DNA with a high purity, without a significant decrease in the DNA yield. To achieve an optimal DNA yield, the wood DNA should be rinsed with ammonium acetate fewer than three times. All the wood DNA obtained using the kit method and treated with the ammonium acetate buffer rinsing solution one to four times was successfully amplified. The NJ phylogenetic tree constructed based on ITS2 can distinguish <i>D. tsoi</i> from other <i>Dalbergia</i> spp., and the predicted ITS2 secondary structure showed the difference between species. This experiment extracted high-quality DNA from wood, without the need for purification kits, thereby improving the efficiency of the extraction process. The extracted DNA was directly used for follow-up molecular experiments. |
| first_indexed | 2024-03-08T20:45:21Z |
| format | Article |
| id | doaj.art-0bb65d123e8246e7a3088f33fc980913 |
| institution | Directory Open Access Journal |
| issn | 1999-4907 |
| language | English |
| last_indexed | 2024-03-08T20:45:21Z |
| publishDate | 2023-11-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Forests |
| spelling | doaj.art-0bb65d123e8246e7a3088f33fc9809132023-12-22T14:09:23ZengMDPI AGForests1999-49072023-11-011412231810.3390/f14122318Study on the Extraction and Identification of DNA from Ten <i>Dalbergia</i> SpeciesChangtao Gan0Haishan He1Jian Qiu2College of Art and Design, Southwest Forestry University, Kunming 650224, ChinaIndustrial Engineering Institute, Yunnan Forestry Technological College, Kunming 650224, ChinaInternational Joint Research Center for Biomass Materials, Southwest Forestry University, Kunming 650224, ChinaMost <i>Dalbergia</i> species are economically valuable and have been over-exploited, which has raised concerns. The regulation and protection of this genus require accurate and rapid authentication and identification processes. To address the issue of high residual inhibitors in extracted DNA from the <i>Dalbergia</i> xylem, an optimized DNA extraction experiment was performed on 10 species of <i>Dalbergia</i> wood stored for 1–5 years; in particular, no gene sequence for <i>D. tsoi</i> can be found in the NCBI database. Additionally, universal primers ITS2 were used for PCR amplification and sequencing to confirm the effectiveness of DNA extraction. The results revealed that rinsing the wood with 0.25 M ammonium acetate buffer produced DNA with a high purity, without a significant decrease in the DNA yield. To achieve an optimal DNA yield, the wood DNA should be rinsed with ammonium acetate fewer than three times. All the wood DNA obtained using the kit method and treated with the ammonium acetate buffer rinsing solution one to four times was successfully amplified. The NJ phylogenetic tree constructed based on ITS2 can distinguish <i>D. tsoi</i> from other <i>Dalbergia</i> spp., and the predicted ITS2 secondary structure showed the difference between species. This experiment extracted high-quality DNA from wood, without the need for purification kits, thereby improving the efficiency of the extraction process. The extracted DNA was directly used for follow-up molecular experiments.https://www.mdpi.com/1999-4907/14/12/2318<i>Dalbergia</i> spp.DNA extractionPCR amplificationITS2 barcodingphylogenetic treesecondary structure |
| spellingShingle | Changtao Gan Haishan He Jian Qiu Study on the Extraction and Identification of DNA from Ten <i>Dalbergia</i> Species Forests <i>Dalbergia</i> spp. DNA extraction PCR amplification ITS2 barcoding phylogenetic tree secondary structure |
| title | Study on the Extraction and Identification of DNA from Ten <i>Dalbergia</i> Species |
| title_full | Study on the Extraction and Identification of DNA from Ten <i>Dalbergia</i> Species |
| title_fullStr | Study on the Extraction and Identification of DNA from Ten <i>Dalbergia</i> Species |
| title_full_unstemmed | Study on the Extraction and Identification of DNA from Ten <i>Dalbergia</i> Species |
| title_short | Study on the Extraction and Identification of DNA from Ten <i>Dalbergia</i> Species |
| title_sort | study on the extraction and identification of dna from ten i dalbergia i species |
| topic | <i>Dalbergia</i> spp. DNA extraction PCR amplification ITS2 barcoding phylogenetic tree secondary structure |
| url | https://www.mdpi.com/1999-4907/14/12/2318 |
| work_keys_str_mv | AT changtaogan studyontheextractionandidentificationofdnafromtenidalbergiaispecies AT haishanhe studyontheextractionandidentificationofdnafromtenidalbergiaispecies AT jianqiu studyontheextractionandidentificationofdnafromtenidalbergiaispecies |