Setsuko Suzuki, Yoshimura Kensuke, Ueno Saneyoshi, Worth James Raymond Peter, Ujino-Ihara Tokuko, Katsuki Toshio, Noshiro Shuichi, Fujii Tomoyuki, Arai Takahisa, Yoshimaru Hiroshi
Department of Forest Molecular Genetics and Biotechnology, Forestry and Forest Products Research Institute, Forest Research and Management Organization, Ibaraki, Japan.
Tama Forest Science Garden, Forestry and Forest Products Research Institute, Forest Research and Management Organization, Tokyo, Japan.
Mol Ecol Resour. 2023 May;23(4):855-871. doi: 10.1111/1755-0998.13748. Epub 2023 Jan 24.
DNA barcode databases are increasingly available for a range of organisms, facilitating the wide application of DNA barcode-based studies. Here we announce the development of a comprehensive DNA barcode reference library of Japanese native woody seed plants representing 43 orders, 99 families, 303 genera and 834 species, and comprising 77.3% of the genera and 72.2% of the species of native woody seed plants in Japan. A total of 6216 plant specimens were collected from 223 sites across the subtropical, temperate, boreal and alpine biomes in Japan with most species represented by multiple accessions. This reference library utilized three chloroplast DNA regions (rbcL, trnH-psbA and matK) and consists of 14,403 barcode sequences. Individual regions varied in their identification rates, with species-level and genus-level rates for rbcL, trnH-psbA and matK based on blast being 57.4%/96.2%, 78.5%/99.1% and 67.8%/98.1%, respectively. Identification rates were higher using region combinations, with total species-level rates for two region combinations (rbcL & trnH-psbA, rbcL & matK and trnH-psbA & matK) ranging between 90.6% and 95.8%, and for all three regions being equal to 98.6%. Genus-level identification rates were even higher, ranging between 99.7% and 100% for two region combinations and being 100% for the three regions. These results indicate that this DNA barcode reference library is an effective resource for investigations of native woody seed plants in Japan using DNA barcodes and provides a useful template for the development of libraries for other components of the Japanese flora.
DNA条形码数据库越来越多地应用于一系列生物，促进了基于DNA条形码研究的广泛应用。在此，我们宣布已开发出一个全面的日本本土木本种子植物DNA条形码参考文库，该文库涵盖43目、99科、303属和834种，占日本本土木本种子植物属的77.3%和种的72.2%。总共从日本亚热带、温带、寒带和高山生物群落的223个地点收集了6216份植物标本，大多数物种有多个样本。该参考文库利用了三个叶绿体DNA区域（rbcL、trnH-psbA和matK），由14403条条形码序列组成。各个区域的识别率有所不同，基于blast的rbcL、trnH-psbA和matK的物种水平和属水平识别率分别为57.4%/96.2%、78.5%/99.1%和67.8%/98.1%。使用区域组合时识别率更高，两个区域组合（rbcL & trnH-psbA、rbcL & matK和trnH-psbA & matK）的总物种水平识别率在90.6%至95.8%之间，三个区域的总物种水平识别率为98.6%。属水平识别率更高，两个区域组合的识别率在99.7%至100%之间，三个区域的识别率为100%。这些结果表明，这个DNA条形码参考文库是利用DNA条形码研究日本本土木本种子植物的有效资源，并为开发日本植物群其他组成部分的文库提供了有用的模板。
