A DNA barcode reference library for the native woody seed plants of Japan

Abstract

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.

Plant DNA barcode library for native flowering plants in the arid region of northwestern China

“…A local library, including all the species in one region/flora, is essential for large‐scale species identification. After nearly two decades of development, many regional DNA barcode libraries have been established, such as in Australia, Canada, Japan, Norway and the UK (Alsos et al, 2020; Costion et al, 2016; Jones et al, 2021; Kuzmina et al, 2017; Setsuko et al, 2023). However, publicly available vascular plant records still need to be increased (Govaerts et al, 2021; Wilkinson et al, 2017).…”

Molecular Structure and Variation Characteristics of the Plastomes from Six Malus baccata (L.) Borkh. Individuals and Comparative Genomic Analysis with Other Malus Species

“…The chloroplast genome has a double-chained structure, and its size and composition are stable [ 42 ]. Due to the influence of gene flow and DNA mutation, the chloroplast genome carries good marker information that can be used as a powerful tool for the study of population evolution, species classification and genetic engineering [ 43 ].…”

Chloroplast genome-based genetic resources for Japan’s threatened subalpine forests via genome skimming

“…This is one of the first studies to develop ultra barcodes for species representing a distinct biome and contributes to an increasing trend to assemble whole chloroplast genomes for genetic resource development studies. For example, Song et al (2023) included whole chloroplast genomes, along with traditional short Sanger-based fragments, in a barcode library of the flowering plants of arid NW China while Krawczyk et al (2018) used whole chloroplast genomes in a barcode library for the genus Stipa. However, studies investigating within species variation of the whole chloroplast genome remain rare.…”

“…Whole mitochondria (De Mandal et al, 2014) and chloroplast (Song et al, 2023) genomes are now being incorporated into barcode libraries (called ultra barcodes) providing greater power to understand the phylogenetic affinity of taxa and increase the ability to identify the small fragments of organelle DNA derived from ancient or environmental samples. The relative low cost of genome skimming means that the whole organelle genome of multiple samples can feasibly be obtained, facilitating the discovery of potentially phylogenetically informative characters and mutational hotspots for the taxonomic level of interest (e.g.…”