Chloroplast genome-based genetic resources via genome skimming for the subalpine forests of Japan and adjacent regions.

Autor: Worth JRP; Department of Forest Molecular Genetics and Biotechnology Forestry and Forest Products Research Institute, Forest Research and Management Organization Tsukuba Ibaraki Japan., Kikuchi S; Hokkaido Research Centre Forestry and Forest Products Research Institute, Forest Research and Management Organization Sapporo Hokkaido Japan., Kanetani S; Kyushu Research Center Forestry and Forest Products Research Institute Kumamoto Japan., Takahashi D; Kawatabi Field Science Centre, Graduate School of Agricultural Science Tohoku University Sendai Miyagi Japan., Aizawa M; Department of Forest Science, School of Agriculture Utsunomiya University Utsunomiya Tochigi Japan., Marchuk EA; Botanical Garden-Institute of the Far Eastern Branch of the Russian Academy of Sciences Vladivostok Russia., Choi HJ; Department of Biology & Chemistry College of Natural Sciences, Changwon National University Changwon Korea., Polezhaeva MA; Institute of Plant and Animal Ecology Russian Academy of Sciences Yekaterinburg Russia., Sheiko VV; Sakhalin Branch of the Botanical Garden-Institute FEB RAS Yuzhno-Sakhalinsk Russia., Ueno S; Department of Forest Molecular Genetics and Biotechnology Forestry and Forest Products Research Institute, Forest Research and Management Organization Tsukuba Ibaraki Japan.
Jazyk: angličtina
Zdroj: Ecology and evolution [Ecol Evol] 2024 Jul 17; Vol. 14 (7), pp. e11584. Date of Electronic Publication: 2024 Jul 17 (Print Publication: 2024).
DOI: 10.1002/ece3.11584
Abstrakt: The Japanese subalpine zone is dominated by an ecologically important forest biome, subalpine coniferous forest, constituting a distinct assemblage of cold-tolerant angiosperm and conifer species. While being relatively intact compared to other forest biomes in Japan, subalpine coniferous forests are under significant threat from deer browsing, global warming and small population size effects. However, there is a severe lack of genetic resources available for this biome's major constituent plant species. This study aimed to develop chloroplast genome-based genetic resources for 12 widespread subalpine tree and shrub species (7 angiosperms and 5 conifers) via genome skimming of whole-genomic DNA using short reads (100-150 bp in length). For 10 species, whole chloroplast genomes were assembled via de novo-based methods from 4 to 10 individuals per species sampled from across their ranges in Japan and, for non-Japanese endemic species, elsewhere in northeast Asia. A total of 566 single nucleotide polymorphisms for Japanese samples and 768 for all samples (varying from 2 to 202 per species) were identified which were distributed in geographically restricted lineages in most species. In addition, between 9 and 58 polymorphic simple sequence repeat regions were identified per species. For two Ericaceae species ( Rhododendron brachycarpum and Vaccinium vitis-idaea ) characterised by large chloroplast genomes, de novo assembly failed, but single nucleotide polymorphisms could be identified using reference mapping. These data will be useful for genetic studies of species taxonomic relationships, investigating phylogeographic patterns within species, developing chloroplast-based markers for conservation genetic studies and has potential application for studies of environmental and ancient DNA.
Competing Interests: The authors declare no conflict of interest.
(© 2024 The Author(s). Ecology and Evolution published by John Wiley & Sons Ltd.)
Databáze: MEDLINE
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