Department of Forest Molecular Genetics and Biotechnology, Forestry and Forest Products Research Institute, Forest Research and Management Organization, 1 Matsunosato, Tsukuba, Ibaraki, 305-8687 Japan.
School of Agriculture, Meiji University, 1-1-1 Higashi-Mita, Tama-ku, Kawasaki, Kanagawa, 214-8571 Japan.
Plant Cell Physiol. 2018 Jun 1;59(6):1276-1284. doi: 10.1093/pcp/pcy058.
Todo-matsu (Abies sachalinensis) is one of the most important forestry species in Hokkaido, Japan and is distributed from near sea level to the alpine zone. Due to its wide spatial distribution, the species adapts to its environment, displaying phenotypes of ecological relevance. In order to identify candidate genes under natural selection, we collected the transcriptome from the female and male flower, leaf and inner bark. De novo assembly with 34.7 Gb of sequencing reads produced 158,542 transcripts from 69,618 loci, whose estimated coverage reached 95.6% of conserved eukaryotic genes. Homology searches against publicly available databases identified 134,190 (84.6%) transcripts with at least one hit. In total, 28,944 simple sequence repeats (SSRs) and 80,758 single nucleotide variants (SNVs) were detected from 23,570 (14.9%) and 25,366 (16.0%) transcripts, which were valuable for use in genetic analysis of the species. All the annotations were included in a relational database, TodoFirGene, which provides an interface for various queries and homology search, and can be accessed at http://plantomics.mind.meiji.ac.jp/todomatsu/. This database hosts not only the A. sachalinensis transcriptome but also links to the proteomes of 13 other species, allowing a comparative genomic study of plant species.
花柏（Abies sachalinensis）是日本北海道最重要的林业物种之一，分布于近海平面到高山带。由于其广泛的空间分布，该物种适应其环境，表现出具有生态相关性的表型。为了鉴定自然选择下的候选基因，我们从雌性和雄性花、叶和内皮中采集了转录组。使用 34.7Gb 的测序reads 进行从头组装，生成了来自 69618 个基因座的 158542 个转录本，其估计覆盖率达到了保守真核基因的 95.6%。与公共数据库的同源性搜索鉴定出 134190 个（84.6%）至少有一个命中的转录本。总共从 23570 个（14.9%）和 25366 个（16.0%）转录本中检测到 28944 个简单序列重复（SSR）和 80758 个单核苷酸变异（SNV），这些都可用于该物种的遗传分析。所有注释都包含在一个关系数据库 TodoFirGene 中，该数据库提供了各种查询和同源性搜索的接口，可在 http://plantomics.mind.meiji.ac.jp/todomatsu/ 访问。该数据库不仅包含 A. sachalinensis 的转录组，还链接到 13 个其他物种的蛋白质组，允许对植物物种进行比较基因组研究。
