De novo genome assembly of Tectona grandis (Teak) with 2993 scaffolds

Teak (Tectona grandis L. f.) is one of the precious bench mark tropical hardwood having qualities of durability, strength and visual pleasantries. Natural teak populations harbour a variety of characteristics that determine their economic, ecological and environmental importance. Sequencing of whole nuclear genome of teak provides a platform for functional analyses and development of genomic tools in applied tree improvement. A draft genome of 317 Mb was assembled at 151× coverage and annotated 36, 172 protein-coding genes. Approximately about 11.18% of the genome was repetitive. Microsatellites or simple sequence repeats (SSRs) are undoubtedly the most informative markers in genotyping, genetics and applied breeding applications. We generated 182,712 SSRs at the whole genome level, of which, 170,574 perfect SSRs were found; 16,252 perfect SSRs showed in silico polymorphisms across six genotypes suggesting their promising use in genetic conservation and tree improvement programmes. Genomic SSR markers developed in this study have high potential in advancing conservation and management of teak genetic resources. Phylogenetic studies confirmed the taxonomic position of the genus Tectona within the family Lamiaceae. Interestingly, estimation of divergence time inferred that the Miocene origin of the Tectona genus to be around 21.4508 million years ago.柚木（Tectona grandis L. f.）是兼具耐用性、结构强度与视觉美感的珍贵标杆级热带硬木之一。天然柚木种群拥有多样的特性，这些特性决定了其经济、生态与环境价值。对柚木全核基因组进行测序，可为功能分析以及林木改良应用中的基因组工具开发提供核心研究平台。本研究以151倍测序覆盖度组装出大小为317 Mb的基因组草图，并注释得到36172个蛋白质编码基因；基因组中约11.18%为重复序列。微卫星（microsatellites）或简单序列重复（simple sequence repeats，SSRs）无疑是基因型分析、遗传学研究及应用育种领域中最具信息价值的分子标记。本研究在全基因组水平开发获得182712个SSRs，其中170574个为完美型SSRs；在6个基因型中检测到16252个完美型SSRs存在计算机模拟多态性，表明其在遗传保护与林木改良项目中具备良好的应用前景。本研究开发的基因组SSR标记，在推动柚木遗传资源的保护与管理方面具有较高应用潜力。系统发育研究确认了柚木属（Tectona）在唇形科（Lamiaceae）中的分类学地位。值得注意的是，分化时间估算结果显示，柚木属的中新世起源时间约为2145.08万年前。