Ecology and Evolutionary Biology Department, University of California, Santa Cruz, Santa Cruz, CA, United States.
Department of Biological Sciences, California State Polytechnic University, Humboldt, Arcata, CA, United States.
J Hered. 2023 May 25;114(3):286-293. doi: 10.1093/jhered/esad018.
The spiral gingers (Costus L.) are a pantropical genus of herbaceous perennial monocots; the Neotropical clade of Costus radiated rapidly in the past few million years into over 60 species. The Neotropical spiral gingers have a rich history of evolutionary and ecological research that can motivate and inform modern genetic investigations. Here, we present the first 2 chromosome-level genome assemblies in the genus, for C. pulverulentus and C. lasius, and briefly compare their synteny. We assembled the C. pulverulentus genome from a combination of short-read data, Chicago and Dovetail Hi-C chromatin-proximity sequencing, and alignment with a linkage map. We annotated the genome by mapping a C. pulverulentus transcriptome and querying mapped transcripts against a protein database. We assembled the C. lasius genome with Pacific Biosciences HiFi long reads and alignment to the C. pulverulentus genome. These 2 assemblies are the first published genomes for non-cultivated tropical plants. These genomes solidify the spiral gingers as a model system and will facilitate research on the poorly understood genetic basis of tropical plant diversification.
螺旋姜属（Costus L.）是一个分布于热带地区的草本多年生单子叶植物属；新热带地区的 Costus 分支在过去的几百万年中迅速辐射出超过 60 个物种。新热带地区的螺旋姜属具有丰富的进化和生态研究历史，这可以激发和为现代遗传研究提供信息。在这里，我们提供了该属的第一个 2 个染色体水平的基因组组装，分别是 C. pulverulentus 和 C. lasius，并简要比较了它们的基因同线性。我们通过结合短读数据、芝加哥和 Dovetail Hi-C 染色质接近测序以及与连锁图谱的比对，组装了 C. pulverulentus 基因组。我们通过映射 C. pulverulentus 转录组并将映射的转录本查询到蛋白质数据库来注释基因组。我们使用 Pacific Biosciences HiFi 长读长和与 C. pulverulentus 基因组的比对来组装 C. lasius 基因组。这两个组装是首次发表的非栽培热带植物的基因组。这些基因组使螺旋姜属成为一个模型系统，并将促进对热带植物多样化的遗传基础的研究，这些基础在很大程度上仍未被理解。
