Ministry of Education Key Laboratory for Transboundary Ecosecurity of Southwest China, Yunnan Key Laboratory of Plant Reproductive Adaptation and Evolutionary Ecology, Institute of Biodiversity, School of Ecology and Environmental Science, Yunnan University, Kunming, Yunnan, 650504, China.
College of Agriculture and Biotechnology, Yunnan Agricultural University, Kunming, Yunnan, 650500, China.
BMC Genom Data. 2024 Aug 27;25(1):77. doi: 10.1186/s12863-024-01261-7.
Roscoea is a Sino-Himalayan alpine genus in pantropical family Zingiberaeae. As traditional Tibetan medicinal plants, many species of this genus are threatened by digging, logging, land clearance, grazing and climate change. Roscoea debilis is an endemic species in the Hengduan Mountains with a narrow distribution range. In this study, the assembled and annotated genome of Roscoea was presented in order to furnish significant resources for comparative and functional genomic investigations. The first complete reference genome of Roscoea is expected to shed light on research on conservation and evolutionary biology.
A chromosome-level genome of 1601.04 Mb was obtained for R. debilis by combining Illumina short reads (107.28 Gb) and PacBio Hi-Fi reads (64.08 Gb), achieving high-quality sequencing coverage of roughly 67 × and 40 ×. The assembly was additionally assisted by 271.65 Gb Hi-C data (169 ×), which resulted in a contig N50 of 136.17 Mb and a scaffold N50 of 90.48 Mb. Benchmarking Universal Single-Copy Orthologs (BUSCO) assessment results revealed that most of the core embryophyta genes (98.7%) in the BUSCO dataset (embryophyta_odb10) were successfully identified. Additionally, 96.44% of the genomic sequences were accurately mapped onto twelve pseudochromosomes.
罗莎草属是姜科姜黄族的一个横断山区泛热带高山特有属。作为传统的藏药植物，该属的许多物种受到挖掘、伐木、土地清理、放牧和气候变化的威胁。柔弱罗莎草是横断山区特有的物种，分布范围狭窄。本研究对柔弱罗莎草进行了基因组组装和注释，为比较和功能基因组研究提供了重要资源。第一个完整的罗莎草属参考基因组有望为保护和进化生物学研究提供新的思路。
通过整合 Illumina 短读序列（107.28Gb）和 PacBio Hi-Fi 读长（64.08Gb），获得了柔弱罗莎草的染色体级基因组，大小为 1601.04Mb，测序深度约为 67×和 40×。组装还得到了 271.65Gb Hi-C 数据（169×）的辅助，最终的 contig N50 为 136.17Mb，scaffold N50 为 90.48Mb。基于通用单拷贝同源基因（BUSCO）的评估结果表明，在 BUSCO 数据集（embryophyta_odb10）中，大多数核心胚植物基因（98.7%）都得到了成功的鉴定。此外，96.44%的基因组序列可以准确地映射到 12 条假染色体上。
