Department of Convergent Bioscience and Informatics, College of Bioscience and Biotechnology, Chungnam National University, Daejeon, 34134, Korea.
Korea Polar Research Institute, Incheon, 21990, Korea.
Sci Data. 2024 Jul 18;11(1):793. doi: 10.1038/s41597-024-03569-6.
To understand the genomic characteristics of Arctic plants, we generated 28-44 Gb of short-read sequencing data from 13 Arctic plants collected from the High Arctic Svalbard. We successfully estimated the genome sizes of eight species by using the k-mer-based method (180-894 Mb). Among these plants, the mountain sorrel (Oxyria digyna) and Greenland scurvy grass (Cochlearia groenlandica) had relatively small genome sizes and chromosome numbers. We obtained 45 × and 121 × high-fidelity long-read sequencing data. We assembled their reads into high-quality draft genomes (genome size: 561 and 250 Mb; contig N50 length: 36.9 and 14.8 Mb, respectively), and correspondingly annotated 43,105 and 29,675 genes using ~46 and ~85 million RNA sequencing reads. We identified 765,012 and 88,959 single-nucleotide variants, and 18,082 and 7,698 structural variants (variant size ≥ 50 bp). This study provided high-quality genome assemblies of O. digyna and C. groenlandica, which are valuable resources for the population and molecular genetic studies of these plants.
为了了解北极植物的基因组特征，我们从采集自北极斯瓦尔巴群岛高海拔地区的 13 种北极植物中生成了 28-44Gb 的短读测序数据。我们成功地使用基于 k-mer 的方法估算了其中 8 个物种的基因组大小（180-894Mb）。在这些植物中，山酢浆草（Oxyria digyna）和格陵兰酸模（Cochlearia groenlandica）的基因组较小，染色体数量也较少。我们获得了 45×和 121×的高保真度长读测序数据。我们将这些reads 组装成高质量的草图基因组（基因组大小分别为 561 和 250Mb；contig N50 长度分别为 36.9 和 14.8Mb），并使用约 46 和 8500 万条 RNA 测序reads 分别注释了 43105 和 29675 个基因。我们鉴定出了 765012 个和 88959 个单核苷酸变异，以及 18082 个和 7698 个结构变异（变异大小≥50bp）。本研究提供了高质量的 O. digyna 和 C. groenlandica 基因组组装，为这些植物的种群和分子遗传学研究提供了有价值的资源。
