Central South University of Forestry and Technology, 498 Shaoshan South Rd, Changsha 410004, China.
Institute of Economic Forest, Yunnan Academy of Forestry and Grassland, 2 Lan'an Rd, Kunming 650201, China.
Gigascience. 2020 Feb 1;9(2). doi: 10.1093/gigascience/giaa006.
Juglans sigillata, or iron walnut, belonging to the order Juglandales, is an economically important tree species in Asia, especially in the Yunnan province of China. However, little research has been conducted on J. sigillata at the molecular level, which hinders understanding of its evolution, speciation, and synthesis of secondary metabolites, as well as its wide adaptability to its plateau environment. To address these issues, a high-quality reference genome of J. sigillata would be useful.
To construct a high-quality reference genome for J. sigillata, we first generated 38.0 Gb short reads and 66.31 Gb long reads using Illumina and Nanopore sequencing platforms, respectively. The sequencing data were assembled into a 536.50-Mb genome assembly with a contig N50 length of 4.31 Mb. Additionally, we applied BioNano technology to identify contacts among contigs, which were then used to assemble contigs into scaffolds, resulting in a genome assembly with scaffold N50 length of 16.43 Mb and contig N50 length of 4.34 Mb. To obtain a chromosome-level genome assembly, we constructed 1 Hi-C library and sequenced 79.97 Gb raw reads using the Illumina HiSeq platform. We anchored ∼93% of the scaffold sequences into 16 chromosomes and evaluated the quality of our assembly using the high contact frequency heat map. Repetitive elements account for 50.06% of the genome, and 30,387 protein-coding genes were predicted from the genome, of which 99.8% have been functionally annotated. The genome-wide phylogenetic tree indicated an estimated divergence time between J. sigillata and Juglans regia of 49 million years ago on the basis of single-copy orthologous genes.
We provide the first chromosome-level genome for J. sigillata. It will lay a valuable foundation for future research on the genetic improvement of J. sigillata.
胡桃属，或铁核桃，属于胡桃目，是亚洲一种重要的经济树种，特别是在中国云南省。然而，在分子水平上对 J. sigillata 的研究甚少，这阻碍了对其进化、物种形成和次生代谢物合成以及对高原环境的广泛适应性的理解。为了解决这些问题，构建 J. sigillata 的高质量参考基因组将是有用的。
为了构建 J. sigillata 的高质量参考基因组，我们首先使用 Illumina 和 Nanopore 测序平台分别生成了 38.0 Gb 的短读和 66.31 Gb 的长读。测序数据组装成一个 536.50-Mb 的基因组组装，其 contig N50 长度为 4.31 Mb。此外，我们应用生物纳米技术来识别contigs 之间的接触，然后将 contigs 组装成 scaffolds，得到一个基因组组装，其 scaffold N50 长度为 16.43 Mb，contig N50 长度为 4.34 Mb。为了获得染色体水平的基因组组装，我们构建了一个 Hi-C 文库，并使用 Illumina HiSeq 平台测序了 79.97 Gb 的原始读数。我们将大约 93%的支架序列锚定到 16 条染色体上，并使用高接触频率热图评估了我们的组装质量。重复元件占基因组的 50.06%，从基因组中预测了 30387 个蛋白质编码基因，其中 99.8%具有功能注释。基于单拷贝直系同源基因的全基因组系统发育树表明，J. sigillata 和 Juglans regia 之间的估计分化时间为 4900 万年前。
我们提供了 J. sigillata 的第一个染色体水平的基因组。它将为未来 J. sigillata 的遗传改良研究奠定宝贵的基础。
