Institute for Advanced Study, Chengdu University, Chengdu 610106, China.
Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China.
DNA Res. 2021 Oct 11;28(6). doi: 10.1093/dnares/dsab022.
Caper spurge, Euphorbia lathyris L., is an important energy crop and medicinal crop. Here, we generated a high-quality, chromosome-level genome assembly of caper spurge using Oxford Nanopore sequencing, Illumina sequencing, and Hi-C technology. The final genome assembly was ∼988.9 Mb in size, 99.8% of which could be grouped into 10 pseudochromosomes, with contig and scaffold N50 values of 32.6 and 95.7 Mb, respectively. A total of 651.4 Mb repetitive sequences and 36,342 protein-coding genes were predicted in the genome assembly. Comparative genomic analysis showed that caper spurge and castor bean clustered together. We found that no independent whole-genome duplication event had occurred in caper spurge after its split from the castor bean, and recent substantial amplification of long terminal repeat retrotransposons has contributed significantly to its genome expansion. Furthermore, based on gene homology searching, we identified a number of candidate genes involved in the biosynthesis of fatty acids and triacylglycerols. The reference genome presented here will be highly useful for the further study of the genetics, genomics, and breeding of this high-value crop, as well as for evolutionary studies of spurge family and angiosperms.
刺叶桂木，Euphorbia lathyris L.，是一种重要的能源作物和药用作物。在这里，我们使用牛津纳米孔测序、Illumina 测序和 Hi-C 技术生成了刺叶桂木的高质量染色体水平基因组组装。最终的基因组组装大小约为 988.9Mb，其中 99.8%可以分组到 10 条假染色体中，contig 和 scaffold N50 值分别为 32.6Mb 和 95.7Mb。在基因组组装中预测了 651.4Mb 的重复序列和 36342 个蛋白质编码基因。比较基因组分析表明，刺叶桂木和蓖麻聚类在一起。我们发现，在与蓖麻分离后，刺叶桂木没有发生独立的全基因组复制事件，最近长末端重复反转录转座子的大量扩增对其基因组的扩张有重要贡献。此外，基于基因同源性搜索，我们鉴定了一些参与脂肪酸和三酰基甘油生物合成的候选基因。这里提供的参考基因组将对进一步研究这种高价值作物的遗传学、基因组学和育种，以及对大戟科和被子植物的进化研究非常有用。
