Genome sequencing reveals chromosome fusion and extensive expansion of genes related to secondary metabolism in Artemisia argyi,Plant Biotechnology Journal

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Genome sequencing reveals chromosome fusion and extensive expansion of genes related to secondary metabolism in Artemisia argyi
Plant Biotechnology Journal ( IF 10.1 ) Pub Date : 2022-06-11 , DOI: 10.1111/pbi.13870
Yuhuan Miao ₁ , Dandan Luo ₁ , Tingting Zhao ₁ , Hongzhi Du ₁ , Zhenhua Liu ₂ , Zhongping Xu ₃ , Lanping Guo ₄ , Changjie Chen ₁ , Sainan Peng ₁ , Jin Xin Li ₁ , Lin Ma ₁ , Guogui Ning ₅ , Dahui Liu ₁ , Luqi Huang ₄

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Artemisia argyi, as famous as Artemisia annua, is a medicinal plant with huge economic value in the genus of Artemisia and has been widely used in the world for about 3000 years. However, a lack of the reference genome severely hinders the understanding of genetic basis for the active ingredient synthesis of A. argyi. Here, we firstly report a complex chromosome-level genome assembly of A. argyi with a large size of 8.03 Gb, with features of high heterozygosity (2.36%), high repetitive sequences (73.59%) and a huge number of protein-coding genes (279 294 in total). The assembly reveals at least three rounds of whole-genome duplication (WGD) events, including a recent WGD event in the A. argyi genome, and a recent burst of transposable element, which may contribute to its large genome size. The genomic data and karyotype analyses confirmed that A. argyi is an allotetraploid with 34 chromosomes. Intragenome synteny analysis revealed that chromosomes fusion event occurred in the A. argyi genome, which elucidates the changes in basic chromosome numbers in Artemisia genus. Significant expansion of genes related to photosynthesis, DNA replication, stress responses and secondary metabolism were identified in A. argyi, explaining the extensive environmental adaptability and rapid growth characteristics. In addition, we analysed genes involved in the biosynthesis pathways of flavonoids and terpenoids, and found that extensive gene amplification and tandem duplication contributed to the high contents of metabolites in A. argyi. Overall, the reference genome assembly provides scientific support for evolutionary biology, functional genomics and breeding in A. argyi and other Artemisia species.

中文翻译：

基因组测序揭示了艾蒿的染色体融合和与次生代谢相关的基因的广泛扩展

艾草与青蒿齐名，是蒿属植物中具有巨大经济价值的药用植物，在世界范围内广泛应用已有约3000年的历史。然而，参考基因组的缺乏严重阻碍了对艾草活性成分合成的遗传基础的理解。在此，我们首次报道了艾叶复杂的染色体水平基因组组装，大小为8.03 Gb，具有高杂合度（2.36%）、高重复序列（73.59%）和大量蛋白质编码基因的特点（总计 279 294）。该组装揭示了至少三轮全基因组复制（WGD）事件，包括最近在艾叶基因组中发生的一次WGD事件，以及最近爆发的转座元件，这可能导致其基因组规模较大。基因组数据和核型分析证实艾草是具有34条染色体的异源四倍体。基因组内同线性分析揭示了艾属基因组中发生了染色体融合事件，阐明了蒿属植物基本染色体数目的变化。艾叶中与光合作用、DNA复制、应激反应和次生代谢相关的基因显着扩增，解释了艾叶广泛的环境适应性和快速生长的特征。此外，我们还分析了黄酮类和萜类化合物生物合成途径中涉及的基因，发现广泛的基因扩增和串联复制导致了艾草中高含量的代谢物。总体而言，参考基因组组装为艾叶和其他蒿属物种的进化生物学、功能基因组学和育种提供了科学支持。

更新日期：2022-06-11

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