Erigeron breviscapus is an important medicinal plant in Compositae and the first species to realize the whole process from the decoding of the draft genome sequence to scutellarin biosynthesis in yeast. However, the previous low‐quality genome assembly has hindered the optimization of candidate genes involved in scutellarin synthesis and the development of molecular‐assisted breeding based on the genome. Here, the E. breviscapus genome was updated using PacBio RSII sequencing data and Hi‐C data, and increased in size from 1.2 Gb to 1.43 Gb, with a scaffold N50 of 156.82 Mb and contig N50 of 140.95 kb, and a total of 43,514 protein‐coding genes were obtained and oriented onto nine pseudo‐chromosomes, thus becoming the third plant species assembled to chromosome level after sunflower and lettuce in Compositae. Fourteen genes with evidence for positive selection were identified and found to be related to leaf morphology, flowering and secondary metabolism. The number of genes in some gene families involved in flavonoid biosynthesis in E. breviscapus have been significantly expanded. In particular, additional candidate genes involved in scutellarin biosynthesis, such as flavonoid‐7‐O‐glucuronosyltransferase genes (F7GATs) were identified using updated genome. In addition, three candidate genes encoding indole‐3‐pyruvate monooxygenase YUCCA2 (YUC2), serine carboxypeptidase‐like 18 (SCPL18), and F‐box protein (FBP), respectively, were identified to be probably related to leaf development and flowering by resequencing 99 individuals. These results provided a substantial genetic basis for improving agronomic and quality traits of E. breviscapus, and provided a platform for improving other draft genome assemblies to chromosome‐level.

中文翻译：

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灯盏花高品质基因组为菊科草本植物提供参考

灯盏花是菊科重要的药用植物，是第一个实现从基因组序列解码到酵母中灯盏花素生物合成全过程的物种。然而，之前低质量的基因组组装阻碍了参与灯盏花素合成的候选基因的优化和基于基因组的分子辅助育种的发展。在这里，E. breviscapus使用PacBio RSII测序数据和Hi-C数据更新基因组，大小从1.2 Gb增加到1.43 Gb，支架N50为156.82 Mb，contig N50为140.95 kb，共获得43,514个蛋白质编码基因并定向到9条假染色体上，成为菊科中继向日葵和生菜之后第三个组装到染色体水平的植物物种。鉴定了具有阳性选择证据的 14 个基因，发现它们与叶片形态、开花和次生代谢有关。参与E. breviscapus中类黄酮生物合成的一些基因家族中的基因数量已显着增加。特别是，参与灯盏花素生物合成的其他候选基因，如 flavonoid-7- O使用更新的基因组鉴定-葡萄糖醛酸基转移酶基因（F7GATs）。此外，通过鉴定分别编码吲哚-3-丙酮酸单加氧酶 YUCCA2 (YUC2)、丝氨酸羧肽酶样 18 (SCPL18) 和 F-box 蛋白 (FBP) 的三个候选基因可能与叶片发育和开花有关。重新测序 99 个人。这些结果为改善短叶松的农艺性状和品质性状提供了坚实的遗传基础，并为将其他基因组组装草图提高到染色体水平提供了平台。