Supporting data for "The genomes of <i>Dahlia pinnata, Cosmos bipinnatus</i> and <i>Bidens alba</i> in tribe Coreopsideae provide insights into polyploid evolution and inulin biosynthesis"

The Coreopsideae tribe, a subset of the Asteraceae family, encompasses economically vital genera like Dahlia, Cosmos, and Bidens, which are widely employed in medicine, horticulture, ecology, and food applications. Nevertheless, the lack of reference genomes hinders evolutionary and biological investigations in this tribe. <br>Here, we present three haplotype-resolved chromosome-level reference genomes of the tribe Coreopsideae, including two famous flower plants <i>Dahlia pinnata</i> and <i>Cosmos bipinnatus</i>, and one invasive weed plant <i>Bidens alba</i>, with assembled genome sizes 3.93 G, 1.02 G and 1.87 G, respectively. We found that <i>Gypsy</i> transposable elements contribute mostly to the larger genome size of <i>D. pinnata</i>, and multiple chromosome rearrangements have occurred in tribe Coreopsideae. Besides the shared whole genome duplication (WGD-2) in the Heliantheae alliance, our analyses showed that <i>D. pinnata</i> and <i>B. alba</i> each underwent an independent recent WGD-3 event: in <i>D. pinnata</i> it is more likely to be a self-WGD, while in <i>B. alba</i> it is from the hybridization of two ancestor species. Further, we identified key genes in the inulin metabolic pathway, and found that the pseudogenization of <i>1-FEH1</i> and <i>1-FEH2</i> genes in <i>D. pinnata</i> and the deletion of three key residues of 1-FFT proteins in <i>C. bipinnatus</i> and <i>B. alba</i> may probably explain why <i>D. pinnata</i> produces much more inulin than the other two plants. <br>Collectively, the genomic resources for the Coreopsideae tribe will promote phylogenomics in Asteraceae plants, facilitate ornamental molecular breeding improvements and inulin production, and help prevent invasive weeds.

菊科（Asteraceae）下的金鸡菊族（Coreopsideae）包含大丽花属（Dahlia）、秋英属（Cosmos）、鬼针草属（Bidens）等具有重要经济价值的类群，这些类群在医药、园艺、生态学及食品领域均有广泛应用。然而，参考基因组的缺失阻碍了该族的演化与生物学研究。
本研究报道了金鸡菊族3个单倍型解析的染色体级参考基因组，分别为两种知名观赏花卉——大丽花（*Dahlia pinnata*）和秋英（*Cosmos bipinnatus*），以及一种入侵性杂草银叶鬼针草（*Bidens alba*），组装后的基因组大小分别为3.93 G、1.02 G和1.87 G。研究发现，Gypsy转座元件是导致大丽花基因组更大的主要原因，且金鸡菊族内发生了多次染色体重排。除向日葵族类群共有的全基因组复制事件WGD-2外，分析显示大丽花和银叶鬼针草各自经历了一次独立的近期全基因组复制事件WGD-3：大丽花的WGD-3更可能为同源多倍化，而银叶鬼针草的WGD-3则来源于两个祖先物种的杂交。此外，本研究鉴定了菊糖代谢通路中的关键基因，发现大丽花中*1-FEH1*和*1-FEH2*基因的假基因化，以及秋英和银叶鬼针草中1-FFT蛋白的三个关键残基缺失，或可解释为何大丽花的菊糖产量远高于另外两种植物。
综上，金鸡菊族的基因组资源将推动菊科植物的系统基因组学研究，助力观赏植物分子育种改良与菊糖生产，并为入侵杂草防控提供支持。