PDF(Pubmed)
Abstract：
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.
Here, we present 3 haplotype-resolved chromosome-level reference genomes of the tribe Coreopsideae, including 2 popular flowering plants (Dahlia pinnata and Cosmos bipinnatus) and 1 invasive weed plant (Bidens alba), with assembled genome sizes 3.93 G, 1.02 G, and 1.87 G, respectively. We found that Gypsy transposable elements contribute mostly to the larger genome size of D. pinnata, 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 D. pinnata and B. alba each underwent an independent recent WGD-3 event: in D. pinnata, it is more likely to be a self-WGD, while in B. alba, it is from the hybridization of 2 ancestor species. Further, we identified key genes in the inulin metabolic pathway and found that the pseudogenization of 1-FEH1 and 1-FEH2 genes in D. pinnata and the deletion of 3 key residues of 1-FFT proteins in C. bipinnatus and B. alba may probably explain why D. pinnata produces much more inulin than the other 2 plants.
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.
Here, we present 3 haplotype-resolved chromosome-level reference genomes of the tribe Coreopsideae, including 2 popular flowering plants (Dahlia pinnata and Cosmos bipinnatus) and 1 invasive weed plant (Bidens alba), with assembled genome sizes 3.93 G, 1.02 G, and 1.87 G, respectively. We found that Gypsy transposable elements contribute mostly to the larger genome size of D. pinnata, 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 D. pinnata and B. alba each underwent an independent recent WGD-3 event: in D. pinnata, it is more likely to be a self-WGD, while in B. alba, it is from the hybridization of 2 ancestor species. Further, we identified key genes in the inulin metabolic pathway and found that the pseudogenization of 1-FEH1 and 1-FEH2 genes in D. pinnata and the deletion of 3 key residues of 1-FFT proteins in C. bipinnatus and B. alba may probably explain why D. pinnata produces much more inulin than the other 2 plants.
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.
摘要：
背景：Coreopsideae部落，菊科的一个子集，包括像大丽花这样重要的经济属，宇宙,还有Bidens,广泛用于医学，园艺,生态学,和食品应用。然而，缺乏参考基因组阻碍了该部落的进化和生物学研究。
结果：这里，我们提出了3个单倍型分辨的染色体水平参考基因组的部落科雷氏，包括2种流行的开花植物（大丽花和Cosmosbipinnatus）和1种入侵杂草植物（Bidensalba），组装的基因组大小为3.93G，1.02G,和1.87G，分别。我们发现吉普赛转座因子主要有助于D.pinnata的更大基因组大小，并且在Coreopsideae部落中发生了多个染色体重排。除了Heliantheae联盟中共享的全基因组复制（WGD-2）之外，我们的分析表明，D.pinnata和B.alba各自经历了一个独立的最近WGD-3事件：在D.pinnata，它更有可能是一个自我WGD，而在B.alba,它来自2种祖先物种的杂交。Further,我们确定了菊粉代谢途径中的关键基因，并发现D.pinnata中1-FEH1和1-FEH2基因的假基因化以及C.bipinnatus和B.alba中1-FFT蛋白的3个关键残基的缺失可能解释了为什么D.pinnata比其他2种植物产生更多的菊粉。
结论：总的来说，Coreopsideae部落的基因组资源将促进菊科植物的系统基因组学，促进观赏分子育种改进和菊粉生产，并帮助防止入侵杂草。
结果：这里，我们提出了3个单倍型分辨的染色体水平参考基因组的部落科雷氏，包括2种流行的开花植物（大丽花和Cosmosbipinnatus）和1种入侵杂草植物（Bidensalba），组装的基因组大小为3.93G，1.02G,和1.87G，分别。我们发现吉普赛转座因子主要有助于D.pinnata的更大基因组大小，并且在Coreopsideae部落中发生了多个染色体重排。除了Heliantheae联盟中共享的全基因组复制（WGD-2）之外，我们的分析表明，D.pinnata和B.alba各自经历了一个独立的最近WGD-3事件：在D.pinnata，它更有可能是一个自我WGD，而在B.alba,它来自2种祖先物种的杂交。Further,我们确定了菊粉代谢途径中的关键基因，并发现D.pinnata中1-FEH1和1-FEH2基因的假基因化以及C.bipinnatus和B.alba中1-FFT蛋白的3个关键残基的缺失可能解释了为什么D.pinnata比其他2种植物产生更多的菊粉。
结论：总的来说，Coreopsideae部落的基因组资源将促进菊科植物的系统基因组学，促进观赏分子育种改进和菊粉生产，并帮助防止入侵杂草。
