A de novo assembled chromosome-level genome of Ainsliaea gracilis Franch. (Pertyeae, Asteraceae) and its comparative phylogenomics within Asteraceae

The genus Ainsliaea DC. is the largest group in the tribe Pertyeae (Pertyoideae, Asteraceae). Ainsliaea gracilis Franch., a medicinal plant endemic to China, is used as a traditional Chinese medicine to treat hemoptysis, phlegmon, and traumatic injuries. However, genomic research of molecular mechanisms of medicinal secondary metabolite biosynthesis for this species is limited by the absence of nuclear genome. To address this gap, we provided a high-quality chromosome-level genome of A. gracilis with comprehensive structural and functional annotations. The genome assembly obtained by PacBio HiFi and Illumina Hi-C sequencing technologies was 1,161 Mb and anchored onto the 13 pseudochromosomes, achieving an anchor rate of 99.14%. The contig and scaffold N50 values were 60.20 Mb and 92.53 Mb, respectively. The BUSCO completeness score was 97.70%. The LTR Assembly Index (LAI) score was 22.75, surpassing the high-quality assembly threshold of 20. The genome annotations indicated 35,803 protein-coding genes (PCGs), 6,058 non-coding RNA genes (ncRNAs) and 72.20% repetitive elements. Gene family expansions and contractions were observed among 13 Asteraceae species, with contractions generally exceeding expansions. Phylogenomic analysis revealed that Pertyoideae was identified as the basal group of Asteraceae. Both A. gracilis and four Carduoideae species experienced a single, most recent whole genome duplication event. Molecular clock estimations pinpointed the divergence of the four subfamilies at 43.98 million years ago. This study fills a critical gap in the nuclear genome data of Pertyoideae (Asteraceae). It provides not only a high-quality genomic resource for developing molecular markers and exploring gene clusters related to medicinal secondary metabolite, but also proposes a practical framework for assembling other complex genomes within Pertyoideae. This work lays a solid foundation for the future phylogenomic studies of Pertyoideae and Asteraceae.