Plastome sequencing of Gymnanthemum amygdalinum and phylogenetic analysis of 17 newly assembled Asteraceae plastomes

Abstract

Asteraceae (sunflower) is a large and diverse family of flowering plants that include numerous economically important and ornamental species. Thorough systematics research has identified 13 subfamilies within Asteraceae. However, some taxa still lack comprehensive genomic data, which hampers the understanding of relationships between these subfamilies. This study sequenced the complete plastome of Gymnanthemum amygdalinum from Vietnam. Additionally, plastomes of 16 Asteraceae species were newly assembled using existing whole genome sequencing data from GenBank. All 17 examined Asteraceae plastomes displayed a quadripartite structure, with lengths ranging from 151,340 bp to 153,670 bp. Of these, G. amygdalinum exhibited a loss of ndhF gene and an expansion of inverted repeat regions, resulting in a smaller small-single copy region. The large single-copy regions of the 16 Asteraceae plastomes, excluding D. popayanense from Barnadesioideae subfamily, showed two inversions: one between the trnE-UUC and trnG-UCC, and another between trnE-UUC and trnC-GCA regions. Our plastome-based phylogenetic analysis of 42 Asteraceae species supported the nuclear gene-based taxonomic classification. However, discrepancies were observed in the phylogenetic relationship among certain less abundant subfamilies. The newly obtained genomic data provide novel insights into the phylogenetic relationships across species in Asteraceae.