Plastid genome variation with phylogenetic implications for the Helichrysum-Anaphalis-Pseudognaphalium (HAP) of the tribe Gnaphalieae (Asteraceae)

As the largest lineage in the tribe Gnaphalieae of Asteraceae, phylogenetic relationships within the Helichrysum-Anaphalis-Pseudognaphalium (HAP) remain poorly resolved. In this study we sequenced chloroplast genomes from 28 representative species from the HAP clade, performing comparative and phylogenetic analyses. Their chloroplast genomes ranged from 151,69 to 153,603 bp and possessed a typical quadripartite structure encoding 131-134 genes, including 87-89 protein-coding genes, 36-37 tRNA genes and 8 rRNA genes. The plastome data recognized the HAP into an early-diverging lineage and a large core clade. The latter was further separated into two subclades, namely core I and core II. Relatively small genomes with more insertion and fewer deletions were found in the early HAP lineage and Anaphalis taxa from core I. The small chloroplast genomes of the early lineage in the HAP clade potentially linked to their dry environmental adaptation in South Africa. The trnT-GGU gene was presented as pseudogenes in the early lineage and a subclade of core II but completely lost in the whole core I. As a distinct lineage within the HAP clade, Pseudognaphalium was characterized by the presence of an ycf15 pseudogene with only 54 bp and the lack of hexanucleotide repetitions. The findings in this study enhance our understanding of the internal structure of chloroplast genomes in the HAP clade and provide valuable insights on the phylogenetics and plastome evolution of this clade.