The complete chloroplast genome and phylogenetic analysis of Dahlia pinnata Cavanilles 1791(Asteraceae: Dahlia)

Abstract

Dahlia pinnata Cavanilles 1791 is an important ornamental plant worldwide. The chloroplast genome has obvious advantages in studies of systematic evolution at the plant classification and species level, making it an important resource for phylogenetic research.Here, we sequenced the full chloroplast genome from D. pinnata 'Chocolate' and found that it exhibited a typical tetrad structure. The full-length D. pinnata chloroplast genome was 152,107 bp, with a GC content of 38.45%. The genome included an 83,704 bp large single-copy (LSC) region, an 18,347 bp small single-copy (SSC) region, and a pair of 25,028 bp inverted repeats (IRa and IRb). A total of 134 genes were annotated, including 86 protein-coding genes, 38 transfer RNA genes, 8 ribosomal RNA genes, and 2 pseudogenes. Analysis of password preferences shows that passwords chosen by D. pinnata tend to end with A/U. A total of 161 SSR markers were detected in the simple sequence repeat (SSR) analysis. Phylogenetic analysis that the Dahlia species formed a monophyly. Dahlia was clustered with Cosmos-Bidens, which differed from studies using nuclear genomic DNA. We suggest that nuclear-cytoplasmic incongruences may be widespread in Asteraceae, and should be thoroughly evaluated in order to understand the true evolutionary history of this economically-important group of plants.

The genomes of Dahlia pinnata, Cosmos bipinnatus, and Bidens alba in tribe Coreopsideae provide insights into polyploid evolution and inulin biosynthesis

“…Recently, chromosome-scale reference genomes have been published for several economically important species in the Heliantheae alliance, including Helianthus annuus [ 20 ], Ambrosia artemisiifolia [ 21 ], Stevia rebaudiana [ 22 ], Mikania micrantha [ 23 ], and Smallanthus sonchifolius [ 15 ]. However, until now, for the tribe Coreopsideae, only the organelle genomes of D. pinnata, C. bipinnatus , and B. alba , as well as a highly fragmented contig-level assembly of the hexaploid Bidens hawaiensis , were available [ 24–29 ]. In this work, we present the chromosome-scale haplotype-resolved genomes of D. pinnata, C. bipinnatus , and B. alba , to explore the evolution of polyploidization and mechanism under inulin metabolism.…”