Complete chloroplast genome comparisons for Pityopsis (Asteraceae)

Abstract

Pityopsis includes several regionally and one federally endangered species of herbaceous perennials. Four species are highly localized, including the federally endangered P. ruthii. The genus includes several ploidy levels and interesting ecological traits such as drought tolerance and fire-dependent flowering. Results from previous cladistic analyses of morphology and from initial DNA sequence studies did not agree with one another or with the infrageneric taxonomic classification, with the result that infrageneric relationships remain unresolved. We sequenced, assembled, and compared the chloroplast (cp) genomes of 12 species or varieties of Pityopsis to better understand generic evolution. A reference cp genome 152,569 bp in length was assembled de novo from P. falcata. Reads from other sampled species were then aligned to the P. falcata reference and individual chloroplast genomes were assembled for each, with manual gapfilling and polishing. After removing the duplicated second inverted region, a multiple sequence alignment of the cp genomes was used to construct a maximum likelihood (ML) phylogeny for the twelve cp genomes. Additionally, we constructed a ML phylogeny from the nuclear ribosomal repeat region after mapping reads to the Helianthus annuus region. The chloroplast phylogeny supported two clades. Previously proposed clades and taxonomic sections within the genus were largely unsupported by both nuclear and chloroplast phylogenies. Our results provide tools for exploring hybridity and examining the physiological and genetic basis for drought tolerance and fire-dependent flowering. This study will inform breeding and conservation practices, and general knowledge of evolutionary history, hybridization, and speciation within Pityopsis.

Fig 1. Visualization of Pityopsis falcata chloroplast gene map with annotations.

The inner circle is GC content. Genes are color coded based on function as per the legend. Genes on the inside of the outer circle are minus (-) strand and genes on the outside of the outer circle are plus (+) strand.

Fig 2. Phylogenetic relationships within Pityopsis using the maximum likelihood approach from whole chloroplast genomes, with Helianthus annuus as the outgroup.

The tree was constructed using the GTR + GAMMA model within RAxML with 1000 replicates. A consensus tree was built using a 50% support threshold. Numbers above nodes are bootstrap values (> 50%).

Fig 3. Phylogenetic tree constructed from nuclear ribosomal region of all sampled Pityopsis taxa with related species Helianthus annuus as an outgroupusing the maximum likelihood approach.

The tree was constructed using the GTR + GAMMA model within RAxML with 1000 replicates. A consensus tree was built using a 50% support threshold. Numbers above nodes are bootstrap values (> 50%).