Complete chloroplast genome comparisons for Pityopsis (Asteraceae)

Authors: HATMAKER, E. ANNE - University Of Tennessee; Wadl, Phillip; Rinehart, Timothy - Tim; Carroll, Jennifer; LANE, THOMAS - University Of Tennessee; TRIGIANO, ROBERT - University Of Tennessee; STATON, MARGARET - University Of Tennessee; SCHILLING, EDWARD - University Of Tennessee

Submitted to: Frontiers in Plant Science
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 12/14/2020
Publication Date: 12/28/2020
Citation: Hatmaker, E., Wadl, P.A., Rinehart, T.A., Carroll, J.B., Lane, T.S., Trigiano, R.N., Staton, M.E., Schilling, E.E. 2020. Complete chloroplast genome comparisons for Pityopsis (Asteraceae). Frontiers in Plant Science. 55:0241391. https://doi.org/10.1371/journal.pone.0241391.
DOI: https://doi.org/10.1371/journal.pone.0241391

Interpretive Summary: Golden asters (Pityopsis spp.) belong to a small genus within the Asteraceae family, which encompasses over 23,000 species including sunflowers, chrysanthemums, and zinnias. The center of diversity for golden asters is in the southeastern United States. The genus includes a wide variety of chromosome levels across species and a large geographic range throughout southeastern North America, in Mexico and Central America, and in the Bahamas. Evolutionary relationships within the genus has been the subject of several studies, but relationships for all species and varieties in the genus have not been fully resolved, resulting in significant variation in the number of species recognized for the golden asters. Golden aster species have several ecologically adaptive traits such as fire-stimulated flowering and drought-tolerance. Studying species relationships often allows for better evolutionary understanding of traits. In golden asters, species distinctions are not well understood, which has been difficult due to the differing chromosome levels and apparent hybridization in the genus. However, a well-supported evolutionary tree for the golden asters could be used to examine the evolution of adaptive traits and the role of hybridity within the context of the varying chromosome levels. Chloroplast genome sequences are a convenient and routine way to find repetitive sequences and regions that are used in for clarifying evolutionary relationships in genera with muddled history, such as the golden asters. Therefore, researchers at the USDA and the University of Tennessee conducted a study where chloroplast genomes of 12 golden asters were sequenced, assembled, compared to other Asteraceae chloroplast genomes, and used to determine evolutionary relationships. The analyses supported two groups of species within the golden asters. 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 the golden asters and benefit researchers working in these areas of study.

Technical 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 twelve 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.