Plastid genomes reveal recurrent formation of allopolyploid Fragaria

Abstract

Recurrent formation of polyploid taxa is a common observation in many plant groups. Haploid, cytoplasmic genomes like the plastid genome can be used to overcome the problem of homeologous genes and recombination in polyploid taxa. Fragaria (Rosaceae) contains several octo-and decaploid species. We use plastome sequences to infer the plastid ancestry of these taxa with special focus on the decaploid Fragaria cascadensis. METHODS: We used genome skimming of 96 polyploid Fragaria samples on a single Illumina HiSeq 3000 lane to obtain whole plastome sequences. These sequences were used for phylogenetic reconstructions and dating analyses. Ploidy of all samples was inferred with flow cytometry, and plastid inheritance was examined in a controlled cross of F. cascadensis. KEY RESULTS: The plastid genome phylogeny shows that only the octoploid F. chiloensis is monophyletic, all other polyploid taxa were supported to be para-or polyphyletic. The decaploid Fragaria cascadensis has biparental plastid inheritance and four different plastid donors. Diversification of the F. cascadensis clades occurred in the last 230,000 years. The southern part of its distribution range harbors considerably higher genetic diversity, suggestive of a potential refugium. CONCLUSIONS: Fragaria cascadensis had at least four independent origins from parents with different plastomes. In contrast, para-and polyphyletic taxa of the octoploid Fragaria species are best explained by incomplete lineage sorting and/or hybridization. Biogeographic patterns in F. cascadensis are probably a result of range shift during the last glacial maximum.

Functional trait divergence and trait plasticity confer polyploid advantage in heterogeneous environments

“…1; Kamneva et al, 2017). Recurrent formation, representing multiple independent origins, has been observed in the 10x and 8x taxa (Dillenberger et al, 2018). The worldwide collection of Fragaria was conducted as an international collaborative effort in 2013-2014; details are available on our Wild Strawberry website (http://wildstrawberry.org/; see also Fig.…”

“…1), among which repeated and independent events of allopolyploid speciation ( Fig. 1) have been revealed by polyploid Fragaria genomes (Tennessen et al, 2014;Kamneva et al, 2017;Wei et al, 2017a,b;Dillenberger et al, 2018).…”

“…vesca , F. viridis and F. mandshurica (Kamneva et al ., ). Recurrent formation* of the same polyploid taxon in different populations has been previously identified (Dillenberger et al ., ), whereas such information remains unclear for the remaining polyploid taxa.…”

Target Capture Sequencing Unravels Rubus Evolution

“…range of plant genera, including Asclepias L. (Weitemier et al, 2014), Heuchera L. (Folk et al, 2017), and Lachemilla L. (Morales-Briones et al, 2018). Although not specifically targeted, chloroplast sequences can be obtained after sequencing target capture libraries, enabling an independent estimate of phylogeny and inference from a predominantly maternally inherited genome (Weitemier et al, 2014;Folk et al, 2017;Dillenberger et al, 2018). Our objectives were to estimate phylogenetic relationships in Rubus using a large molecular dataset over a genus-wide species sampling; estimate divergence times between major Rubus clades; and examine the biogeography of species diversification.…”

A roadmap for research in octoploid strawberry

“…virginiana from North America [1][2][3][4][5] . Several additional wild octoploid subspecies have since been used as parents in breeding, creating an admixed population of F. × ananassa individuals with genomes that are mosaics of phylogenetically and demographically diverse progenitor genomes 4,[6][7][8][9][10][11][12][13] .…”