Journal Articles
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Item Comparative analysis of plastid genomes from allopolyploid Tragopogon miscellus and its diploid parents(John Wiley and Sons Ltd on behalf of German Society for Plant Sciences, Royal Botanical Society of the Netherlands, 2025-09-15) Mukhtar U; Newmarch SC; Winkworth RC; Soltis PS; Soltis DE; Tate JA; Wang X-QTragopogon is a model system for the study of recent, recurrent, and reciprocal allopolyploid formation. Recent research has focused on the fates of nuclear genes duplicated in the allopolyploid T. miscellus relative to the parental diploids, T. dubius and T. pratensis. In contrast, little attention has been given to organellar genomes, which interact with the duplicated nuclear genomes via their gene products. Here we reconstructed plastid genomes (plastomes) for representatives of these three species to investigate their structure and variability among natural and synthetic allopolyploids. Genomic libraries were Illumina-sequenced for several individuals of the allopolyploid T. miscellus and its diploid parents. Whole plastomes were assembled from skimmed data with comparative analyses used to quantify structural and nucleotide variation. Tragopogon plastomes have a typical quadripartite structure and are similar in size to those of other Asteraceae. The 12 plastomes were highly similar, sharing ~99.5%–100% identity. In all but one case, the plastome sequence for each of the polyploids was most similar to that of its expected maternal parent. The exception involved a polyploid that unexpectedly had a T. dubius plastome type, likely as the result of backcrossing with its presumed paternal parent. Such backcrossing events may have contributed to the demise of this polyploid population. Plastome sequences can be used to infer the maternal origins of polyploids as well as investigate ongoing population-level dynamics. More fully assessing plastome variation across the geographic distribution of polyploids and their diploid progenitors may provide additional insights into polyploid formation, population dynamics, and subsequent evolution.Item Ploidy variation in Rhododendron subsection Maddenia and its implications for conservation.(Oxford University Press on behalf of the Annals of Botany Company, 2023-06-01) Hu L; Tate JA; Gardiner SE; MacKay M; Loureiro JPolyploidy, which is common in plants, can confound taxon recognition and hence conservation assessments. In the taxonomically complex genus Rhododendron, 25 % of the over 1,300 taxa are considered under threat and 27 % Near Threatened or Data Deficient, with their taxonomy needing to be resolved urgently. Although ploidy levels of Rhododendron taxa range from diploid (2x) to dodecaploid (12x) according to previous reports, the extent of polyploidy across the genus has not been examined. We first summarized the taxonomic distribution of polyploids in the genus based on the literature. Then as a case study, we estimated ploidy levels of 47 taxa in subsection Maddenia (subgenus Rhododendron, section Rhododendron) using flow cytometry, together with verification of meiotic chromosome counts for representative taxa. The summary of reported ploidy in Rhododendron indicates that polyploidy is most common in subgenera Pentanthera and Rhododendron. In subsection Maddenia, all examined taxa are diploids except for the R. maddenii complex that shows a high ploidy variation (2-8x, 12x). We investigated ploidy level of 12 taxa in subsection Maddenia for the first time, and estimated genome sizes of two Rhododendron species. Knowledge of ploidy levels will inform phylogenetic analysis of unresolved species complexes. Overall, our study of subsection Maddenia provides a model for examining multiple issues including taxonomic complexity, ploidy variation and geographic distribution in relation to biodiversity conservation.Item A roadmap of phylogenomic methods for studying polyploid plant genera(John Wiley and Sons, Inc., on behalf of Botanical Society of America, 2024-04-22) Ning W; Meudt HM; Tate JAPhylogenetic inference of polyploid species is the first step towards understanding their patterns of diversification. In this paper, we review the challenges and limitations of inferring species relationships of polyploid plants using traditional phylogenetic sequencing approaches, as well as the mischaracterization of the species tree from single or multiple gene trees. We provide a roadmap to infer interspecific relationships among polyploid lineages by comparing and evaluating the application of current phylogenetic, phylogenomic, transcriptomic, and whole-genome approaches using different sequencing platforms. For polyploid species tree reconstruction, we assess the following criteria: (1) the amount of prior information or tools required to capture the genetic region(s) of interest; (2) the probability of recovering homeologs for polyploid species; and (3) the time efficiency of downstream data analysis. Moreover, we discuss bioinformatic pipelines that can reconstruct networks of polyploid species relationships. In summary, although current phylogenomic approaches have improved our understanding of reticulate species relationships in polyploid-rich genera, the difficulties of recovering reliable orthologous genes and sorting all homeologous copies for allopolyploids remain a challenge. In the future, assembled long-read sequencing data will assist the recovery and identification of multiple gene copies, which can be particularly useful for reconstructing the multiple independent origins of polyploids.