Project: Transposable element dynamics of a Cape radiation
Research group: Plant Evolutionary Cytogenomics
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Understanding key drivers of radiations means understanding the triggers of speciation. Whole genome duplication (WGD) is discussed as such a key driver. It is considered as intrinsic genomic stress that could fuel changes in genome structure and gene expression induced by the activation of transposable elements (TEs). TE-mediated genomic changes could also be the result of environmental stress (e.g., climatic, edaphic). Up to now nothing is known about the role of TEs in radiating organismic groups and their interrelation with WGDs and environmental stress, and this project aims to fill this gap of knowledge. It focuses on the radiating southern African Oxalis clade (SoAO). Within-species ploidy diversity in SoAO is more than three times higher than global estimates of angiosperm intraspecific ploidy variation (Schmickl et al., unpublished; see Figure), and the >200 SoAO species grow under diverse environmental conditions. Genome sizes of diploids are small but vary largely, which is indicative of different TE content. In this project I aim to (i) characterize the TE landscape of SoAO diploids, (ii) test if WGDs resulted in a burst of TEs for selected SoAO polyploids, and (iii) test if particular TE classes accumulate in species/cytotypes that are restricted to specific environmental conditions.
Du Preez B., Dreyer L., Schmickl R., Suda J., Oberlander K. (2018) Plastid capture and resultant fitness costs of hybridization in the Hirta clade of southern African Oxalis. S. Afr. J. Bot. 118: 329–341.
Carlsen M.M., Fér T., Schmickl R., Leong-Škorničková J., Newman M., Kress W.J. (2018) Resolving the rapid plant radiation of early diverging lineages in the tropical Zingiberales: Pushing the limits of genomic data. Mol. Phylogenet. Evol. 128: 55–68.
Fér T., Schmickl R.E. (2018) HybPhyloMaker: target enrichment data analysis from raw reads to species trees. Evol. Bioinform. 14.1176934317742613.
Schmickl R., Marburger S., Bray S., Yant L. (2017) Hybrids and horizontal transfer: introgression allows adaptive allele discovery. J. Exp. Bot. 68: 5453–5470.
Schmickl R., Liston A., Zeisek V., Oberlander K., Weitemier K., Straub S.C.K., Cronn R.C., Dreyer L.L., Suda J. (2016) Phylogenetic marker development for target enrichment from transcriptome and genome skim data: the pipeline and its application in southern African Oxalis (Oxalidaceae). Mol. Ecol. Resour. 16: 1124–1135.
Junior GAČR GJ16-15134Y, 01/2016-12/2018. 6,291,928 CZK
Primus Research Programme PRIMUS/17/SCI/23, 01/2018-12/2020. 5,982,000 CZK
Primus Research Programme PRIMUS/17/SCI/23
Deadline is closed