Genomes carry the information for organisms to develop, respond and change, and understanding the genome dynamics underlying plant biology, provides insight into the capacity of lineages to respond to challenges and change.
Genome dynamics
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Genome assembly
We aim to generate high-quality telomere-to-telomere (T2T) genome assemblies for studying differences between species.
We are testing genome assembly software and developing pipelines to support staff and students in producing accurate and well annotated reference genomes.
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Genetic maps and transcriptomes
A genome sequence is just the beginning in understanding the genetics of a species.
We are studying the patterns of gene expression (transcriptomics) and the patterns of inheritance of genetic markers (genetic maps). We use these to bridge the gap between the variation in the genomes (genotype) and the variation in how species look, grow, and behave (phenotype).
Our aim is to identify the genetic changes underlying the patterns of plant diversity, giving us a better understanding of how plants have evolved and how they can change in the future.
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Cyto-genomics
Cytology allows us to visualise chromosomes. This allows us to anchor genomic information to a physical location.
Knowing the number and arrangement of chromosomes is vital for producing accurate genome assemblies and for studying how they change, through repeat expansion, chromosome breakage and fusion, and large-scale repeats and inversions.
These large-scale changes can underlie speciation events. We use a wide range of classical cytology techniques and more detailed focus on specific sequences (FISH) to examine genome evolution.
Campos-Dominguez L, J Pellicer, A Matthews, IJ Leitch, CA Kidner (2022). Evolutionary patterns of genome size and chromosome number variation in Begoniaceae. http://dx.doi.org/10.24823/ejb.2022.1876
Canales, NA, OA Pérez-Escobar, RF Powell, M Töpel, C Kidner, M Nesbitt, C Maldonado et al. (2022) A highly contiguous, scaffold-level nuclear genome assembly for the fever tree (Cinchona pubescens Vahl) as a novel resource for Rubiaceae research. GigaByte 2022. https://doi.org/10.46471/gigabyte.71
Chen YY, K Nishii, S Barber, C Hackett, C Kidner, K Gharbi, AJ Nagano, A Iwamoto, M Möller (2018). Building a genetic map: Comparison between de novo and reference-based approaches using RAD sequencing data in Streptocarpus (Gesneriaceae). South African Journal of Botany 117: 158–168. https://doi.org/10.1016/j.sajb.2018.05.009
Denduangboripant J, QCB Cronk, G Kokubugata, M Möller (2007). Variation and inheritance of nuclear ribosomal DNA clusters in Streptocarpus (Gesneriaceae) and their biological and phylogenetic implications. International Journal of Plant Sciences 168(4): 455–467. https://doi.org/10.1086/512103
Ferrari G, L Esselens, ML Hart, S Janssens, C Kidner, M Mascarello, JV Peñalba et al. (2023). Developing the protocol infrastructure for DNA sequencing natural history collections. Biodiversity Data Journal 11. https://doi.org/10.3897/BDJ.11.e102317
Li L, X Chen, D Fang, S Dong, X Guo, N Li, L Campos‐Dominguez et al. (2022). Genomes shed light on the evolution of Begonia, a mega‐diverse genus. New Phytologist 234, no. 1: 295-310. https://doi.org/10.1111/nph.17949
Michel T, Y-H Tseng, H Wilson, K-F Chung, C Kidner (2022). A hybrid capture bait set for Begonia. Edinburgh Journal of Botany 79: 1-33. https://doi.org/10.24823/ejb.2022.409
Möller M (2018). Nuclear DNA C-values are correlated with pollen size at tetraploid but not diploid level and linked to phylogenetic descent in Streptocarpus (Gesneriaceae). South African Journal of Botany 114: 323–344. https://doi.org/10.1016/j.sajb.2017.11.017
Möller M, N Kelso, K Nishii (2023). Meiotic behavior and postmeiotic pollen formation in the F1 hybrid Streptocarpus grandis × S. rexii (Gesneriaceae) and its parents. Cytologia 88(2): 95–103. https://doi.org/10.1508/cytologia.88.95
Nishii K, M Hart, N Kelso, S Barber, YY Chen, M Thomson, U Trivedi, AD Twyford, M Möller (2022). The first genome for the Cape Primrose Streptocarpus rexii (Gesneriaceae), a model plant for studying meristem-driven shoot diversity. Plant Direct 6(4): e388. https://doi.org/10.1002/pld3.388
Percival‐Alwyn L, I Barnes, MD Clark, J Cockram, MP Coffey, S Jones, PJ Kersey et al. (2024). UKCropDiversity‐HPC: A collaborative high‐performance computing resource approach for sustainable agriculture and biodiversity conservation. Plants, People, Planet. https://doi.org/10.1002/ppp3.10607
Schley R J, RT Pennington, AD Twyford, KG Dexter, C Kidner, TP Michael, Wellcome Sanger Institute Tree of Life (2024). The genome sequence of Inga laurina (Sw.) Willd. Wellcome Open Research 9: 567. https://doi.org/10.12688/wellcomeopenres.23057.1
Schley R J, RT Pennington, AD Twyford, KG Dexter, C Kidner, TP Michael, Wellcome Sanger Institute Tree of Life (2024). The genome sequence of Inga leiocalycina Benth. Wellcome Open Research 9: 606. https://doi.org/10.12688/wellcomeopenres.23131.1
Schley RJ, RT Pennington, AD Twyford, KG Dexter, C Kidner, TP Michael, Wellcome Sanger Institute Tree of Life (2024). The genome sequence of Inga oerstediana Benth. Wellcome Open Research 9: 607. https://doi.org/10.12688/wellcomeopenres.23146.1
Tseng Y-H, C-L Hsieh, L Campos-Domínguez, A-Q Hu, C-C Chang, Y-Ting Hsu, CA Kidner et al. (2022). Insights into the evolution of the chloroplast genome and the phylogeny of Begonia. Edinburgh Journal of Botany 79 : 1-32. https://doi.org/10.24823/ejb.2022.408
Ye LJ, M Möller, YH Luo, JY Zou, W Zheng, J Liu, DZ Li, LM Gao (2023). Variation in gene expression along an elevation gradient of Rhododendron sanguineum var. haemaleum assessed in a comparative transcriptomic analysis. Frontiers in Plant Science, Section Functional Plant Ecology 14: 1133065. https://doi.org/10.3389/fpls.2023.1133065
Ye LJ, M Möller, YH Luo, JY Zou, W Zheng, YH Wang, J Liu, AD Zhu, JY Hu, DZ Li, LM Gao (2021). Differential expressions of anthocyanin synthesis genes underlie flower color divergence in a sympatric Rhododendron sanguineum complex. BMC Plant Biology 21, e204: 1–16. https://doi.org/10.1186/s12870-021-02977-9