Kidner Lab

Understanding Diversity

We are interested in determining the genetics underlying differences between species. We would like to know how many genetic changes and what type of changes determine differences in plant growth and form. A combination of classical genetics and new sequencing technologies is being used to link the variation in form to variation in the sequence and expression of genes. We are particularly interested applying these techniques to tropical species, as the tropics contain most of the world’s diversity but have been genetically understudied.

Methodology

We are interested in the application of large scale comparative sequence analysis to understanding patterns of diversity. We use NGS to produce transcriptomes, genomes and phylogenies to explore the diversity of tropical plants. We use the resources of the living collections at RBGE for expression analysis and are using Hyb-Seq to mine genetic data from herbarium samples.

Study Systems

Begonia

Begonia is one of the largest angiosperm genera and well represented in flora across the tropics. Understanding the drivers and the results of speciation patterns in Begonia will help us understand tropical diversity. We have produced a genetic map, several transcriptomes, a reference genome and several draft genomes for the group and are using these to identify the genetics underlying species-level diversity patterns.

Inga

Inga is a group of about 300 species of leguminous trees of the neotropics. It is cultivated as a shade tree in agro-forestry. We have been using Hyb-Seq to produce a well resolved phylogeny for the genus and are using comparative transcriptomics to identify traits associated with species-level variation, particularly in herbivore defence.

Other groups

We are interested all aspects of comparative genetics and genomics in underexplored plants.

 

Current Projects and lab members

Hyb-Seb for phylogenetics of Begonia Coelocentrum

Collaboration with Kuo-Fang Chung and Yu-Hsin Tseng, Academia Sinica.

 

Evolution of secondary metabolism in Inga

Collaboration with Toby Pennington (Exeter), Graham Stone (UoE),  Phyllis Kusar (University of Utah)

 

Generation of a better Begonia genome

Collaboration with Aureliano Bombarely, University of Milan.

 

Does a dynamic genome drive speciation in Begonia?

Lucia Campos Dominguez – PhD project

 

Mutational meltdown in a mega diverse genus

Thibauld Michel - Phd Project with Plant.ID

 

The genetics of Begonia leaf shape

Cynthia Fan - PhD Project

 

Colonisation of the Chocó

Kelly Gonzalez - PhD Project

 

Past Group Members

Leila Imcharen April 2020 - Sept 2020 Evolution of Shade tolerance genes in Begonia

Carolina Armijos May 2020 – Sept 2020 Evolution of Terpene synthase genes in Begonia

Angèle Demouveaux Sept 2019 – Jan 2020 Plastid markers from Hyb-Seq data

Philippa Stone April 2019 - Sept 2019 Does horticultural breeding preserve rare alleles from endangered species?

Mayra Breiceno April 2019 - Sept 2019 Morphometrics of Begonia leaves

Rachel Callaghan  April 2018 - Sept 2018 Begonia terpenes

Ethan Roos – April 2018 - Sept 2018 A TRIPAL database for Begonia

Andrea Martinez-Martinez April 2017 - Sept 2017 A draft genome of Hillebrandia

Eloi Durrant April 2017 - Sept 2017 SOM analysis of gene expression Begonia

Yue Wang April 2016 - Sept 2016 KTI proteins in Inga

Katie Emelianova 2013 – 2017 Gene duplication patterns in Begonia

Lucia Campos Dominguez March – August 2016 QTL analysis of lens cell anatomy in Begonia

Tessa Pronk Sept 2015 – April 2016 - CHS genes in Begonia

Aleix Soler 2014 Chracterisation of the draft Begonia Genome

Mansour Abdullah 2012 - 2016 Barcoding the Flora of Kuwait

Mobina Shaukat Ali 2008 - 2012 Genetic architecture of variation between species in leaf structure and ecophysiology in Begonia

Nikki Harrison 2006 - 2012 Plastid genomes for phylogenetics

Alex Twyford 2007 - 2011 Hybridisation and introgression in Mexican Begonia

Saima Umbreen 2005 – 2011 ARP and KNOX genes and leaf form

Julie Bluhm Summer 2011 Microsatellite markers for Begonia

Adrian Brennan 2010-2011 A genetic map of Begonia based on AFLPs and SNPs.

Aaron Marrubi Spring 2011 Candidate genes for stomatal patterning

Emily Johnston Spring 2011 CAM metabolism in Begonia

Chris White Spring 2010 QTL analysis of petal form

Stephen Wrigley 2010 – 2012 Ectopic leaves in hybrid Begonia

Qasim Hayat 2010 – Phylogenetic realtionships in Central Asian Artemisia

Iro Kouzali Summer 2010 Paternal chloroplast inheritance

Keith Gardner 2008-2010 Genetic map of Begonia

Ninette Rowlands – Summer 2009, CUC genes and leaf dissection in B. carolineifolia and B. heracleifolia

Stewart Nicholson – Summer 2009, Species delimitation in B. serconeura.

Samantha Dobbie – Spring 2009 Transformation of Begonia

Olivia Moss –Summer 2008. Segregation of vegetative traits in an F1BC1 population.

Melanie Oakley - Spring 2008. KNOX gene and Begonia leaf form

Neil Young –Summer 2007. Pollen germination in interspecific interspecific hybrids

Sergio Piso-Martin – Spring 2007. – Methylation at the CYC and DIC loci in Linaria purpurea

Clare Rickerby – Spring 2007. KNOX1-like genes and leaf dissection

Rhydian Beydon-Davies –Spring 2007. Interspecific hybrids in Begonia

Andrew Matthews –Spring 2007. F1 fertility in Begonia

Emma Laidlaw –Summer 2006. Genetics of Leaf form in Begonia F1 hybrids

Katie Glass – Spring 2006. DNA fingerprinting in schools

Fatima Dahmani – Spring-summer 2006. KNOX1-like genes and compound leaves in Begonia

Rachel Kenneil – Summer 2005. QTL mapping of serrations in Arabidopsis

Claire Webster – Summer 2005. Sequencing and genotyping

Pierre Cattenoz – Spring-Summer 2005. ARP genes and leaf form in Begonia

Jack Cavers – Spring 2005. KNOX1 and ectopic leaflets in Begonia luxurians

Publications

QTL dissection of floral traits in Streptocarpus (Gesneriaceae). Yun-Yu Chen, Kanae Nishii, Catherine Kidner, Christine Anne Hackett, Michael Möller Euphytica 216 (7), 1-20

The Origin of the Legumes is a Complex Paleopolyploid Phylogenomic Tangle closely associated with the Cretaceous-Paleogene (K-Pg) Mass Extinction Event.  Erik JM Koenen, Dario I Ojeda, Freek T Bakker, Jan J Wieringa, Catherine Kidner, Olivier J Hardy, R Toby Pennington, Patrick S Herendeen, Anne Bruneau, Colin E Hughes (2020) Systematic Biology https://doi.org/10.1093/sysbio/syaa041

Large‐scale genomic sequence data resolve the deepest divergences in the legume phylogeny and support a near‐simultaneous evolutionary origin of all six subfamilies.  Erik JM Koenen, Dario I Ojeda, Royce Steeves, Jérémy Migliore, Freek T Bakker, Jan J Wieringa, Catherine Kidner, Olivier J Hardy, R Toby Pennington, Anne Bruneau, Colin E Hughes. (2020) New Phytologist 225 (3), 1355-1369. doi: 10.1111/nph.16290.

Phylogeny and biogeography of Ceiba Mill.(Malvaceae, Bombacoideae) Flavia Fonseca Pezzini, Kyle G Dexter, Jefferson G Carvalho-Sobrinho, Catherine A.Kidner, James A Nicholls, Luciano P Queiroz, R Toby Pennington (2020) BioarXiv

The limits of Hyb-Seq for herbarium specimens: impact of preservation techniques.  LL Forrest,Laura Lowe Forrest, Michelle Louise Hart, Mark Hughes, Hannah Phoebe Wilson, Kuo-Fang Chung, Yu-Hsin Tseng, Catherine A.Kidner (2019) Front. Ecol. Evol 7:439. doi:10.3389/fevo.2019.00439

Phyllis D. Coley, María-José Endar, Gabrielle Ghabash, Catherine A.Kidner, James A.Nicholls, R. Toby Pennington, Anthony G. Mills, Abrianna J. Soule¹ Maristerra R. Lemes and Thomas A. Kursar (2019) Macroevolutionary patterns in overexpression of tyrosine: an anti-herbivore defence in a speciose tropical tree genus, Inga (Fabaceae). Journal of           Ecology 107:1620-1632

María-José Endara, James Nicholls, Phyllis Coley, Dale Forrister, Gordon Younkin, Kyle Dexter, Catherine Kidner, RTP Pennington, Graham Stone, Thomas Kursar.(2018) Tracking of Host Defenses and Phylogeny During the Radiation of Neotropical Inga-Feeding Sawflies (Hymenoptera; Argidae). Front Plant Sci. 9:1237. doi: 10.3389/fpls.2018.01237.

Y-Y Chen, K Nishii, S Barber, C Hackett, CA Kidner, K Gharbi, AJ Nagano, A Iwamoto, M Möller (2018) A first genetic map in the genus Streptocarpus generated with RAD sequencing based SNP markers. South African Journal of Botany 117, 158-168

María-José Endara, Phyllis Coley, Natasha Wiggins,  Dale Forrister, Gordon Younkin, James Nicholls, RTP Pennington, Kyle Dexter, Catherine Kidner, Graham Stone, Thomas Kursar (2018) Chemocoding as an identification tool where morphological- and DNA-based methods fall short: Inga as a case study. New Phytologist  218: 847-858

Eugenio Valderrama Escallon. James E.Richardson, Catherine A.Kidner, Santiago Madriñán, Graham S.Stone (2017) Transcriptome mining for phylogenetic markers in a recently radiated genus of tropical plants (Renealmia L.f., Zingiberaceae) Molecular Phylogenetics and Evolution in press doi.org/10.1016/j.ympev.2017.10.001

Paula J. Rudall, Adele C. M. Julier and Catherine A. Kidner (2017) Ultrastructure and development of non-contiguous stomatal clusters and helicocytic patterning in Begonia. Annals of Botany, in press

Michelle L. Hart, Laura L. Forrest, James A. Nicholls, and Catherine A. Kidner (2016) Retrieval of hundreds of nuclear loci from herbarium specimens Taxon, 65 1081-1092 doi.org/10.12705/655.9

Nikki Harrison , Richard J. Harrison RJ, Catherine A. Kidner. (2016) Comparative Analysis of Begonia Plastid Genomes and Their Utility for Species-Level Phylogenetics. PLoS One. 11(4):e0153248. doi: 10.1371/journal.pone.0153248

James A. Nicholls, R. Toby Pennington, Erik J.M. Koenen, Colin E. Hughes, Jack Hearn, Lynsey Bunnefeld, Kyle G. Dexter, Graham N. Stone and Catherine A. Kidner (2015). Using targeted enrichment of nuclear genes to increase phylogenetic resolution in the the neotropical rain forest genus Inga (Leguminosae: Mimosoideae) Frontiers in Plant Biology 6:710. doi: 10.3389/fpls.2015.00710

Alex Twyford Catherine Kidner, Richard Ennos (2015) Maintenance of species boundaries in a Neotropical radiation of Begonia. Molecular ecology, 24:4982-4993

Catherine Kidner, Andrew Groover, Daniel Thomas, Katie Emelianova, Claudia Soliz-Gamboa, Frederic Lens (2014) First steps in studying origins of secondary woodiness in Begonia (Begoniaceae): combining anatomy, phylogenetics, and stem transcriptomics. Bot. J. Linn. Soc 117: 121-138 10.1111/bij.12492

Alex Twyford, Richard Ennos, Chris White, Mobina Shaukat Ali, Catherine Kidner. (2014) The evolution of sex ratio differences and inflorescence architectures in Begonia (Begoniaceae) - Am. J. Bot, 101: 308-17

Alex Twyford Catherine Kidner, Richard Ennos (2013) Genetic differentiation and species cohesion in two widespread Central American Begonia species. Heredity (doi:10.1038)

Alex Twyford, Richard A. Ennos and Catherine A. Kidner (2013) Development and Characterization of Microsatellite Markers for Central American Begonia sect. Gireoudia (Begoniaceae). Applications in Plant Sciences 1:1200499. doi: 10.3732

Adrian Brennan, Stephen Bridgett, Mobina Shaukat Ali, Nicola Harrison, Andrew Mathews, Jaume Pellicer, Alex Twyford, and Catherine Kidner (2012) Genomic resources for evolutionary studies in the large, diverse tropical genus Begonia. Tropical Plant Biology 5:261-276

Alex Twyford, Catherine Kidner, Nicola Harrison and Richard Ennos (2012) Population history and seed dispersal in widespread Central American Begonia species (Begoniaceae) inferred from plastome derived microsatellite markers. Bot. J. Linn. Soc. DOI: 10.1111/j.1095-8339.2012.01265.x

Nicola Harrison and Catherine Kidner (2011) Next-generation sequencing and systematics. What can a billion base pairs of DNA sequence do for you? Taxon 6:1552-1566

Angelo Dewitte, Alex Twyford, Daniel Thomas, Catherine Kidner and Jan Van Huylenbroeck (2011) The Origin of Diversity in Begonia: Genome dynamism, population processes and phylogenetic patterns. In: The Dynamical Processes of Biodiversity - Case Studies of Evolution and Spatial Distribution (InTech)

Catherine Kidner and Marja Timmermans (2010) Signaling sides: adaxial-abaxial patterning in leaves. Current Topics in Developmental Biology 91:141-68.

Catherine Kidner and Steven Wrigley (2010) Patches, pegs and piggies. New Phytol. 187:13-7.

Catherine Kidner and Saima Umbreen (2010) Why is leaf shape so variable? International Journal of Plant Developmental Biology 4: 64-75.

Kanae Nishii, Michael Möller, Catherine Kidner, Albert Spada, Raffaella Mantegazza, Chun-Neng Wang, Tochiyuka Nagata. (2010) A complex case of simple leaves: indeterminate leaves co-express ARP and KNOX1 genes. Dev Genes Evol. 220:25-40.

Catherine Kidner (2010) Plant Organ Primordia. In: Encyclopedia of Life Sciences (ELS). John Wiley & Sons, Ltd: Chichester. DOI:10.1002/9780470015902.a0002055.pub2

Catherine Kidner (2010) The many roles of small RNAs in leaf development. Journal of Genetics and Genomics 37:13-21

Catherine Kidner (2007) Leaf evolution: working with what's to hand. Evol Dev. 9:321-2.

Catherine Kidner and Marja Timmermans (2007) Mixing and matching pathways in leaf polarity. Curr Opp Pl. Sci10:13-20.

Sophie Neale, Will Goodall-Copespeak and Catherine Kidner (2006b) The Evolution of Diversity in Begonia. In: ‘Floriculture, Ornamental and Plant Biotechnology: Advances and Topical Issues’. J. A. Teixeira da Silva (Ed.) Global Science Books

Catherine Kidner and Marja Timmermans (2006a). In situ hybridization as a tool to study the role of miRNAs in plant development. In: ‘MicroRNA protocols’ Methods in Molecular Biology. Shao-Yao Ying (Ed). Humana press Inc.

Catherine Kidner and Robert Martienssen (2005b) The role of ARGONAUTE1(AGO1) in meristem formation and identity. Developmental Biology 280:504-17

Catherine Kidner and Robert Martienssen (2005a). The developmental role of microRNA in plants. Curr Opin Plant Biol. 8:38-44.

Catherine Kidner and Robert Martienssen (2004) Spatially restricted microRNA directs leaf polarity via ARGONAUTE1. Nature. 428:81-4

Mary E. Byrne, Catherine A. Kidner and Robert A. Martienssen (2003) Plant stem cells: divergent pathways and common themes in shoots and roots. Curr. Opin .Genet. Dev.. 5:551-7.

Rob Martienssen, Tom Volpe, Zach Lippman, Ann-Valerie Genrel, Catherine Kidner, Pablo Rabinowicz and Vincent Colot. (2003) Transposable elements, RNA interference and the origin of heterochromatin. In ‘RNAi – A guide to gene silencing’ Ed. Gregory J Hannon CSHL Press, NY.

Catherine A Kidner and Robert A Martienssen. (2003) Macro effects of microRNAs in plants. Trends in Genetics 19: 13-16

Catherine Kidner, Marja Timmermans, Mary Byrne, and Robert Martienssen. (2002) Developmental Genetics of the Angiosperm Leaf. Advances in Botanical Research Vol 38: 192-234

Tom Volpe, Catherine Kidner, Ira Hall, Grace Teng, Shiv Grewel and Robert Martienssen. (2002) Regulation of Heterochromatic Silencing and Histone H3 Lysine-9 Methylation by RNAi. Science. 297: 1833-1837.

Mary Byrne, Marja Timmermans, Catherine Kidner and Robert Martienssen. (2001) Development of leaf shape. Current Opinion in Plant Biology 4:38-43.

Catherine Kidner, Vendkatesan Sundaresan , Keith Roberts, and Liam Dolan. (2000) Clonal analysis of the Arabidopsis root confirms that position, not lineage, determines cell fate. Planta. 211:191-9.

Liam Dolan, Paul Linstead, Catherine Kidner, Kurt Boudonck, Cao Xiao-Feng, Frederic Berger. (1998) Cell fate specification in Plants - Lessons from the Arabidopsis root. Society for Experimental Biology Symposium Seris. 51:11-17.

Jane A. Langdale and Catherine A. Kidner (1994) bundle sheath defective, a mutation that disrupts cellular differentiation in maize leaves. Development 120, 673-681.

Links

Evo-devo research at RBGE (http://www.rbge.org.uk/science/tropical-diversity/evolutionary-development)

Kidner lab at Edinburgh University (http://www.research.ed.ac.uk/portal/en/persons/catherine-kidner)

PlantID DTP (http://www.plantid.uio.no/)