Plant Evolutionary Genetics

My long-term research encompasses large-scale sequencing studies to address questions in molecular evolution, demographic history and the impact of mating system differences, using cultivated tomatoes and their wild relatives (Solanum section Lycopersicon) as a model system. Moreover, in collaboration with a large network of tomato genome biologists, we have contributed to analyses of the domestication history of the cultivated tomato, a commercially important crop.

My group also studies postzygotic reproductive isolation among species of wild tomatoes, taking advantage of the variable proportion of hybrid seed failure among different pairs of taxa. Specifically, we are interested in (possibly disturbed) genomic imprinting and other epigenetic phenomena as an avenue to evaluate their potential involvement in hybrid seed failure. To these ends, we employ controlled crosses in the greenhouse, laser-assisted microdissection of different seed components, and high-throughput transcriptome sequencing.

• Plant evolutionary genetics
• Speciation and reproductive isolation
• Plant mating system evolution
• Genomic imprinting
• Molecular evolution

► ORCID: https://orcid.org/0000-0003-4513-8583

• Graph pangenome captures missing heritability and empowers tomato breeding
  Zhou, Y; Zhang, ZY; (...); Huang, SW
  Nature, 10.1038/s41586-022-04808-9   Jun 2022
• Transcriptomic Profiling Reveals Shared Signalling Networks Between Flower Development and Herbivory-Induced Responses in Tomato
  Ke, Lanlan; Wang, Yangzi; Schaefer, Martin; Staedler, Thomas; Zeng, Rensen; et al.
  Frontiers In Plant Science 10.3389/fpls.2021.722810 SEP 21 2021
• Endosperm and Seed Transcriptomes Reveal Possible Roles for Small RNA Pathways in Wild Tomato Hybrid Seed Failure
  Florez-Rueda, Ana Marcela; Fiscalini, Flurin; Roth, Morgane; Grossniklaus, Ueli; Staedler, Thomas
  Genome Biology And Evolution 10.1093/gbe/evab107  AUG 2021
• Population Genomics of the "Arcanum" Species Group in Wild Tomatoes: Evidence for Separate Origins of Two Self-Compatible Lineages
  Florez-Rueda, Ana M.; Scharmann, Mathias; Roth, Morgane; Stadler, Thomas
  Frontiers In Plant Science 10.3389/fpls.2021.624442 Published: MAR 19 2021
• Adaptive reduction of male gamete number in the selfing plant Arabidopsis thaliana
  Tsuchimatsu, T; Kakui, H; Yamazaki, M; Marona, C; Tsutsui, H; Hedhly, A; Meng, D; Sato, Y; Stadler, T;Grossniklaus, U; Kanaoka, MM; Lenhard, M; Nordborg, M; Shimizu, KK
  Nature Communications  8 June 2020., 10.1038/s41467-020-16679-7
• Differences in Effective Ploidy Drive Genome-Wide Endosperm Expression Polarization and Seed Failure in Wild Tomato Hybrids
  Roth, M; Florez-Rueda, AM; Stadler, T
  GENETICS, 212 (1):141-152; 10.1534/genetics.119.302056 MAY 2019
• Wild tomato endosperm transcriptomes reveal common roles of genomic imprinting in both nuclear and cellular endosperm
  Morgane Roth, Ana M. Florez‐Rueda, Margot Paris, Thomas Städler
  The Plant Journal 95(6) · June 2018  https://doi.org/10.1111/tpj.14012
• Incidence and developmental timing of endosperm failure in post-zygotic isolation between wild tomato lineages
  Morgane Roth, Ana M Florez-Rueda, Stephan Griesser, Margot Paris, Thomas Städler
  Annals of Botany, Volume 121, Issue 1, Pages 107–118, 25 January 2018, https://doi.org/10.1093/aob/mcx133
• Genomic Imprinting in the Endosperm Is Systematically Perturbed in Abortive Hybrid Tomato Seeds 
  Florez-Rueda, Ana M.; Paris, Margot; Schmidt, Anja; et al. 
  MOLECULAR BIOLOGY AND EVOLUTION, 33 (11): 2935-2946, 10.1093/molbev/msw175  NOV 2016
• Genomic analyses provide insights into the history of tomato breeding 
  Lin T, Zhu G, Zhang J et al.
  NATURE GENETICS, 46 (11): 1220-1226, 10.1038/ng.3117   2014
• A genomic variation map provides insights into the genetic basis of cucumber domestication and diversity 
  Qi, Jianjian; Liu, Xin; Shen, Di; et al. 
  Nature Genetics, 45 (12): , 10.1038/ng.2801 DEC 2013
• Testing for "Snowballing" Hybrid Incompatibilities in Solanum: Impact of Ancestral Polymorphism and Divergence Estimates 
  Staedler, Thomas; Florez-Rueda, Ana Marcela; Paris, Margot 
  MOLECULAR BIOLOGY AND EVOLUTION, 29 (1): 31-34, 10.1093/molbev/msr218 JAN 2012
• Evolution of self-compatibility in Arabidopsis by a mutation in the male specificity gene 
  Tsuchimatsu, T; Suwabe, K; Shimizu-Inatsugi, R; et al. 
  NATURE 464 (7293): 1342-U2, 10.1038/nature08927 APR 2010

• Ultra-high throughput sequencing
• Evolution of genomic imprinting
• Adaptation and speciation