Evolutionary Genomics

Our group is fascinated by the diversity and evolution of living organisms, populations and ecological systems. Our primary goal is to understand the basic principles underlying both macro- and microevolutionary changes using plants as model organisms. In particular, our interest extends over several fields of plant biology, including ecology, population genomics, molecular evolution, evo-devo, systematics and comparative genomics with special attention to basal groups of land plants. We combine field-based ecological and lab-based molecular/reverse genetic approaches including computationally intensive modeling and genome analysis to understand evolutionary processes both at the macro- and microevolutionary scales.

• The hornworts: morphology, evolution and development
  Frangedakis, Eftychios; Shimamura, Masaki; Villarreal, Juan Carlos; Li, Fay-Wei; Tomaselli, Marta; et al.
  New Phytologist  DOI: 10.1111/nph.16874 SEP 2020
• Evolutionary History of the Marchantia polymorpha Complex
  Linde, Anna-Malin; Sawangproh, Weerachon; Cronberg, Nils; Szoevenyi, Peter; Lagercrantz, Ulf
  Frontiers In Plant Science  DOI: 10.3389/fpls.2020.00829  JUN 26 2020
• Transcriptional Landscapes of Divergent Sporophyte Development in Two Mosses, Physcomitrium (Physcomitrella) patens and Funaria hygrometrica
  Kirbis, Alexander; Waller, Manuel; Ricca, Mariana; Bont, Zoe; Neubauer, Anna; et al.
  Frontiers In Plant Science  DOI: 10.3389/fpls.2020.00747 JUN 10 2020
• A pseudomolecule-scale genome assembly of the liverwort Marchantia polymorpha
  Diop, Seydina I.; Subotic, Oliver; Giraldo-Fonseca, Alejandro; Waller, Manuel; Kirbis, Alexander; et al.
  Plant Journal  DOI: 10.1111/tpj.14602  Published: MAR 2020
• Development and characterization of novel SSR markers in the endangered endemic species Ferula sadleriana
  Malkocs, Tamas; Laczko, Levente; Bereczki, Judit; Meglecz, Emese; Szoevenyi, Peter; et al.
  Applications In Plant Sciences 8(2) Special Issue, DOI: 10.1002/aps3.11321 FEB 2020
• Anthoceros genomes illuminate the origin of land plants and the unique biology of hornworts
  Fay-Wei Li, Tomoaki Nishiyama, Manuel Waller, Eftychios Frangedakis, Jean Keller, Zheng Li, Noe Fernandez-Pozo, Michael S. Barker, Tom Bennett, Miguel A. Blázquez, Shifeng Cheng, Andrew C. Cuming, Jan de Vries, Sophie de Vries, Pierre-Marc Delaux, Issa S. Diop, C. Jill Harrison, Duncan Hauser, Jorge Hernández-García, Alexander Kirbis, John C. Meeks, Isabel Monte, Sumanth K. Mutte, Anna Neubauer, Dietmar Quandt, Tanner Robison, Masaki Shimamura, Stefan A. Rensing, Juan Carlos Villarreal, Dolf Weijers, Susann Wicke, Gane K.-S. Wong, Keiko Sakakibara & Péter Szövényi
  Nature Plants. March 13, 2020. DOI: 10.1038/s41477-020-0618-2
• Towards a plant model for enigmatic U-to-C RNA editing: the organelle genomes, transcriptomes, editomes and candidate RNA editing factors in the hornwort Anthoceros agrestis
  Gerke, Philipp; Szovenyi, Peter; Neubauer, Anna; Lenz, Henning; Gutmann, Bernard; et al.
  New Phytologist, 10.1111/nph.16297
• Organellomic data sets confirm a cryptic consensus on (unrooted) land-plant relationships and provide new insights into bryophyte molecular evolution
  Bell, David; Lin, Qianshi; Gerelle, Weslery K.; Joya, Steve; Chang, Ying; et al.
  American Journal Of Botany,  DOI: 10.1002/ajb2.1397
  
• One thousand plant transcriptomes and the phylogenomics of green plants
  Leebens-Mack, James H.; Barker, Michael S.; Carpenter, Eric J.; Deyholos, Michael K.; Gitzendanner, Matthew A.; et al.
  Nature DOI: 10.1038/s41586-019-1693-2  2019
• The lichen symbiosis re-viewed through the genomes of Cladonia grayi and its algal partner Asterochloris glomerata
  Armaleo, D; Muller, O; Lutzoni, F; Andresson, OS; Blanc, G; Bode, HB; Collart, FR; Dal Grande, F; Dietrich, F; Grigoriev, IV; Joneson, S; Kuo, A; Larsen, PE; Logsdon, JM; Lopez, D; Martin, F; May, SP; McDonald, TR; Merchant, SS; Miao, V; Morin, E; Oono, R; Pellegrini, M; Rubinstein, N; Sanchez-Puerta, MV; Savelkoul, E; Schmitt, I; Slot, JC; Soanes, D; Szovenyi, P; Talbot, NJ; Veneault-Fourrey, C; Xavier, B
  BMC GENOMICS, 20 10.1186/s12864-019-5629-x  JUL 2019
• Evolution of the plant body plan
  Szovenyi, P; Waller, M; Kirbis, A
  PLANT DEVELOPMENT AND EVOLUTION, 131 1-+; 10.1016/bs.ctdb.2018.11.005 2019
• CLAVATA Was a Genetic Novelty for the Morphological Innovation of 3D Growth in Land Plants
  Whitewoods, CD; Cammarata, J; Venza, ZN; Sang, S; Crook, AD; Aoyama, T; Wang, XY; Waller, M; Kamisugi, Y; Cuming, AC; Szovenyi, P; Nimchuk, ZL; Roeder, AHK; Scanlon, MJ; Harrison, CJ
  CURRENT BIOLOGY, 28 (15):2365-+; 10.1016/j.cub.2018.05.068 AUG 6 2018
• The Physcomitrella patens gene atlas project: large-scale RNA-seq based expression data
  Perroud, PF; Haas, FB; Hiss, M; Ullrich, KK; Alboresi, A; Amirebrahimi, M; Barry, K; Bassi, R; Bonhomme, S; Chen, HD; Coates, JC; Fujita, T; Guyon-Debast, A; Lang, D; Lin, JY; Lipzen, A; Nogue, F; Oliver, MJ; de Leon, IP; Quatrano, RS; Rameau, C; Reiss, B; Reski, R; Ricca, M; Saidi, Y; Sun, N; Szovenyi, P; Sreedasyam, A; Grimwood, J; Stacey, G; Schmutz, J; Rensing, SA
  PLANT JOURNAL, 95 (1):168-182; 10.1111/tpj.13940 JUL 2018
• The Sphagnome Project: enabling ecological and evolutionary insights through a genus-level sequencing project 
  Weston, David J.; Turetsky, Merritt R.; Johnson, Matthew G.; et al. 
  NEW PHYTOLOGIST, 217 (1): 16-25 JAN 2018 10.1111/nph.14860
• …

• The evolution of life cycle transitions in plants
• The evolution of the land plant sporophyte
• The effect of ploidy on evolutionary processes
• Sex chromosome evolution and sex determination in haploid dioecy
• The genetics and epigenetics of inbreeding and outbreeding depression
• Genomic imprinting in plants lacking endosperm

• Comparative evolutionary developmental biology
• Evolutionary genomics
• Adaptation to changing climate
• Evolutionary transcriptomics
• Breeding system evolution