Plant Cytogenomics - Martin Lysák

Research areas

• Karyotype and genome evolution in plants
• Chromosome rearrangements in speciation
• Whole-genome duplications (polyploidy)
• Chromosome structure
• Evolution of repetitive DNA
• Comparative and evolutionary phylogenomics
• Molecular phylogenetics

Main objectives

• Investigation into the evolution of chromosome complements (karyotypes) in land plants.
• Understanding the role of chromosome repatterning and whole-genome duplication events in genome evolution and speciation.
• Analysis of chromosome and genome collinearity using comparative molecular cytogenetics and sequence genomics methods.

Content of research

The overarching objective of the Plant Cytogenomics group is to document, analyze and compare genome structure across the plant kingdom at different levels of complexity:

1. DNA level (genome size, repetitive elements),
2. chromosomal level (karyotype evolution, chromosome collinearity),
3. whole-genome level (genome collinearity, polyploidy),
4. species level (molecular phylogenetic frameworks, paleobiogeography).

The primary focus of the research group is comparative cytogenomics in species and plant groups with contrasting genome features and well-documented phylogenetic frameworks. The prime focus of our research is comparative and evolutionary genomics of the mustard family (crucifers, Brassicaceae). Several collaborative projects explore principles of chromosome evolution in other angiosperm groups

Our research concentrates on understanding (1) the role of chromosome rearrangements in reproductive isolation and speciation, (2) the impact of whole-genome duplication events on genome structure and cladogenesis, and (3) the evolutionary dynamics and chromosome organization of repetitive elements.

list / cards

SELECTED PUBLICATIONS

2017

• LEE, CR; WANG, B; MOJICA, JP; MANDÁKOVÁ, T; PRASAD, KV; GOICOECHEA, JL; PERERA, N; HELLSTEN, U; HUNDLEY, HN; JOHNSON, J; GRIMWOOD, J; BARRY, K; FAIRCLOUGH, S; JENKINS, JW; YU, Y; KUDRNA, D; ZHANG, J; TALAG, J; GOLSER, W; GHATTAS, K; SCHRANZ, ME; WING, R; LYSAK, MA; SCHMUTZ, J; ROKHSA,R DS; MITCHELL-OLDS, T, 2017:Young inversion with multiple linked QTLs under selection in a hybrid zone. Nature Ecology & Evolution
• MANDAKOVA, T; HLOUSKOVA, P; GERMAN, DA; LYSAKA, MA, 2017:Monophyletic Origin and Evolution of the Largest Crucifer Genomes. PLANT PHYSIOLOGY 174 (4), p. 2062 - 2071.
• MANDAKOVA, T; LI, Z; BARKER, MS; LYSAK, MA, 2017:Diverse genome organization following 13 independent mesopolyploid events in Brassicaceae contrasts with convergent patterns of gene retention. PLANT JOURNAL 91 (1), p. 3 - 21.
• MANDAKOVA, T; POUCH, M; HARMANOVA, K; ZHAN, SH; MAYROSE, I; LYSAK, MA, 2017:Multispeed genome diploidization and diversification after an ancient allopolyploidization. MOLECULAR ECOLOGY 26 (22), p. 6445 - 6462.
• RABANAL, FA; MANDAKOVA, T; SOTO-JIMENEZ, LM; GREENHALGH, R; PARROTT, DL; LUTZMAYER, S; STEFFEN, JG; NIZHYNSKA, V; MOTT, R; LYSAK, MA; CLARK, RM; NORDBORG, M, 2017:Epistatic and allelic interactions control expression of ribosomal RNA gene clusters in Arabidopsis thaliana. GENOME BIOLOGY 18

2016

• CAO, HX; VU, GTH; WANG, WQ; APPENROTH, KJ; MESSING, J; SCHUBERT, I, 2016:The map-based genome sequence of Spirodela polyrhiza aligned with its chromosomes, a reference for karyotype evolution. NEW PHYTOLOGIST 209 (1), p. 354 - 363.
• GEISER, C; MANDAKOVA, T; ARRIGO, N; LYSAK, MA; PARISOD, C, 2016:Repeated Whole-Genome Duplication, Karyotype Reshuffling, and Biased Retention of Stress-Responding Genes in Buckler Mustard. PLANT CELL 28 (1), p. 17 - 27.
• JANECKA, J; LYSAK, MA, 2016:chromDraw: an R package for visualization of linear and circular karyotypes. CHROMOSOME RESEARCH 24 (2), p. 217 - 223.
• LYSAK, MA; MANDAKOVA, T; SCHRANZ, ME, 2016:Comparative paleogenomics of crucifers: ancestral genomic blocks revisited. CURRENT OPINION IN PLANT BIOLOGY 30 , p. 108 - 115.
• MANDAKOVA T; LYSAK MA, 2016:Chromosome preparation for cytogenetic analyses in Arabidopsis. CURRENT PROTOCOLS IN PLANT BIOLOGY (1), p. 43 - 51.
• MANDAKOVA T; LYSAK MA, 2016:Painting of Arabidopsis chromosomes with chromosome-specific BAC Clones. CURRENT PROTOCOLS IN PLANT BIOLOGY , p. 359 - 371.
• MANDAKOVA, T; GLOSS, AD; WHITEMAN, NK; LYSAK, MA, 2016:How diploidization turned a tetraploid into a pseudotriploid. AMERICAN JOURNAL OF BOTANY 103 (7), p. 1187 - 1196.
• WATANABE, K; BREIER, U; HENSEL, G; KUMLEHN, J; SCHUBERT, I; REISS, B, 2016:Stable gene replacement in barley by targeted double-strand break induction. JOURNAL OF EXPERIMENTAL BOTANY 67 (5), p. 1433 - 1445.

2015

• HOHMANN, N; WOLF, EM; LYSAK, MA; KOCH, MA, 2015:A time-calibrated road map of Brassicaceae species radiation and evolutionary history. PLANT CELL 27 , p. 2770 - 2784.
• CHENG, F; LYSAK, MA; MANDÁKOVÁ, T; WANG, X, 2015:The common ancestral genome of the Brassica species. In: Wang X, Kole Ch (eds.) The Brassica rapa Genome. Springer. , p. 97 - 106.
• CHUMOVA, Z; KREJCIKOVA, J; MANDAKOVA, T; SUDA, J; TRAVNICEK, P, 2015:Evolutionary and Taxonomic Implications of Variation in Nuclear Genome Size: Lesson from the Grass Genus Anthoxanthum (Poaceae). PLOS ONE 10 (7), p. e0133748 - .
• KELLY, LJ; RENNY-BYFIELD; PELLICER, J; MACAS, J; NOVÁK, P; NEUMANN, P; LYSAK, MA; DAY, PD; BERGER, M; FAY, MF; NICHOLS, RA; LEITCH, AR; LEITCH, IJ, 2015:Analysis of the giant genomes of Fritillaria (Liliaceae) indicates that a lack of DNA removal characterizes extreme expansions in genome size. NEW PHYTOLOGIST 208 (2), p. 596 - 607.
• KOLÁŘ, F; LUČANOVÁ, M; ZÁVESKÁ, E; FUXOVÁ, G; MANDÁKOVÁ, T; ŠPANIEL, S; SENKO, D; SVITOK, M; KOLNÍK, M; GUDŽINSKAS, Z; MARHOLD, K, 2015:Ecological segregation does not drive the intricate parapatric distribution of diploid and tetraploid cytotypes of the Arabidopsis arenosa group (Brassicaceae). BIOLOGICAL JOURNAL OF THE LINNEAN SOCIETY
• LYSAK, MA, 2015:Chromosome "fusions" in karyotype evolution. MCGRAW-HILL YEARBOOK OF SCIENCE & TECHNOLOGY 2015 , p. 50 - 53.
• MANDAKOVA, T; SCHRANZ, ME; SHARBEL, TF; DE JONG, H; LYSAK, MA, 2015:Karyotype evolution in apomictic Boechera and the origin of the aberrant chromosomes. PLANT JOURNAL 82 (5), p. 785 - 793.
• MANDAKOVA, T; SINGH, V; KRAMER, U; LYSAK, MA, 2015:Genome Structure of the Heavy Metal Hyperaccumulator Noccaea caerulescens and Its Stability on Metalliferous and Nonmetalliferous Soils. PLANT PHYSIOLOGY 169 (1), p. 674 - 689.
• TAN, EH; HENRY, IM; RAVI, M; BRADNAM, KR; MANDAKOVA, T; MARIMUTHU, MP; KORF, I; LYSAK, MA; COMAI, L; CHAN, SW, 2015:Catastrophic chromosomal restructuring during genome elimination in plants. ELIFE 4 , p. e06516 - .
• TRAN, TD; CAO, HX; JOVTCHEV, G; NEUMANN, P; NOVAK, P; FOJTOVA, M; VU, GTH; MACAS, J; FAJKUS, J; SCHUBERT, I; FUCHS, J, 2015:Centromere and telomere sequence alterations reflect the rapid genome evolution within the carnivorous plant genus Genlisea. PLANT JOURNAL 84 (6), p. 1087 - 1099.
• WICKER, T; WING, RA; SCHUBERT, I, 2015:Recurrent sequence exchange between homeologous grass chromosomes. PLANT JOURNAL 84 (4), p. 747 - 759.
• WILLING, E-M; RAWAT, V; MANDÁKOVÁ, T; MAUMUS, F; VELIKKAKAM JAMES, G; NORDSTRÖM, KJV; BECKER, C; WARTHMANN, N; CHICA, C; SZARZYNSKA, B; ZYTNICKI, M; ALBANI, MC; KIEFER, C; BERGONZI, S; CASTAINGS, L; MATEOS, JL; BERNS, MC; BUJDOSO, N; PIOFCZYK, T; DE LORENZO, L; BARRERO-SICILIA, C; MATEOS, I; PIEDNOËL, M; HAGMANN, J; CHEN-MIN-TAO, R; IGLESIAS-FERNÁNDEZ, R; SCHUSTER, SC; ALONSO-BLANCO, C; ROUDIER, F; CARBONERO, P; PAZ-ARES, J; DAVIS, SJ; PECINKA, A; QUESNEVILLE, H; COLOT, V; LYSAK, MA; WEIGEL, D; COUPLAND, G; SCHNEEBERGER, K, 2015:Genome expansion of Arabis alpina linked with retrotransposition and reduced symmetric DNA methylation. NATURE PLANTS 1 (2), p. 1 - 7.

2014

• HAY, AS; PIEPER, B; COOKE, E; MANDAKOVA, T; CARTOLANO, M; TATTERSALL, AD; IOIO, RD; MCGOWAN, SJ; BARKOULAS, M; GALINHA, C; RAST, MI; HOFHUIS, H; THEN, C; PLIESKE, J; GANAL, M; MOTT, R; MARTINEZ-GARCIA, JF; CARINE, MA; SCOTLAND, RW; GAN, XC; FILATOV, DA; L, 2014:Cardamine hirsuta: a versatile genetic system for comparative studies. PLANT JOURNAL 78 (1), p. 1 - 15.
• KIEFER, M; SCHMICKL, R; GERMAN, DA; MANDAKOVA, T; LYSAK, MA; AL-SHEHBAZ, IA; FRANZKE, A; MUMMENHOFF, K; STAMATAKIS, A; KOCH, MA, 2014:BrassiBase: Introduction to a Novel Knowledge Database on Brassicaceae Evolution. PLANT AND CELL PHYSIOLOGY 55 (1), p. e3 - .
• LYSAK, MA, 2014:Live and let die: centromere loss during evolution of plant chromosomes. NEW PHYTOLOGIST 203 (4), p. 1082 - 1089.
• MAJEROVA, E; MANDAKOVA, T; VU, GTH; FAJKUS, J; LYSAK, MA; FOJTOVA, M, 2014:Chromatin features of plant telomeric sequences at terminal vs. internal positions. FRONTIERS IN PLANT SCIENCE 5 , p. 593 - .
• MANDAKOVA, T; MARHOLD, K; LYSAK, MA, 2014:The widespread crucifer species Cardamine flexuosa is an allotetraploid with a conserved subgenomic structure. NEW PHYTOLOGIST 201 (3), p. 982 - 992.
• ZOZOMOVA-LIHOVA, J; KRAK, K; MANDAKOVA, T; SHIMIZU, KK; SPANIEL, S; VIT, P; LYSAK, MA, 2014:Multiple hybridization events in Cardamine (Brassicaceae) during the last 150 years: revisiting a textbook example of neoallopolyploidy. ANNALS OF BOTANY 113 (5), p. 817 - 830.
• ZOZOMOVA-LIHOVA, J; MANDAKOVA, T; KOVARIKOVA, A; MUHLHAUSEN, A; MUMMENHOFF, K; LYSAK, MA; KOVARIK, A, 2014:When fathers are instant losers: homogenization of rDNA loci in recently formed Cardamine X schulzii trigenomic allopolyploid. NEW PHYTOLOGIST 203 (4), p. 1096 - 1108.

2013

• HAUDRY, A; PLATTS, AE; VELLO, E; HOEN, DR; LECLERCQ, M; WILLIAMSON, RJ; FORCZEK, E; JOLY-LOPEZ, Z; STEFFEN, JG; HAZZOURI, KM; DEWAR, K; STINCHCOMBE, JR; SCHOEN, DJ; WANG, XW; SCHMUTZ, J; TOWN, CD; EDGER, PP; PIRES, JC; SCHUMAKER, KS; JARVIS, DE; MANDAKOVA, 2013:An atlas of over 90,000 conserved noncoding sequences provides insight into crucifer regulatory regions. NATURE GENETICS 45 (8), p. 891 - U228.
• LONG, Q; RABANAL, FA; MENG, DZ; HUBER, CD; FARLOW, A; PLATZER, A; ZHANG, QR; VILHJALMSSON, BJ; KORTE, A; NIZHYNSKA, V; VORONIN, V; KORTE, P; SEDMAN, L; MANDAKOVA, T; LYSAK, MA; SEREN, U; HELLMANN, I; NORDBORG, M, 2013:Massive genomic variation and strong selection in Arabidopsis thaliana lines from Sweden. NATURE GENETICS 45 (8), p. 884 - U218.
• MANDAKOVA, T; KOVARIK, A; ZOZOMOVA-LIHOVA, J; SHIMIZU-INATSUGI, R; SHIMIZU, KK; MUMMENHOFF, K; MARHOLD, K; LYSAK, MA, 2013:The More the Merrier: Recent Hybridization and Polyploidy in Cardamine. PLANT CELL 25 (9), p. 3280 - 3295.
• SLOTTE, T; HAZZOURI, KM; AGREN, JA; KOENIG, D; MAUMUS, F; GUO, YL; STEIGE, K; PLATTS, AE; ESCOBAR, JS; NEWMAN, LK; WANG, W; MANDAKOVA, T; VELLO, E; SMITH, LM; HENZ, SR; STEFFEN, J; TAKUNO, S; BRANDVAIN, Y; COOP, G; ANDOLFATTO, P; HU, TT; BLANCHETTE, M; CL, 2013:The Capsella rubella genome and the genomic consequences of rapid mating system evolution. NATURE GENETICS 45 (7), p. 831 - U165.
• ZD'ARSKA, M; ZATLOUKALOVA, P; BENITEZ, M; SEDO, O; POTESIL, D; NOVAK, O; SVACINOVA, J; PESEK, B; MALBECK, J; VASICKOVA, J; ZDRAHAL, Z; HEJATKO, J, 2013:Proteome Analysis in Arabidopsis Reveals Shoot- and Root-Specific Targets of Cytokinin Action and Differential Regulation of Hormonal Homeostasis. PLANT PHYSIOLOGY 161 (2), p. 918 - 930.

2012

• MANDAKOVA, T; MUMMENHOFF, K; AL-SHEHBAZ, IA; MUCINA, L; MUHLHAUSEE, A; LYSAK, MA, 2012:Whole-genome triplication and species radiation in the southern African tribe Heliophileae (Brassicaceae). TAXON 61 (5), p. 989 - 1000.

2011

• FRANZKE, A; LYSAK, MA; AL-SHEHBAZ, IA; KOCH, MA; MUMMENHOFF, K, 2011:Cabbage family affairs: the evolutionary history of Brassicaceae. TRENDS IN PLANT SCIENCE 16 (2), p. 108 - 116.
• SCHUBERT, I; LYSAK, MA, 2011:Interpretation of karyotype evolution should consider chromosome structural constraints. TRENDS IN GENETICS 27 (6), p. 207 - 216.

2010

• MANDAKOVA, T; JOLY, S; KRZYWINSKI, M; MUMMENHOFF, K; LYSAK, MA, 2010:Fast Diploidization in Close Mesopolyploid Relatives of Arabidopsis. PLANT CELL 22 (7), p. 2277 - 2290.

GRANTY

• Establishing Czech-Icelandic collaboration in plant cytogenomics (EHP-CZ07-MOP-1-1052014), Ministry of Finance - EEA / Norway Grants, 2015 - 2016
• Genome evolution and spatiotemporal diversity of the Arabideae (GA15-18545S), Czech Science Foundation - Standard Grants, 2015 - 2017
• Evolution and function of complex plant genomes (P501/12/G090), Czech Science Foundation - Projects for promotion of excellence in basic research, 2012 - 2018
• Evolutionary patterns in polyploid complexes: congruent or discordant histories in three examples from the Brassicaceae family (GAP506/12/0668), Czech Science Foundation - Standard Grants, 2012 - 2015
• Development of excellence in evolutionary cytogenomics, epigenetics and cell Signalling (CZ.1.07/2.3.00/20.0189), MEYS - OP Education for Competiteveness, 2012 - 2015

CURRENT RESEARCH INFRASTRUCTURE

The current infrastructure includes equipment for molecular cytogenetics and phylogenetics, such as high-end fluorescence microscopes, PCR cyclers, electrophoreses, gel documentation system, and other standard laboratory equipment for molecular biology. Experimental materials are accommodated in spacious greenhouses and walk-in growth chambers.

1. Genome evolution in the Brassicales

Supervisor: doc. Mgr. Martin Lysák, Ph.D.

Annotation

The order Brassicales contains ca. 4,700 species in 17 families including several model families for evolutionary biology. The aim of the project is to reconstruct key evolutionary events which shaped the extant genome of this angiosperm clade. PhD student will use combination of phylogenomic tools to characterize selected Brassicales genomes and reconstruct past evolutionary events. Although experience of bioinformatics would be a distinct advantage, applications are welcome from enthusiastic and committed students.

Keywords: Brassicales, evolutionary biology, phylogenomic tools

2. Repeatome evolution in crucifers

Supervisor: doc. Mgr. Martin Lysák, Ph.D., DSc.

Annotation

Repeats are prominent componenents of plant genomes. The work will be centred on analysis of diversity and evolution of repetitive elements in crucifer genomes using next-generation sequencing platforms. The evolution of sequenced repeatomes will be analyzed within existin and newly built phylogenetic frameworks.

Keywords: crucifer genomes, next-generation sequencing, phylogenetic, repeatome evolution