Martin Lysak

Masaryk University, Central European Institute of Technology, Faculty Member

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The Aquilegia genome provides insight into adaptive radiation and reveals an extraordinarily polymorphic chromosome with a unique history

eLife, 2018

The columbine genus Aquilegia is a classic example of an adaptive radiation, involving a wide var... more The columbine genus Aquilegia is a classic example of an adaptive radiation, involving a wide variety of pollinators and habitats. Here we present the genome assembly of A. coerulea ‘Goldsmith’, complemented by high-coverage sequencing data from 10 wild species covering the world-wide distribution. Our analyses reveal extensive allele sharing among species and demonstrate that introgression and selection played a role in the Aquilegia radiation. We also present the remarkable discovery that the evolutionary history of an entire chromosome differs from that of the rest of the genome – a phenomenon that we do not fully understand, but which highlights the need to consider chromosomes in an evolutionary context.

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The Aquilegia genome provides insight into adaptive radiation and reveals an extraordinarily polymorphic chromosome with a unique history

by Daniele Filiault, Juying Yan, and Martin Lysak

eLife, 2018

The columbine genus Aquilegia is a classic example of an adaptive radiation, involving a wide var... more The columbine genus Aquilegia is a classic example of an adaptive radiation, involving a wide variety of pollinators and habitats. Here we present the genome assembly of A. coerulea 'Goldsmith', complemented by high-coverage sequencing data from 10 wild species covering the worldwide distribution. Our analyses reveal extensive allele sharing among species and demonstrate that introgression and selection played a role in the Aquilegia radiation. We also present the remarkable discovery that the evolutionary history of an entire chromosome differs from that of the rest of the genome-a phenomenon that we do not fully understand, but which highlights the need to consider chromosomes in an evolutionary context.

format_quoteChromosome four shows exceptionally high polymorphism, with levels strikingly higher than other chromosomes, tied to inbreeding metrics.format_quote

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Cytogenetic analyses of Arabidopsis

Methods in molecular biology (Clifton, N.J.), 2006

For a long time, Arabidopsis thaliana was not a favorite of cytogeneticists because of its small ... more For a long time, Arabidopsis thaliana was not a favorite of cytogeneticists because of its small chromosomes. Nevertheless, most cytogenetic approaches have become applicable to this model plant during the past decade. Recently, the very small genome, the low content, and strong clustering of repetitive sequences even turned out to be advantageous for the first establishment of chromosome painting in a euploid plant. Chromosome painting together with the high-resolution fluorescence in situ hybridization (FISH) mapping on Arabidopsis pachytene chromosomes has opened new perspectives for plant cytogenetics. In this chapter, we describe standard cytogenetic methods including preparation of chromosomes and chromatin fibers, isolation of interphase nuclei, FISH and immunostaining, painting of Arabidopsis chromosomes, and comparative chromosome painting in other Brassicaceae species.

Cytogenetic Analyses of <i>Arabidopsis</i>

Arabidopsis Protocols, 2006

Comparative Cytogenetics of Wild Crucifers (Brassicaceae)

Biology and Breeding of Crucifers, 2009

Phylogenetic analyses of ITS and rbcL DNA sequences for sixteen genera of Australian and New Zealand Brassicaceae result in the expansion of the tribe Microlepidieae

Sequence data from the internal transcribed spacer (ITS) nrDNA and rbcL cpDNA regions were used t... more Sequence data from the internal transcribed spacer (ITS) nrDNA and rbcL cpDNA regions were used to determine relationships of genera of Brassicaceae from Australia and New Zealand (NZ) that were previously unassigned to a tribe. Maximum likelihood analysis of 71 ITS sequences identified a monophyletic clade of Australian genera, including Carina valva and Microlepidium that had previously been assigned to the tribe Microlepidieae. Pachycladon is not supported as monophyletic, comprising a clade of the NZ species and another clade of the Tasmanian P. radicatum. These two Pachycladon clades form a polytomy with the Australian clade. Maximum likelihood analysis of the rbcL region generally supports the ITS analysis with the Australian genera forming a monophyletic clade with Pachycladon. Arabidella is polyphyletic in the rbcL phylogeny as A. eremigena is member of the Australian clade but A. trisecta is placed in a sister clade that comprises mainly genera of tribe Camelineae. As a result of these phylogenetic analyses the tribe Microlepidieae is expanded and now includes 16 genera and 56 species endemic to Australia and New Zealand. Genera included in the Microlepidieae are Arabidella, Ballantinia, Blen nodia, Carinavalva, Cuphonotus, Drabastrum, Geococcus, Harmsiodoxa, Irenepharsus, Menkea, Microlepidium, Pachycladon, Pachymitus, Phlegmatospermum, Scambopus and Stenopetalum. Whole-genome duplication has previously been shown to have occurred in the ancestry of Arabidella, Ballantinia, Pachycladon and Stenopetalum and is likely to be a defining feature of the tribe Microlepidieae. Future research needs to investigate circumscription of the Australian genera as there is a predominance of closely related monotypic genera in the Microlepidieae. With resolution of the tribal placement of these Australian and New Zealand genera, ca. 94% (302) of the 321 genera in the family have been assigned to a tribe.

format_quoteThe ITS analysis identified 14 Australian genera as a monophyletic clade, while Pachycladon was found not to be monophyletic.format_quote

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Correlation between GC content ond genome size in plants

... Original title: Correlation between GC content ond genome size in plants. Authors: Petr Bure... more

Plant Genome Size Estimation by Flow Cytometry: Inter-laboratory Comparison

Annals of Botany, 1998

Flow cytometry is a convenient and rapid method that has been used extensively for estimation of ... more Flow cytometry is a convenient and rapid method that has been used extensively for estimation of nuclear genome size in plants. In contrast to general expectations, results obtained in different laboratories showed some striking discrepancies. The aim of this joint experiment was to test the reliability and reproducibility of methods. Care was taken to avoid a bias due to the quantity of DNA in the nucleus, the procedure for nuclei isolation or the type of instrument. Nuclear DNA content was estimated in nine plant species representing a typical range of genome size (2C = approx. 03-30 pg DNA). Each of the four laboratories involved in this study used a different buffer and/or procedure for nuclei isolation. Two laboratories used arc lamp-based instruments while the other two used laser-based instruments. The results obtained after nuclei staining with propidium iodide (a DNA intercalator) agreed well with those obtained using Feulgen densitometry. On the other hand, results obtained after staining with DAPI (binding preferentially to AT-rich regions) did not agree with those obtained using Feulgen densitometry. Small, but statistically significant, differences were found between data obtained with individual instruments. Differences between the same type of instruments were negligible, while larger differences were observed between lamp-and laserbased instruments. Ratios of fluorescence intensity obtained by laser instruments were higher than those obtained by lamp-based cytometers or by Feulgen densitometry. The results obtained in this study demonstrate that flow cytometry with DNA intercalators is a reliable method for estimation of nuclear genome size in plants. However, the study confirmed an urgent need for an agreement on standards. Given the small but systematic differences between different types of flow cytometers, analysis of very small differences in genome size should be made in the same laboratory and using the same instrument.

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Running head: Triplication of ancestral chromosomal blocks in Brassiceae Research area: Genetics, Genomics, and Molecular Evolution

The paleopolyploid character of genomes of the economically important genus Brassica and closely ... more The paleopolyploid character of genomes of the economically important genus Brassica and closely related species (tribe Brassiceae) is still fairly controversial. Here we report on the comparative painting analysis of the block F of the crucifer Ancestral Karyotype (AK; n=8), consisting of 24 conserved genomic blocks, in ten species traditionally treated as members of the tribe Brassiceae.

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Genome structure of the heavy metal hyperaccumulator Noccaea caerulescens and its stability on metalliferous and non-metalliferous soils

Plant physiology, Jan 20, 2015

Noccaea caerulescens (Thlaspi caerulescens), an extremophile heavy metal hyperaccumulator model p... more Noccaea caerulescens (Thlaspi caerulescens), an extremophile heavy metal hyperaccumulator model plant in the Brassicaceae family, is a morphologically and phenotypically diverse species exhibiting metal tolerance and leaf accumulation of zinc, cadmium and nickel. Here we provide a detailed genome structure of the ~267-Mb N. caerulescens genome, which has descended from seven chromosomes of the ancestral Proto-Calepineae Karyotype (PCK, n = 7) through an unusually high number of pericentric inversions. Genome analysis in two other related species, N. jankae and Raparia bulbosa, showed that all three species - and thus probably entire Coluteocarpeae tribe - have descended from the PCK. All three analyzed species share the chromosome structure of six out of seven chromosomes and an unusually high metal accumulation in leaves, which remains moderate in N. jankae and R. bulbosa, and is extreme in N. caerulescens. Among these species, N. caerulescens has the most derived karyotype with sp...

Estimation of nuclear DNA content in Sesleria (Poaceae)

Caryologia, 1998

ABSTRACT

On the age of the mustard family (Brassicaceae)

Nature

This is a detailed comment on a "Research Highlight Contribution": On the age of the mu... more This is a detailed comment on a "Research Highlight Contribution": On the age of the mustard family (Brassicaceae) Andreas Franzke^a^, Marcus A. Koch^b^, Thomas L.P. Couvreur^c^, Martin A. Lysak^d^, and Klaus Mummenhoff^e^ ^a^Botanical Garden, Heidelberg Institute of Plant Sciences, Heidelberg University, D-69120 Heidelberg ^b^Department Biodiversity and Plant Systematics, Heidelberg Institute of Plant Sciences, University of Heidelberg, Im Neuenheimer Feld 345, D-69120 Heidelberg ^c^The New York Botanical Garden, 200th St. and Kazimiroff Blvd., Bronx, NY 10458-5126 ^d^Department of Functional Genomics and Proteomics, Faculty of Science, Masaryk University, Kamenice 5, CZ-62500 Brno ^e^Department of Biology, Botany, University of OsnabrÃ¼ck, Barbarastrasse 11, D-49076 OsnabrÃ¼ck New age estimates for the mustard and related families (Brassicales) were recently published by Beilstein et al. (1), based on a relaxed-clock model calibrated with four fossils including a potenti...

Karyotype evolution in apomictic Boechera and the origin of the aberrant chromosomes

The Plant journal : for cell and molecular biology, Jan 10, 2015

Chromosome rearrangements may result in both decrease and increase of chromosome numbers. Here we... more Chromosome rearrangements may result in both decrease and increase of chromosome numbers. Here we have used comparative chromosome painting (CCP) to reconstruct the pathways of descending and ascending dysploidy in the genus Boechera (tribe Boechereae, Brassicaceae). We describe the origin and structure of three Boechera genomes and establish the origin of the previously described aberrant Het and Del chromosomes found in Boechera apomicts with euploid (2n = 14) and aneuploid (2n = 15) chromosome number. CCP analysis allowed us to reconstruct the origin of seven chromosomes in sexual B. stricta and apomictic B. divaricarpa from the ancestral karyotype (n = 8) of Brassicaceae lineage I. Whereas three chromosomes (BS4, BS6, and BS7) retained their ancestral structure, five chromosomes were reshuffled by reciprocal translocations to form chromosomes BS1-BS3 and BS5. The reduction of the chromosome number (from x = 8 to x = 7) was accomplished through the inactivation of a paleocentrome...

Live and let die: centromere loss during evolution of plant chromosomes

New Phytologist, 2014

Functional centromeres, ensuring regular chromosome segregation in mitosis and meiosis, are a pre... more Functional centromeres, ensuring regular chromosome segregation in mitosis and meiosis, are a prerequisite for the evolutionary success of pre-existing and new chromosome variants. The rapid progress in plant comparative genomics and cytogenetics brings new insights into the evolutionary fate of centromeres and mechanisms of chromosome number reduction (descending dysploidy). Centromere loss and relocation in chromosome regions with otherwise conserved collinearity can be explained by conventional mechanisms of chromosome rearrangements or, as newly available phylogenomic and cytogenomic data suggest, by centromere inactivation through epigenetic chromatin modifications and/or intra-and inter-chromosomal recombination.

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A bicontinental origin of polyploid Australian/New Zealand Lepidium species (Brassicaceae)? Evidence from genomic in situ hybridization

Annals of botany, 2009

Incongruence between chloroplast and nuclear DNA phylogenies, and single additive nucleotide posi... more Incongruence between chloroplast and nuclear DNA phylogenies, and single additive nucleotide positions in internal transcribed spacer (ITS) sequences of polyploid Australian/New Zealand (NZ) Lepidium species have been used to suggest a bicontinental hybrid origin. This pattern was explained by two trans-oceanic dispersals of Lepidium species from California and Africa and subsequent hybridization followed by homogenization of the ribosomal DNA sequence either to the Californian (C-clade) or to the African ITS-type (A-clade) in two different ITS-lineages of Australian/NZ Lepidium polyploids. Genomic in situ hybridization (GISH) was used to unravel the genomic origin of polyploid Australian/NZ Lepidium species. Fluorescence in situ hybridization (FISH) with ribosomal DNA (rDNA) probes was applied to test the purported ITS evolution, and to facilitate chromosome counting in high-numbered polyploids. In Australian/NZ A-clade Lepidium polyploids, GISH identified African and Australian/NZ...

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Inter laboratory comparison for reliability and reproducibility of plant DNA flow cytometry

European journal of histochemistry : EJH, 1997

Search by Subject Search using Medical Subject Headings (&amp;amp;amp;amp;amp;amp;lt; b&a... more Search by Subject Search using Medical Subject Headings (&amp;amp;amp;amp;amp;amp;lt; b&amp;amp;amp;amp;amp;amp;gt; MeSH&amp;amp;amp;amp;amp;amp;lt;/b&amp;amp;amp;amp;amp;amp;gt;), a controlled vocabulary for indexing life sciences content.&amp;amp;amp;amp;amp;amp;lt; br/&amp;amp;amp;amp;amp;amp;gt; Note that some records do not have MeSH. These include Patents and the latest PubMed and PubMed Central records.

From transposon to chromosome and polyploidy. An update on cytogenetics and genomics of Arabidopsis

by Martin Lysak and Paul Fransz

Chromosome research : an international journal on the molecular, supramolecular and evolutionary aspects of chromosome biology, 2014

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FISH analysis of meiosis in Arabidopsis allopolyploids

Chromosome research : an international journal on the molecular, supramolecular and evolutionary aspects of chromosome biology, 2003

Although allopolyploids are common in nature and in agriculture, knowledge of their origin, evolu... more Although allopolyploids are common in nature and in agriculture, knowledge of their origin, evolution and genomic regulation is limited. We study synthetic allotetraploids of Arabidopsis thaliana and Arabidopsis arenosa as well as the natural allotetraploid Arabidopsis suecica. To elucidate the composition and behavior of the allotetraploid genome, we used chromosome painting with probes from contiguous regions of chromosome 4 of A. thaliana and fluorescent in-situ hybridization with centromeric (CEN) probes specific for each parental genome. We documented the presence of 16 A. arenosa and 10 A. thaliana chromosomes and demonstrate that two different A. arenosa chromosomes are homeologous to chromosome 4 of A. thaliana. Although chromosome pairing in pollen mother cells was predominantly homologous, CENs of different parental origin coalesced at early prophase I, but resolved into proper pairs by metaphase. In addition, CENs of homologous chromosomes were not paired in tapetum cells...

Analysis of Plant Meiotic Chromosomes by Chromosome Painting

Methods in Molecular Biology, 2013

Chromosome painting (CP) refers to visualization of large chromosome regions, entire chromosome a... more Chromosome painting (CP) refers to visualization of large chromosome regions, entire chromosome arms, or entire chromosomes via fluorescence in situ hybridization (FISH). For CP in plants, contigs of chromosome-specific bacterial artificial chromosomes (BAC) from the target species or from a closely related species (comparative chromosome painting, CCP) are typically applied as painting probes. Extended pachytene chromosomes provide the highest resolution of CP in plants. CP enables identification and tracing of particular chromosome regions and/or entire chromosomes throughout all meiotic stages as well as corresponding chromosome territories in premeiotic interphase nuclei. Meiotic pairing and structural chromosome rearrangements (typically inversions and translocations) can be identified by CP. Here, we describe step-by-step protocols of CP and CCP in plant species including chromosome preparation, BAC DNA labeling, and multicolor FISH.

The origin, evolution and proposed stabilization of the terms 'genome size' and 'C-value' to describe nuclear DNA contents

Annals of botany, 2005

Perusing the literature on nuclear 'genome size' shows that the term is not stabilized, b... more Perusing the literature on nuclear 'genome size' shows that the term is not stabilized, but applied with different meanings. It is used for the DNA content of the complete chromosome complement (with chromosome number n), for which others use 'C-value', but also for the DNA content of the monoploid chromosome set only (with chromosome number x). Reconsideration of the terminology is required. Our purpose is to discuss the currently unstable usage of the terms 'genome…

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