Papers by Václav Bačovský
Molecular biology and evolution, Apr 12, 2024
Journal of experimental botany, Apr 23, 2024
Y chromosomes are thought to undergo progressive degeneration due to stepwise loss of recombinati... more Y chromosomes are thought to undergo progressive degeneration due to stepwise loss of recombination and subsequent reduction in selection efficiency. However, the timescales over which degeneration occurs and the evolutionary forces driving degeneration remain unclear. In order to characterize the evolution of sex chromosomes on multiple timescales, we generated a high-quality phased genome assembly of the massive older (7-9 MYA) and neo (<200,000 years) sex chromosomes in the XYY cytotype of the plant Rumex hastatulus, along with a hermaphroditic outgroup Rumex salicifolius. Our assemblies confirmed the neo-sex chromosomes were formed by two key events: an X-autosome fusion and a reciprocal translocation between the homologous autosome and the Y chromosome. The enormous sex-linked regions of the X (296 MB) and the two Y chromosomes (503 MB) both arose in a large repeat-rich genome with low recombination, however the complete loss of recombination on the Y still led to over 30% g...
Methods in molecular biology, Oct 20, 2017
Significant advances in chromosome preparation and other techniques have greatly increased the po... more Significant advances in chromosome preparation and other techniques have greatly increased the potential of plant cytogenetics in recent years. Increase in longitudinal resolution using DNA extended fibers as well as new developments in imaging and signal amplification technologies have enhanced the ability of FISH to detect small gene targets. The combination of fluorescence in situ hybridization with immunocytochemistry allows the investigation of cell events, chromosomal rearrangements and chromatin features typical for plant nuclei. Chromosome manipulation techniques using microdissection and flow sorting have accelerated the analysis of complex plant genomes. Together, the different cytogenetic approaches are invaluable for the unravelling of detailed structures of plant chromosomes, which are of utmost importance for the study of genome properties, DNA replication and gene regulation. In this technical review, different cytogenetic approaches are discussed for the analysis of plant chromosomes, with a focus on mitotic chromosomes.
Heart, Vessels and Transplantation
Genetic variability was studied in two species of the genus Aesculus L.: A. turbinata and A. hipp... more Genetic variability was studied in two species of the genus Aesculus L.: A. turbinata and A. hippocastanum; ten clones of explant cultures of A. hippocastanum L. derived by organogenesis and somatic embryogenesis from donor resistant and susceptible to horse chestnut leaf-miner (Cameraria ohridella) were compared using microsatellite (SSR) markers. A total of 28 alleles were detected at the 8 SSR loci. The number of alleles generated by each marker ranged from 1 to 5 with an average of 3.5 alleles per locus. Statistical indicators were calculated for each SSR marker. We found low level of genetic variability. The value of polymorphic information content ranged from 0.00 to 0.74 (average 0.43). Conformity of donor plant resistant to C. ohridella and its in vitro horse chestnut clones (cultivar ‘Mertelík’) was demonstrated. No changes caused by in vitro cultivation were observed on molecular level. On the contrary, explant cultures of the susceptible genotype of A. hippocastanum did n...
Methods in Molecular Biology, 2017
Significant advances in chromosome preparation and other techniques have greatly increased the po... more Significant advances in chromosome preparation and other techniques have greatly increased the potential of plant cytogenetics in recent years. Increase in longitudinal resolution using DNA extended fibers as well as new developments in imaging and signal amplification technologies have enhanced the ability of FISH to detect small gene targets. The combination of fluorescence in situ hybridization with immunocytochemistry allows the investigation of cell events, chromosomal rearrangements and chromatin features typical for plant nuclei. Chromosome manipulation techniques using microdissection and flow sorting have accelerated the analysis of complex plant genomes. Together, the different cytogenetic approaches are invaluable for the unravelling of detailed structures of plant chromosomes, which are of utmost importance for the study of genome properties, DNA replication and gene regulation. In this technical review, different cytogenetic approaches are discussed for the analysis of plant chromosomes, with a focus on mitotic chromosomes.
Philosophical Transactions of the Royal Society B: Biological Sciences
Microscopically dimorphic sex chromosomes in plants are rare, reducing our ability to study them.... more Microscopically dimorphic sex chromosomes in plants are rare, reducing our ability to study them. One difficulty has been the paucity of cultivatable species pairs for cytogenetic, genomic and experimental work. Here, we study the newly recognized sisters Coccinia grandis and Coccinia schimperi , both with large Y chromosomes as we here show for Co. schimperi . We built genetic maps for male and female Co. grandis using a full-sibling family, inferred gene sex-linkage, and, with Co. schimperi transcriptome data, tested whether X- and Y-alleles group by species or by sex. Most sex-linked genes for which we could include outgroups grouped the X- and Y-alleles by species, but some 10% instead grouped the two species' X-alleles. There was no relationship between XY synonymous-site divergences in these genes and gene position on the non-recombining part of the X, suggesting recombination arrest shortly before or after species divergence, here dated to about 3.6 Ma. Coccinia grandis a...
Philosophical Transactions of the Royal Society B: Biological Sciences
In a minority of flowering plants, separate sexes are genetically determined by sex chromosomes. ... more In a minority of flowering plants, separate sexes are genetically determined by sex chromosomes. The Y chromosome has a non-recombining region that degenerates, causing a reduced expression of Y genes. In some species, the lower Y expression is accompanied by dosage compensation (DC), a mechanism that re-equalizes male and female expression and/or brings XY male expression back to its ancestral level. Here, we review work on DC in plants, which started as early as the late 1960s with cytological approaches. The use of transcriptomics fired a controversy as to whether DC existed in plants. Further work revealed that various plants exhibit partial DC, including a few species with young and homomorphic sex chromosomes. We are starting to understand the mechanisms responsible for DC in some plants, but in most species, we lack the data to differentiate between global and gene-by-gene DC. Also, it is unknown why some species evolve many dosage compensated genes while others do not. Final...
This collection of supplementary data include raw RNA-seq data for each sample in the main manusc... more This collection of supplementary data include raw RNA-seq data for each sample in the main manuscript in triplicate (male, female, two generations of hermaphrodites), 12 Supplementary figures, 5 Supplementary Tables, 8 Datasets and. RNA-seq data were not processed. The supplementary figures and tables support major findings of the main article titled "Chemical genetics in Silene latifolia elucidate regulatory pathways involved in gynoecium development" and include schematic workflow of the experimental procedure regarding in vitro assay, phenotyping and bioinformatic analysis. Further collection of figures includes a pedigree of androhermahroditic inheritance, the effect of chemical treatment on developing seedlings, electron micrographs of female flower in the androhermaphrodite progeny, viability staining, carpel examination, RNA-seq data validation, Volcano plots, TEs expression, gene ontology and clustering analysis. Tables include data for transcriptomic analysis. Sup...
bioRxiv, 2021
Dioecious plants possess diverse sex determination systems and unique mechanisms of reproductive ... more Dioecious plants possess diverse sex determination systems and unique mechanisms of reproductive organ development; however, little is known about how sex-linked genes shape the expression of regulatory cascades that lead to developmental differences between sexes. In Silene latifolia, a dioecious plant with stable dimorphism in floral traits, early experiments suggested that female-regulator genes act on the factors that determine the boundaries of the flower whorls. To identify these regulators, we sequenced the transcriptome of male flowers with fully developed gynoecia induced by rapid demethylation in the parental generation. As the hermaphrodite flower trait is holandric (transmitted only from male to male, inherited on the Y chromosome), we screened for genes that are differentially expressed between male, female, and hermaphrodite flowers. Dozens of candidate genes that are upregulated in hermaphrodite flowers compared to male and female flowers were detected and found to ha...
Journal of Experimental Botany, 2021
Dioecious plants possess diverse sex determination systems and unique mechanisms of reproductive ... more Dioecious plants possess diverse sex determination systems and unique mechanisms of reproductive organ development; however, little is known about how sex-linked genes shape the expression of regulatory cascades that lead to developmental differences between sexes. In Silene latifolia, a dioecious plant with stable dimorphism in floral traits, early experiments suggested that female-regulator genes act on the factors that determine the boundaries of the flower whorls. To identify these regulators, we sequenced the transcriptome of male flowers with fully developed gynoecia, induced by rapid demethylation in the parental generation. Eight candidates were found to have a positive role in gynoecium promotion, floral organ size, and whorl boundary, and affect the expression of class B MADS-box flower genes. To complement our transcriptome analysis, we closely examined the floral organs in their native state using field emission environmental scanning electron microscopy, and examined th...
Some species of the genus Aesculus are every year heavily infested by horse chestnut leaf miner (... more Some species of the genus Aesculus are every year heavily infested by horse chestnut leaf miner (Cameraria ohridella), whose larvae are mining the leaves, and under appropriate conditions may damage up to 100% of the leaf area. The effect of lower defense capability of infested trees lead to invasion of fungal (Erysiphe flexuosa, Guignardia aesculi) and bacterial (Pseudomonas syringae pv. aesculi) pathogens, and later to higher mortality of infected individuals. In this study were measured the genetic diversity of species A.hippocastanum, A. turbinata, A. glabra, A. parviflora, A. glabra var. arguta, A. x carnea, A. marilandica, A. pavia, and their genotypes with different susceptibility to the leaf miner. Analysis of 8 microsatellite loci, using the SB buffer for separation, showed high polymorfic information content 0.45 -- 0.77 (0,60 in average) and high genetic diversity. For each loci was found average 5.5 aleles. During two vegetation period, leaf area damage of these genotypes was evaluated in statistical software Assess 2.0. Different pressure of leaf miner and different development at each locality was recorded, and even in some cases lower damage was found, in one case it occured permanently. According to the data obtained, the pathological scale was established and the dendogram of similarity was created. Three groups of resistant, non -- resistant and immune individuals were distinguished and five main section of Aesculus was found. By cloning and analysing the inner transcribed spacers, ITS1 and ITS2, inner and inter species variability was examined. For the sequence of hybrid species A. x carnea no compliance was found in NBCI, therefore first sequence of this genotype was obtained
Frontiers in Plant Science, 2020
The genus Silene includes a plethora of dioecious and gynodioecious species. Two species, Silene ... more The genus Silene includes a plethora of dioecious and gynodioecious species. Two species, Silene latifolia (white campion) and Silene dioica (red campion), are dioecious plants, having heteromorphic sex chromosomes with an XX/XY sex determination system. The X and Y chromosomes differ mainly in size, DNA content and posttranslational histone modifications. Although it is generally assumed that the sex chromosomes evolved from a single pair of autosomes, it is difficult to distinguish the ancestral pair of chromosomes in related gynodioecious and hermaphroditic plants. We designed an oligo painting probe enriched for X-linked scaffolds from currently available genomic data and used this probe on metaphase chromosomes of S. latifolia (2n = 24, XY), S. dioica (2n = 24, XY), and two gynodioecious species, S. vulgaris (2n = 24) and S. maritima (2n = 24). The X chromosome-specific oligo probe produces a signal specifically on the X and Y chromosomes in S. latifolia and S. dioica, mainly in the subtelomeric regions. Surprisingly, in S. vulgaris and S. maritima, the probe hybridized to three pairs of autosomes labeling their p-arms. This distribution suggests that sex chromosome evolution was accompanied by extensive chromosomal rearrangements in studied dioecious plants.
Frontiers in Plant Science, 2020
Interspecific hybridization represents one of the main mechanisms of plant speciation. Merging of... more Interspecific hybridization represents one of the main mechanisms of plant speciation. Merging of two genomes from different subspecies, species, or even genera is frequently accompanied by whole-genome duplication (WGD). Besides its evolutionary role, interspecific hybridization has also been successfully implemented in multiple breeding programs. Interspecific hybrids combine agronomic traits of two crop species or can be used to introgress specific loci of interests, such as those for resistance against abiotic or biotic stresses. The genomes of newly established interspecific hybrids (both allopolyploids and homoploids) undergo dramatic changes, including chromosome rearrangements, amplifications of tandem repeats, activation of mobile repetitive elements, and gene expression modifications. To ensure genome stability and proper transmission of chromosomes from both parental genomes into subsequent generations, allopolyploids often evolve mechanisms regulating chromosome pairing. Such regulatory systems allow only pairing of homologous chromosomes and hamper pairing of homoeologs. Despite such regulatory systems, several hybrid examples with frequent homoeologous chromosome pairing have been reported. These reports open a way for the replacement of one parental genome by the other. In this review, we provide an overview of the current knowledge of genomic changes in interspecific homoploid and allopolyploid hybrids, with strictly homologous pairing and with relaxed pairing of homoeologs.
Planta, 2019
Main conclusion Contrasting patterns of histone modifications between the X and Y chromosome in S... more Main conclusion Contrasting patterns of histone modifications between the X and Y chromosome in Silene latifolia show euchromatic histone mark depletion on the Y chromosome and indicate hyperactivation of one X chromosome in females.
Trees, 2016
Key message Species of Aesculus genus are divided into five main sections according to their susc... more Key message Species of Aesculus genus are divided into five main sections according to their susceptibility and resistance to horse chestnut leaf miner using molecular markers. Abstract Some species of the genus Aesculus are yearly severely infested by horse chestnut leaf miner (Cameraria ohridella). The larvae mine the leaves and under appropriate conditions can damage up to 100% of the leaf area. In this study, we assessed the genetic diversity of eight species of horse chestnut and their genotypes which have varying susceptibility to the leaf miner. Analysis of eight microsatellite loci showed high polymorphic information content 0.45-0.77 (0.60 in average) and high genetic diversity. For each locus, we found on average 5.50 alleles. During three vegetation periods, the leaf area damage of these genotypes was evaluated using the statistical software Assess 2.0. Different pressure of leaf miner and different development at each locality was recorded, and in some cases less damage was found, in one case the lesser damage was permanent. From the data, a pathological scale was established and a dendogram of similarity was created. Based on SSR analysis, four groups of Aesculus trees were distinguished according to their resistance or susceptibility and five main section?Hybrid were found. By cloning and analysing the inner transcribed spacers, the ITS1 and ITS2, inner and inter species variability was examined. For the sequence of hybrid species A. 9 carnea, no compliance was revealed in NBCI database. For this reason, the first sequence of this genotype was obtained.
Genetic variability was studied in two species of the genus Aesculus L.: A. turbinata and A. hipp... more Genetic variability was studied in two species of the genus Aesculus L.: A. turbinata and A. hippocastanum; ten clones of explant cultures of A. hippocastanum L. derived by organogenesis and somatic embryogenesis from donor resistant and susceptible to horse chestnut leaf-miner (Cameraria ohridella) were compared using microsatellite (SSR) markers. A total of 28 alleles were detected at the 8 SSR loci. The number of alleles generated by each marker ranged from 1 to 5 with an average of 3.5 alleles per locus. Statistical indicators were calculated for each SSR marker. We found low level of genetic variability. The value of polymorphic information content ranged from 0.00 to 0.74 (average 0.43). Conformity of donor plant resistant to C. ohridella and its in vitro horse chestnut clones (cultivar ‘Mertelík’) was demonstrated. No changes caused by in vitro cultivation were observed on molecular level. On the contrary, explant cultures of the susceptible genotype of A. hippocastanum did n...
International Journal of Molecular Sciences, 2022
Young sex chromosomes possess unique and ongoing dynamics that allow us to understand processes t... more Young sex chromosomes possess unique and ongoing dynamics that allow us to understand processes that have an impact on their evolution and divergence. The genus Silene includes species with evolutionarily young sex chromosomes, and two species of section Melandrium, namely Silene latifolia (24, XY) and Silene dioica (24, XY), are well-established models of sex chromosome evolution, Y chromosome degeneration, and sex determination. In both species, the X and Y chromosomes are strongly heteromorphic and differ in the genomic composition compared to the autosomes. It is generally accepted that for proper cell division, the longest chromosomal arm must not exceed half of the average length of the spindle axis at telophase. Yet, it is not clear what are the dynamics between males and females during mitosis and how the cell compensates for the presence of the large Y chromosome in one sex. Using hydroxyurea cell synchronization and 2D/3D microscopy, we determined the position of the sex c...
Some species of the genus Aesculus are yearly
severely infested by horse chestnut leaf miner (Cam... more Some species of the genus Aesculus are yearly
severely infested by horse chestnut leaf miner (Cameraria
ohridella). The larvae mine the leaves and under appropriate
conditions can damage up to 100% of the leaf area.
In this study, we assessed the genetic diversity of eight
species of horse chestnut and their genotypes which have
varying susceptibility to the leaf miner. Analysis of eight
microsatellite loci showed high polymorphic information
content 0.45–0.77 (0.60 in average) and high genetic
diversity. For each locus, we found on average 5.50 alleles.
During three vegetation periods, the leaf area damage of
these genotypes was evaluated using the statistical software
Assess 2.0. Different pressure of leaf miner and different
development at each locality was recorded, and in some
cases less damage was found, in one case the lesser damage
was permanent. From the data, a pathological scale was
established and a dendogram of similarity was created.
Based on SSR analysis, four groups of Aesculus trees were
distinguished according to their resistance or susceptibility
and five main section?Hybrid were found. By cloning and
analysing the inner transcribed spacers, the ITS1 and ITS2,
inner and inter species variability was examined. For the
sequence of hybrid species A. 9 carnea, no compliance
was revealed in NBCI database. For this reason, the first
sequence of this genotype was obtained.
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Papers by Václav Bačovský
severely infested by horse chestnut leaf miner (Cameraria
ohridella). The larvae mine the leaves and under appropriate
conditions can damage up to 100% of the leaf area.
In this study, we assessed the genetic diversity of eight
species of horse chestnut and their genotypes which have
varying susceptibility to the leaf miner. Analysis of eight
microsatellite loci showed high polymorphic information
content 0.45–0.77 (0.60 in average) and high genetic
diversity. For each locus, we found on average 5.50 alleles.
During three vegetation periods, the leaf area damage of
these genotypes was evaluated using the statistical software
Assess 2.0. Different pressure of leaf miner and different
development at each locality was recorded, and in some
cases less damage was found, in one case the lesser damage
was permanent. From the data, a pathological scale was
established and a dendogram of similarity was created.
Based on SSR analysis, four groups of Aesculus trees were
distinguished according to their resistance or susceptibility
and five main section?Hybrid were found. By cloning and
analysing the inner transcribed spacers, the ITS1 and ITS2,
inner and inter species variability was examined. For the
sequence of hybrid species A. 9 carnea, no compliance
was revealed in NBCI database. For this reason, the first
sequence of this genotype was obtained.
severely infested by horse chestnut leaf miner (Cameraria
ohridella). The larvae mine the leaves and under appropriate
conditions can damage up to 100% of the leaf area.
In this study, we assessed the genetic diversity of eight
species of horse chestnut and their genotypes which have
varying susceptibility to the leaf miner. Analysis of eight
microsatellite loci showed high polymorphic information
content 0.45–0.77 (0.60 in average) and high genetic
diversity. For each locus, we found on average 5.50 alleles.
During three vegetation periods, the leaf area damage of
these genotypes was evaluated using the statistical software
Assess 2.0. Different pressure of leaf miner and different
development at each locality was recorded, and in some
cases less damage was found, in one case the lesser damage
was permanent. From the data, a pathological scale was
established and a dendogram of similarity was created.
Based on SSR analysis, four groups of Aesculus trees were
distinguished according to their resistance or susceptibility
and five main section?Hybrid were found. By cloning and
analysing the inner transcribed spacers, the ITS1 and ITS2,
inner and inter species variability was examined. For the
sequence of hybrid species A. 9 carnea, no compliance
was revealed in NBCI database. For this reason, the first
sequence of this genotype was obtained.