In most studied eukaryotes, chromosomes are monocentric, with centromere activity confined to a single region. However, the rush family (Juncaceae) includes species with both monocentric (Juncus) and holocentric (Luzula) chromosomes, where centromere activity is distributed along the entire chromosome length. Here, we combine chromosome-scale genome assembly, epigenetic analysis, immuno-FISH and super-resolution microscopy to study the transition to holocentricity in Luzula sylvatica. We report repeat-based holocentromeres with an irregular distribution of features along the chromosomes. Luzula sylvatica holocentromeres are predominantly associated with two satellite DNA repeats (Lusy1 and Lusy2), while CENH3 also binds satellite-free gene-poor regions. Comparative repeat analysis suggests that Lusy1 plays a crucial role in centromere function across most Luzula species. Furthermore, synteny analysis between L. sylvatica (n = 6) and Juncus effusus (n = 21) suggests that holocentric chromosomes in Luzula could have arisen from chromosome fusions of ancestral monocentric chromosomes, accompanied by the expansion of CENH3-associated satellite repeats.

• MeSH
• centromera * genetika   MeSH
• chromozomy rostlin * genetika   MeSH
• DNA rostlinná genetika   MeSH
• genom rostlinný MeSH
• hybridizace in situ fluorescenční MeSH
• molekulární evoluce MeSH
• repetitivní sekvence nukleových kyselin genetika   MeSH
• satelitní DNA * genetika   MeSH
• syntenie MeSH
• Publikační typ
• časopisecké články MeSH
• Názvy látek
• DNA rostlinná MeSH
• satelitní DNA * MeSH

The oxidation of 5-methylcytosine (5mC) to 5-hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC), and 5-carboxylcytosine (5caC), known as oxi-mCs, garners significant interest in plants as potential epigenetic marks. While research in mammals has established a role in cell reprogramming, carcinogenesis, and gene regulation, their functions in plants remain unclear. In rice, 5hmC has been associated with transposable elements (TEs) and heterochromatin. This study utilizes Silene latifolia, a dioecious plant with heteromorphic sex chromosomes and a genome with a large proportion of TEs, which provides a favourable environment for the study of oxi-mCs in individual sexes. Notably, we detected surprisingly high levels of oxi-mCs in S. latifolia comparable with mammals. Nuclei showed enrichment in heterochromatic regions, except for 5hmC whose signal was homogeneously distributed. Intriguingly, the same X chromosome in females displayed overall enrichment of 5hmC and 5fC compared with its counterpart. This fact is shared with 5mC, resembling dosage compensation. Co-localization showed higher correlation between 5mC and 5fC than with 5hmC, indicating no potential relationship between 5hmC and 5fC. Additionally, the promoter of several sex-linked genes and sex-biased TEs clustered in a clear sex-dependent way. Together, these findings unveil a hypothetical role for oxi-mCs in S. latifolia sex chromosome development, warranting further exploration.

• Klíčová slova
• Silene latifolia, Cytosine modifications, dosage compensation, oxi-mCs, sex chromosomes, transposable elements,
• MeSH
• 5-methylcytosin metabolismus   analogy a deriváty   MeSH
• chromozomy rostlin * genetika   MeSH
• epigeneze genetická MeSH
• pohlavní chromozomy * genetika   MeSH
• Silene * genetika   MeSH
• transpozibilní elementy DNA genetika   MeSH
• Publikační typ
• časopisecké články MeSH
• Názvy látek
• 5-methylcytosin MeSH
• transpozibilní elementy DNA MeSH

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. Silene latifolia (white campion) is a dioecious plant with heteromorphic sex chromosomes (24, XX in females and 24, XY in males), and a genetically degenerated Y chromosome that is 1.4 times larger than the X chromosome. Although the two sex chromosomes differ in their DNA content, information about epigenetic histone marks and evidence of their function are scarce. We performed immunolabeling experiments using antibodies specific for active and suppressive histone modifications as well as pericentromere-specific histone modifications. We show that the Y chromosome is partially depleted of histone modifications important for transcriptionally active chromatin, and carries these marks only in the pseudo-autosomal region, but that it is not enriched for suppressive and pericentromere histone marks. We also show that two of the active marks are specifically enriched in one of the X chromosomes in females and in the X chromosome in males. Our data support recent findings that genetic imprinting mediates dosage compensation of sex chromosomes in S. latifolia.

• Klíčová slova
• Posttranslational histone modifications, Pseudo-autosomal region, Sex chromosomes,
• MeSH
• chromozomy rostlin genetika   MeSH
• epigeneze genetická * MeSH
• histonový kód genetika   MeSH
• Silene genetika   MeSH
• Publikační typ
• časopisecké články MeSH

BACKGROUND: The rise and fall of the Y chromosome was demonstrated in animals but plants often possess the large evolutionarily young Y chromosome that is thought has expanded recently. Break-even points dividing expansion and shrinkage phase of plant Y chromosome evolution are still to be determined. To assess the size dynamics of the Y chromosome, we studied intraspecific genome size variation and genome composition of male and female individuals in a dioecious plant Silene latifolia, a well-established model for sex-chromosomes evolution. RESULTS: Our genome size data are the first to demonstrate that regardless of intraspecific genome size variation, Y chromosome has retained its size in S. latifolia. Bioinformatics study of genome composition showed that constancy of Y chromosome size was caused by Y chromosome DNA loss and the female-specific proliferation of recently active dominant retrotransposons. We show that several families of retrotransposons have contributed to genome size variation but not to Y chromosome size change. CONCLUSIONS: Our results suggest that the large Y chromosome of S. latifolia has slowed down or stopped its expansion. Female-specific proliferation of retrotransposons, enlarging the genome with exception of the Y chromosome, was probably caused by silencing of highly active retrotransposons in males and represents an adaptive mechanism to suppress degenerative processes in the haploid stage. Sex specific silencing of transposons might be widespread in plants but hidden in traditional hermaphroditic model plants.

• Klíčová slova
• Epigenetics, Genome size, Silene latifolia, Transposable elements, Y chromosome,
• MeSH
• chromozomy rostlin * MeSH
• délka genomu MeSH
• DNA rostlinná * MeSH
• genom rostlinný MeSH
• hybridizace in situ fluorescenční MeSH
• koncové repetice MeSH
• mapování chromozomů MeSH
• molekulární evoluce * MeSH
• repetitivní sekvence nukleových kyselin MeSH
• retroelementy * MeSH
• sekvenční delece * MeSH
• Silene klasifikace   genetika   MeSH
• umlčování genů * MeSH
• variabilita počtu kopií segmentů DNA MeSH
• zastoupení bazí MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Názvy látek
• DNA rostlinná * MeSH
• retroelementy * MeSH

In contrast to animals, separate sexes and sex chromosomes in plants are very rare. Although the evolution of sex chromosomes has been the subject of numerous studies, the impact of repetitive sequences on sex chromosome architecture is not fully understood. New genomic approaches shed light on the role of satellites and transposable elements in the process of Y chromosome evolution. We discuss the impact of repetitive sequences on the structure and dynamics of sex chromosomes with specific focus on Rumex acetosa and Silene latifolia. Recent papers showed that both the expansion and shrinkage of the Y chromosome is influenced by sex-specific regulation of repetitive DNA spread. We present a view that the dynamics of Y chromosome formation is an interplay of genetic and epigenetic processes.

• Klíčová slova
• Y chromosome, satellites, sex chromosomes, transposable elements,
• Publikační typ
• časopisecké články MeSH
• přehledy MeSH

Structurally and functionally diverged sex chromosomes have evolved in many animals as well as in some plants. Sex chromosomes represent a specific genomic region(s) with locally suppressed recombination. As a consequence, repetitive sequences involving transposable elements, tandem repeats (satellites and microsatellites), and organellar DNA accumulate on the Y (W) chromosomes. In this paper, we review the main types of repetitive elements, their gathering on the Y chromosome, and discuss new findings showing that not only accumulation of various repeats in non-recombining regions but also opposite processes form Y chromosome. The aim of this review is also to discuss the mechanisms of repetitive DNA spread involving (retro) transposition, DNA polymerase slippage or unequal crossing-over, as well as modes of repeat removal by ectopic recombination. The intensity of these processes differs in non-recombining region(s) of sex chromosomes when compared to the recombining parts of genome. We also speculate about the relationship between heterochromatinization and the formation of heteromorphic sex chromosomes.

• Klíčová slova
• microsatellites, recombination, repetitive sequences, sex chromosomes, tandem repeats (satellites), transposable elements,
• MeSH
• chromozomy rostlin * MeSH
• DNA rostlinná * MeSH
• molekulární evoluce * MeSH
• pohlavní chromozomy genetika   MeSH
• regulace genové exprese u rostlin MeSH
• repetitivní sekvence nukleových kyselin * MeSH
• rostliny genetika   MeSH
• transpozibilní elementy DNA MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Názvy látek
• DNA rostlinná * MeSH
• transpozibilní elementy DNA MeSH

BACKGROUND: Silene latifolia represents one of the best-studied plant sex chromosome systems. A new approach using RNA-seq data has recently identified hundreds of new sex-linked genes in this species. However, this approach is expected to miss genes that are either not expressed or are expressed at low levels in the tissue(s) used for RNA-seq. Therefore other independent approaches are needed to discover such sex-linked genes. RESULTS: Here we used 10 well-characterized S. latifolia sex-linked genes and their homologs in Silene vulgaris, a species without sex chromosomes, to screen BAC libraries of both species. We isolated and sequenced 4 Mb of BAC clones of S. latifolia X and Y and S. vulgaris genomic regions, which yielded 59 new sex-linked genes (with S. vulgaris homologs for some of them). We assembled sequences that we believe represent the tip of the Xq arm. These sequences are clearly not pseudoautosomal, so we infer that the S. latifolia X has a single pseudoautosomal region (PAR) on the Xp arm. The estimated mean gene density in X BACs is 2.2 times lower than that in S. vulgaris BACs, agreeing with the genome size difference between these species. Gene density was estimated to be extremely low in the Y BAC clones. We compared our BAC-located genes with the sex-linked genes identified in previous RNA-seq studies, and found that about half of them (those with low expression in flower buds) were not identified as sex-linked in previous RNA-seq studies. We compiled a set of ~70 validated X/Y genes and X-hemizygous genes (without Y copies) from the literature, and used these genes to show that X-hemizygous genes have a higher probability of being undetected by the RNA-seq approach, compared with X/Y genes; we used this to estimate that about 30% of our BAC-located genes must be X-hemizygous. The estimate is similar when we use BAC-located genes that have S. vulgaris homologs, which excludes genes that were gained by the X chromosome. CONCLUSIONS: Our BAC sequencing identified 59 new sex-linked genes, and our analysis of these BAC-located genes, in combination with RNA-seq data suggests that gene losses from the S. latifolia Y chromosome could be as high as 30 %, higher than previous estimates of 10-20%.

• MeSH
• chromozomy rostlin genetika   MeSH
• molekulární evoluce * MeSH
• molekulární sekvence - údaje MeSH
• pohlavní chromozomy genetika   MeSH
• procesy určující pohlaví * MeSH
• regulace genové exprese u rostlin MeSH
• sekvence nukleotidů MeSH
• Silene genetika   růst a vývoj   MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH

Rumex acetosa is a dioecious plant with the XY1Y2 sex chromosome system. Both Y chromosomes are heterochromatic and are thought to be degenerated. We performed low-pass 454 sequencing and similarity-based clustering of male and female genomic 454 reads to identify and characterize major groups of R. acetosa repetitive DNA. We found that Copia and Gypsy retrotransposons dominated, followed by DNA transposons and nonlong terminal repeat retrotransposons. CRM and Tat/Ogre retrotransposons dominated the Gypsy superfamily, whereas Maximus/Sireviruses were most abundant among Copia retrotransposons. Only one Gypsy subfamily had accumulated on Y1 and Y2 chromosomes, whereas many retrotransposons were ubiquitous on autosomes and the X chromosome, but absent on Y1 and Y2 chromosomes, and others were depleted from the X chromosome. One group of CRM Gypsy was specifically localized to centromeres. We also found that majority of previously described satellites (RAYSI, RAYSII, RAYSIII, and RAE180) are accumulated on the Y chromosomes where we identified Y chromosome-specific variant of RAE180. We discovered two novel satellites-RA160 satellite dominating on the X chromosome and RA690 localized mostly on the Y1 chromosome. The expression pattern obtained from Illumina RNA sequencing showed that the expression of transposable elements is similar in leaves of both sexes and that satellites are also expressed. Contrasting patterns of transposable elements (TEs) and satellite localization on sex chromosomes in R. acetosa, where not only accumulation but also depletion of repetitive DNA was observed, suggest that a plethora of evolutionary processes can shape sex chromosomes.

• MeSH
• chromozomy rostlin genetika   MeSH
• fylogeneze MeSH
• molekulární evoluce MeSH
• molekulární sekvence - údaje MeSH
• pohlavní chromozomy genetika   MeSH
• retroelementy * MeSH
• Rumex klasifikace   genetika   MeSH
• satelitní DNA * MeSH
• sekvence nukleotidů MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Názvy látek
• retroelementy * MeSH
• satelitní DNA * MeSH

In this study, we investigated repetitive sequences localized on Y chromosomes. Repetitive DNA sequences represent a substantial part of the eukaryotic genome and, among them, a large portion comprises sequences repeated in tandem. Efficient and rapid isolation of repeat units is possible due to a laser microdissection technique used for Y chromosome separation, followed by polymerase chain reaction (PCR), cloning, and sequence analysis. We applied the derived repeat units to members of nine tribes within the Bovidae. Apart from the Y chromosomes of Bos taurus and Bubalus bubalis, where we used known sequences of repetition, the derived sequences were used as probes for fluorescent in situ cross-hybridization to members of the nine tribes of the Bovidae. We investigated the distribution of repeat units within the tribes and their localization on the Y chromosome. Sharing of sequence variants would indicate common descent, while the rapid horizontal evolution should allow discrimination between closely related species or subspecies.

• MeSH
• chromozom Y chemie   genetika   MeSH
• druhová specificita MeSH
• fluorescenční barviva chemie   MeSH
• fylogeneze MeSH
• hybridizace in situ fluorescenční veterinární   MeSH
• laserová záchytná mikrodisekce metody   veterinární   MeSH
• metafáze MeSH
• molekulární evoluce MeSH
• populační genetika metody   MeSH
• repetitivní sekvence nukleových kyselin * MeSH
• sekvence nukleotidů MeSH
• sekvenční analýza DNA metody   veterinární   MeSH
• sekvenční seřazení MeSH
• sexuální faktory MeSH
• skot klasifikace   genetika   MeSH
• zvířata MeSH
• Check Tag
• mužské pohlaví MeSH
• skot klasifikace   genetika   MeSH
• zvířata MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Názvy látek
• fluorescenční barviva MeSH

BACKGROUND: Genome size evolution is a complex process influenced by polyploidization, satellite DNA accumulation, and expansion of retroelements. How this process could be affected by different reproductive strategies is still poorly understood. METHODOLOGY/PRINCIPAL FINDINGS: We analyzed differences in the number and distribution of major repetitive DNA elements in two closely related species, Silene latifolia and S. vulgaris. Both species are diploid and possess the same chromosome number (2n = 24), but differ in their genome size and mode of reproduction. The dioecious S. latifolia (1C = 2.70 pg DNA) possesses sex chromosomes and its genome is 2.5× larger than that of the gynodioecious S. vulgaris (1C = 1.13 pg DNA), which does not possess sex chromosomes. We discovered that the genome of S. latifolia is larger mainly due to the expansion of Ogre retrotransposons. Surprisingly, the centromeric STAR-C and TR1 tandem repeats were found to be more abundant in S. vulgaris, the species with the smaller genome. We further examined the distribution of major repetitive sequences in related species in the Caryophyllaceae family. The results of FISH (fluorescence in situ hybridization) on mitotic chromosomes with the Retand element indicate that large rearrangements occurred during the evolution of the Caryophyllaceae family. CONCLUSIONS/SIGNIFICANCE: Our data demonstrate that the evolution of genome size in the genus Silene is accompanied by the expansion of different repetitive elements with specific patterns in the dioecious species possessing the sex chromosomes.

• MeSH
• chromozomy rostlin MeSH
• délka genomu * MeSH
• genetická variace MeSH
• genom rostlinný MeSH
• genomika MeSH
• hybridizace in situ fluorescenční MeSH
• hybridizace nukleových kyselin MeSH
• Magnoliopsida genetika   MeSH
• mikrosatelitní repetice genetika   MeSH
• modely genetické MeSH
• molekulární evoluce MeSH
• polyploidie MeSH
• repetitivní sekvence nukleových kyselin genetika   MeSH
• rostlinné geny MeSH
• rostlinné proteiny genetika   MeSH
• satelitní DNA genetika   MeSH
• Silene klasifikace   genetika   MeSH
• výpočetní biologie metody   MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Názvy látek
• rostlinné proteiny MeSH
• satelitní DNA MeSH