Satellite DNA (satDNA) is one of the major fractions of the eukaryotic nuclear genome. Highly variable satDNA is involved in various genome functions, and a clear link between satellites and phenotypes exists in a wide range of organisms. However, little is known about the origin and temporal dynamics of satDNA. The "library hypothesis" indicates that the rapid evolutionary changes experienced by satDNAs are mostly quantitative. Although this hypothesis has received some confirmation, a number of its aspects are still controversial. A recently developed next-generation sequencing (NGS) method allows the determination of the satDNA landscape and could shed light on unresolved issues. Here, we explore low-coverage NGS data to infer satDNA evolution in the phylogenetic context of the diploid species of the Chenopodium album aggregate. The application of the Illumina read assembly algorithm in combination with Oxford Nanopore sequencing and fluorescent in situ hybridization allowed the estimation of eight satDNA families within the studied group, six of which were newly described. The obtained set of satDNA families of different origins can be divided into several categories, namely group-specific, lineage-specific and species-specific. In the process of evolution, satDNA families can be transmitted vertically and can be eliminated over time. Moreover, transposable element-derived satDNA families may appear repeatedly in the satellitome, creating an illusion of family conservation. Thus, the obtained data refute the "library hypothesis", rather than confirming it, and in our opinion, it is more appropriate to speak about "the library of the mechanisms of origin".
- MeSH
- Chenopodium album genetika růst a vývoj MeSH
- diploidie * MeSH
- DNA rostlinná analýza genetika MeSH
- druhová specificita MeSH
- fylogeneze MeSH
- genom rostlinný * MeSH
- genová knihovna MeSH
- molekulární evoluce * MeSH
- satelitní DNA analýza genetika MeSH
- vysoce účinné nukleotidové sekvenování MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
Extensive and complex links exist between transposable elements (TEs) and satellite DNA (satDNA), which are the two largest fractions of eukaryotic genome. These relationships have a crucial effect on genome structure, function and evolution. Here, we report a novel case of mutual relationships between TEs and satDNA. In the genomes of Chenopodium s. str. species, the deletion derivatives of tnp2 conserved domain of the newly discovered CACTA-like TE Jozin are involved in generating monomers of the most abundant satDNA family of the Chenopodium satellitome. The analysis of the relative positions of satDNA and different TEs utilizing assembled Illumina reads revealed several associations between satDNA arrays and the transposases of putative CACTA-like elements when an ~ 40 bp fragment of tnp2 served as the start monomer of the satDNA array. The high degree of identity of the consensus satDNA monomers of the investigated species and the tnp2 fragment (from 82.1 to 94.9%) provides evidence of the genesis of CficCl-61-40 satDNA family monomers from analogous regions of their respective parental elements. The results were confirmed via molecular genetic methods and Oxford Nanopore sequencing. The discovered phenomenon leads to the continuous replenishment of species genomes with new identical satDNA monomers, which in turn may increase species satellitomes similarity.
- Publikační typ
- časopisecké články MeSH
Retrotransposable elements are widely distributed and diverse in eukaryotes. Their copy number increases through reverse-transcription-mediated propagation, while they can be lost through recombinational processes, generating genomic rearrangements. We previously identified extensive structurally uniform retrotransposon groups in which no member contains the gag, pol, or env internal domains. Because of the lack of protein-coding capacity, these groups are non-autonomous in replication, even if transcriptionally active. The Cassandra element belongs to the non-autonomous group called terminal-repeat retrotransposons in miniature (TRIM). It carries 5S RNA sequences with conserved RNA polymerase (pol) III promoters and terminators in its long terminal repeats (LTRs). Here, we identified multiple extended tandem arrays of Cassandra retrotransposons within different plant species, including ferns. At least 12 copies of repeated LTRs (as the tandem unit) and internal domain (as a spacer), giving a pattern that resembles the cellular 5S rRNA genes, were identified. A cytogenetic analysis revealed the specific chromosomal pattern of the Cassandra retrotransposon with prominent clustering at and around 5S rDNA loci. The secondary structure of the Cassandra retroelement RNA is predicted to form super-loops, in which the two LTRs are complementary to each other and can initiate local recombination, leading to the tandem arrays of Cassandra elements. The array structures are conserved for Cassandra retroelements of different species. We speculate that recombination events similar to those of 5S rRNA genes may explain the wide variation in Cassandra copy number. Likewise, the organization of 5S rRNA gene sequences is very variable in flowering plants; part of what is taken for 5S gene copy variation may be variation in Cassandra number. The role of the Cassandra 5S sequences remains to be established.
- MeSH
- chromozomy hmyzu MeSH
- fylogeneze MeSH
- genom rostlinný MeSH
- genomika metody MeSH
- interakce hostitele a parazita genetika MeSH
- koncové repetice * MeSH
- konformace nukleové kyseliny MeSH
- molekulární evoluce MeSH
- můry genetika MeSH
- rekombinace genetická MeSH
- retroelementy * MeSH
- RNA ribozomální 5S genetika MeSH
- rostliny genetika parazitologie MeSH
- zvířata MeSH
- Check Tag
- zvířata MeSH
- Publikační typ
- časopisecké články MeSH
BACKGROUND: Interspecific hybridisation resulting in polyploidy is one of the major driving forces in plant evolution. Here, we present data from the molecular cytogenetic analysis of three cytotypes of Elytrigia ×mucronata using sequential fluorescence (5S rDNA, 18S rDNA and pSc119.2 probes) and genomic in situ hybridisation (four genomic probes of diploid taxa, i.e., Aegilops, Dasypyrum, Hordeum and Pseudoroegneria). RESULTS: The concurrent presence of Hordeum (descended from E. repens) and Dasypyrum + Aegilops (descended from E. intermedia) chromosome sets in all cytotypes of E. ×mucronata confirmed the assumed hybrid origin of the analysed plants. The following different genomic constitutions were observed for E. ×mucronata. Hexaploid plants exhibited three chromosome sets from Pseudoroegneria and one chromosome set each from Aegilops, Hordeum and Dasypyrum. Heptaploid plants harboured the six chromosome sets of the hexaploid plants and an additional Pseudoroegneria chromosome set. Nonaploid cytotypes differed in their genomic constitutions, reflecting different origins through the fusion of reduced and unreduced gametes. The hybridisation patterns of repetitive sequences (5S rDNA, 18S rDNA, and pSc119.2) in E. ×mucronata varied between and within cytotypes. Chromosome alterations that were not identified in the parental species were found in both heptaploid and some nonaploid plants. CONCLUSIONS: The results confirmed that both homoploid hybridisation and heteroploid hybridisation that lead to the coexistence of four different haplomes within single hybrid genomes occur in Elytrigia allopolyploids. The chromosomal alterations observed in both heptaploid and some nonaploid plants indicated that genome restructuring occurs during and/or after the hybrids arose. Moreover, a specific chromosomal translocation detected in one of the nonaploids indicated that it was not a primary hybrid. Therefore, at least some of the hybrids are fertile. Hybridisation in Triticeae allopolyploids clearly and significantly contributes to genomic diversity. Different combinations of parental haplomes coupled with chromosomal alterations may result in the establishment of unique lineages, thus providing raw material for selection.
- MeSH
- cytogenetické vyšetření MeSH
- DNA rostlinná analýza MeSH
- genotyp * MeSH
- hybridizace genetická * MeSH
- hybridizace in situ fluorescenční MeSH
- hybridizace in situ MeSH
- lipnicovité genetika MeSH
- polyploidie * MeSH
- RNA ribozomální 18S analýza MeSH
- RNA ribozomální 5S analýza MeSH
- Publikační typ
- časopisecké články MeSH
- Geografické názvy
- Česká republika MeSH
Satellite DNA (satDNA) is the most variable fraction of the eukaryotic genome. Related species share a common ancestral satDNA library and changing of any library component in a particular lineage results in interspecific differences. Although the general developmental trend is clear, our knowledge of the origin and dynamics of satDNAs is still fragmentary. Here, we explore whole genome shotgun Illumina reads using the RepeatExplorer (RE) pipeline to infer satDNA family life stories in the genomes of Chenopodium species. The seven diploids studied represent separate lineages and provide an example of a species complex typical for angiosperms. Application of the RE pipeline allowed by similarity searches a determination of the satDNA family with a basic monomer of ~40 bp and to trace its transformation from the reconstructed ancestral to the species-specific sequences. As a result, three types of satDNA family evolutionary development were distinguished: (i) concerted evolution with mutation and recombination events; (ii) concerted evolution with a trend toward increased complexity and length of the satellite monomer; and (iii) non-concerted evolution, with low levels of homogenization and multidirectional trends. The third type is an example of entire repeatome transformation, thus producing a novel set of satDNA families, and genomes showing non-concerted evolution are proposed as a significant source for genomic diversity.
- MeSH
- Chenopodium genetika MeSH
- diploidie MeSH
- DNA rostlinná genetika MeSH
- druhová specificita MeSH
- fylogeneze MeSH
- genom rostlinný MeSH
- komponenty genomu MeSH
- molekulární evoluce MeSH
- satelitní DNA genetika MeSH
- sekvenční analýza DNA MeSH
- vysoce účinné nukleotidové sekvenování MeSH
- Publikační typ
- časopisecké články MeSH
Hybridization and polyploidization represent an important speciation mechanism in the diploid-polyploid complex of the Chenopodium album aggregate. In the present study we successfully reconstructed the evolutionary histories of the majority of Eurasian representatives of the C. album aggregate, resulting in the most comprehensive phylogenetic analysis of this taxonomically intricate group of species to date. We applied a combination of classical karyology for precise chromosome number determination, genomic in-situ hybridization for the determination of genomic composition, flow cytometry for the estimation of genome size and sequencing of plastid (cpDNA) and nuclear (ribosomal internal transcribed spacer - ITS and the introns of the FLOWERING LOCUS T LIKE genes - FTL) markers for a phylogenetic reconstruction and the identification of parental genomes in polyploid taxa. The FTL markers identified eight well supported evolutionary lineages. Five of them include at least one diploid species, and the remaining three comprise solely the subgenomes of polyploids that probably represent extinct or unknown diploid taxa. The existence of eight basic diploid lineages explains the origin of seven Eurasian polyploid groups and brings evidence of a nearly unlimited number of subgenomic combinations. The supposed promiscuity generated new species wherever different diploid lineages met each other and gave rise to tetraploid species or whenever they met other tetraploid species to produce hexaploid species throughout their evolutionary history. Finally, we unravelled a surprisingly simple scheme of polyploid species formation within the C. album aggregate. We determined seven groups of polyploid species differing in their origin in either Eurasia or Africa and convincingly demonstrated that (1) all Chenopodium polyploid species under study are of allopolyploid origin, (2) there are eight major monophyletic evolutionary lineages represented by extant or extinct/unknown diploid taxa, (3) those monophyletic lineages represent individual subgenomes, (4) hybridization among the lineages created seven subgenomic combinations of polyploid taxa, (5) taxa represented by particular subgenome combinations were further subjected to diversification, and (6) the majority of species are relatively young, not exceeding the age of the Quaternary period.
- MeSH
- Chenopodium album cytologie genetika MeSH
- chromozomy rostlin genetika MeSH
- délka genomu MeSH
- fylogeneze MeSH
- genetické lokusy MeSH
- genetické markery MeSH
- hybridizace genetická * MeSH
- molekulární evoluce MeSH
- polyploidie * MeSH
- sekvence nukleotidů MeSH
- tetraploidie MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
We evaluated copy number variation (CNV) for four genes in rat strains differing in nervous system excitability. rpl13a copy number is significantly reduced in hippocampus and bone marrow in rats with a high excitability threshold and stress. The observed phenomenon may be associated with a role for rpl13a in lipid metabolism.
- MeSH
- hipokampus metabolismus fyziologie MeSH
- kortikální excitabilita genetika fyziologie MeSH
- kostní dřeň metabolismus fyziologie MeSH
- krysa rodu rattus MeSH
- nervový systém - fyziologické jevy genetika MeSH
- ribozomální proteiny genetika MeSH
- variabilita počtu kopií segmentů DNA genetika MeSH
- zvířata MeSH
- Check Tag
- krysa rodu rattus MeSH
- zvířata MeSH
- Publikační typ
- časopisecké články MeSH
The role of the nucleolus and autophagy in maintenance of nuclear integrity is poorly understood. In addition, the mechanisms of nuclear destruction in cancer cells senesced after conventional chemotherapy are unclear. In an attempt to elucidate these issues, we studied teratocarcinoma PA1 cells treated with Etoposide (ETO), focusing on the nucleolus. Following treatment, most cells enter G2 arrest, display persistent DNA damage and activate p53, senescence, and macroautophagy markers. 2-5 µm sized nucleolar aggresomes (NoA) containing fibrillarin (FIB) and damaged rDNA, colocalized with ubiquitin, pAMPK, and LC3-II emerge, accompanied by heterochromatin fragments, when translocated perinuclearly. Microscopic counts following application of specific inhibitors revealed that formation of FIB-NoA is dependent on deficiency of the ubiquitin proteasome system coupled to functional autophagy. In contrast, the accompanying NoAs release of pericentric heterochromatin, which exceeds their frequency, is favored by debilitation of autophagic flux. Potential survivors release NoA in the cytoplasm during rare mitoses, while exit of pericentric fragments often depleted of H3K9Me3, with or without encompassing by NoA, occurs through the nucleolar protrusions and defects of the nuclear envelope. Foci of LC3-II are accumulated in the nucleoli undergoing cessation of rDNA transcription. As an origin of heterochromatin fragmentation, the unscheduled DNA synthesis and circular DNAs were found in the perinucleolar heterochromatin shell, along with activation and retrotransposition of ALU elements, colocalized with 45S rDNA in NoAs. The data indicate coordination of the basic nucleolar function with autophagy regulation in maintenance of the integrity of the nucleolus associated domains secured by inactivity of retrotransposons.
- MeSH
- autofagie účinky léků genetika MeSH
- buněčné jadérko účinky léků genetika metabolismus MeSH
- chromozomální proteiny, nehistonové metabolismus MeSH
- etoposid toxicita MeSH
- heterochromatin účinky léků metabolismus MeSH
- inhibitor p16 cyklin-dependentní kinasy metabolismus MeSH
- kontrolní body buněčného cyklu účinky léků genetika MeSH
- lidé MeSH
- mutageny toxicita MeSH
- nádorové buněčné linie MeSH
- poškození DNA MeSH
- retroelementy účinky léků genetika MeSH
- ribozomální DNA genetika metabolismus MeSH
- stárnutí buněk účinky léků genetika MeSH
- Check Tag
- lidé MeSH
- Publikační typ
- časopisecké články MeSH
Reticulate evolution is characterized by occasional hybridization between two species, creating a network of closely related taxa below and at the species level. In the present research, we aimed to verify the hypothesis of the allopolyploid origin of hexaploid C. album s. str., identify its putative parents and estimate the frequency of allopolyploidization events. We sampled 122 individuals of the C. album aggregate, covering most of its distribution range in Eurasia. Our samples included putative progenitors of C. album s. str. of both ploidy levels, i.e. diploids (C. ficifolium, C. suecicum) and tetraploids (C. striatiforme, C. strictum). To fulfil these objectives, we analysed sequence variation in the nrDNA ITS region and the rpl32-trnL intergenic spacer of cpDNA and performed genomic in-situ hybridization (GISH). Our study confirms the allohexaploid origin of C. album s. str. Analysis of cpDNA revealed tetraploids as the maternal species. In most accessions of hexaploid C. album s. str., ITS sequences were completely or nearly completely homogenized towards the tetraploid maternal ribotype; a tetraploid species therefore served as one genome donor. GISH revealed a strong hybridization signal on the same eighteen chromosomes of C. album s. str. with both diploid species C. ficifolium and C. suecicum. The second genome donor was therefore a diploid species. Moreover, some individuals with completely unhomogenized ITS sequences were found. Thus, hexaploid individuals of C. album s. str. with ITS sequences homogenized to different degrees may represent hybrids of different ages. This proves the existence of at least two different allopolyploid lineages, indicating a polyphyletic origin of C. album s. str.
