The linked units of 5S rDNA and U1 snDNA of razor shells (Mollusca: Bivalvia: Pharidae)

[Abstract] The linkage between 5S ribosomal DNA and other multigene families has been detected in many eukaryote lineages, but whether it provides any selective advantage remains unclear. In this work, we report the occurrence of linked units of 5S ribosomal DNA (5S rDNA) and U1 small nuclear DNA (U1 snDNA) in 10 razor shell species (Mollusca: Bivalvia: Pharidae) from four different genera. We obtained several clones containing partial or complete repeats of both multigene families in which both types of genes displayed the same orientation. We provide a comprehensive collection of razor shell 5S rDNA clones, both with linked and nonlinked organisation, and the first bivalve U1 snDNA sequences. We predicted the secondary structures and characterised the upstream and downstream conserved elements, including a region at −25 nucleotides from both 5S rDNA and U1 snDNA transcription start sites. The analysis of 5S rDNA showed that some nontranscribed spacers (NTSs) are more closely related to NTSs from other species (and genera) than to NTSs from the species they were retrieved from, suggesting birth-and-death evolution and ancestral polymorphism. Nucleotide conservation within the functional regions suggests the involvement of purifying selection, unequal crossing-overs and gene conversions. Taking into account this and other studies, we discuss the possible mechanisms by which both multigene families could have become linked in the Pharidae lineage. The reason why 5S rDNA is often found linked to other multigene families seems to be the result of stochastic processes within genomes in which its high copy number is determinan

Contrasting patterns of the 5S and 45S rDNA evolutions in the Byblis liniflora complex (Byblidaceae)

To clarify the evolutionary dynamics of ribosomal RNA genes (rDNAs) in the Byblis liniflora complex (Byblidaceae), we investigated the 5S and 45S rDNA genes through (1) chromosomal physical mapping by fluorescence in situ hybridization (FISH) and (2) phylogenetic analyses using the nontranscribed spacer of 5S rDNA (5S-NTS) and the internal transcribed spacer of 45S rDNA (ITS). In addition, we performed phylogenetic analyses based on rbcL and trnK intron. The complex was divided into 2 clades: B. aquatica–B. filifolia and B. guehoi–B. liniflora–B. rorida. Although members of the complex had conservative symmetric karyotypes, they were clearly differentiated on chromosomal rDNA distribution patterns. The sequence data indicated that ITS was almost homogeneous in all taxa in which two or four 45S rDNA arrays were frequently found at distal regions of chromosomes in the somatic karyotype. ITS homogenization could have been prompted by relatively distal 45S rDNA positions. In contrast, 2–12 5S rDNA arrays were mapped onto proximal/interstitial regions of chromosomes, and some paralogous 5S-NTS were found in the genomes harboring 4 or more arrays. 5S-NTS sequence type-specific FISH analysis showed sequence heterogeneity within and between some 5S rDNA arrays. Interlocus homogenization may have been hampered by their proximal location on chromosomes. Chromosomal location may have affected the contrasting evolutionary dynamics of rDNAs in the B. liniflora complex

Are ribosomal DNA clusters rearrangement hotspots? A case study in the genus Mus (Rodentia, Muridae)

<p>Abstract</p> <p>Background</p> <p>Recent advances in comparative genomics have considerably improved our knowledge of the evolution of mammalian karyotype architecture. One of the breakthroughs was the preferential localization of evolutionary breakpoints in regions enriched in repetitive sequences (segmental duplications, telomeres and centromeres). In this context, we investigated the contribution of ribosomal genes to genome reshuffling since they are generally located in pericentromeric or subtelomeric regions, and form repeat clusters on different chromosomes. The target model was the genus <it>Mus </it>which exhibits a high rate of karyotypic change, a large fraction of which involves centromeres.</p> <p>Results</p> <p>The chromosomal distribution of rDNA clusters was determined by <it>in situ </it>hybridization of mouse probes in 19 species. Using a molecular-based reference tree, the phylogenetic distribution of clusters within the genus was reconstructed, and the temporal association between rDNA clusters, breakpoints and centromeres was tested by maximum likelihood analyses. Our results highlighted the following features of rDNA cluster dynamics in the genus <it>Mus</it>: i) rDNA clusters showed extensive diversity in number between species and an almost exclusive pericentromeric location, ii) a strong association between rDNA sites and centromeres was retrieved which may be related to their shared constraint of concerted evolution, iii) 24% of the observed breakpoints mapped near an rDNA cluster, and iv) a substantial rate of rDNA cluster change (insertion, deletion) also occurred in the absence of chromosomal rearrangements.</p> <p>Conclusions</p> <p>This study on the dynamics of rDNA clusters within the genus <it>Mus </it>has revealed a strong evolutionary relationship between rDNA clusters and centromeres. Both of these genomic structures coincide with breakpoints in the genus <it>Mus</it>, suggesting that the accumulation of a large number of repeats in the centromeric region may contribute to the high level of chromosome repatterning observed in this group. However, the elevated rate of rDNA change observed in the chromosomally invariant clade indicates that the presence of these sequences is insufficient to lead to genome instability. In agreement with recent studies, these results suggest that additional factors such as modifications of the epigenetic state of DNA may be required to trigger evolutionary plasticity.</p

Actinidia seed-born latent virus is transmitted paternally and maternally at high rates

AbstractActinidia seed-borne latent virus (ASbLV, Betaflexiviridae), was detected at high frequency in healthy seedlings grown from lines of imported seed in a New Zealand post-entry quarantine facility. To better understand how to manage this virus in a dioecious crop species, we developed a rapid molecular protocol to detect infected progeny and to identify a reliable plant tissue appropriate to detect transmission rates from paternal and maternal parents under quarantine environment.The frequency of ASbLV detection from true infection of F1 progeny was distinguished by testing whole seeds and progeny seedling tissues from a controlled cross between two unrelated parents; an ASbLV-infected staminate (male) plant and an uninfected pistillate (female) plant, and the process was repeated with an ASbLV uninfected staminate (male) plant and an infected pistillate (female) plant. Individual whole seeds, or single cotyledons from newly-emerged seedlings, true leaf or a root from those positive-tested seedlings, were assessed for presence of ASbLV by reverse transcription-polymerase chain reaction (RT-PCR) analysis. The virus was detected at a high incidence (98%) in individual seeds, but at a much lower incidence in seedling cotyledons (62%). Since detection results were consistent (P=95%) across the three seedling tissues (i.e. cotyledons, leaves and roots) only cotyledons were tested thereafter to determine ASbLV transmission to F1 progeny. F1 seedlings from three crosses were used to compare transmission rates from infected staminate versus infected pistillate parents. One cross from a single flower used an uninfected pistillate vine pollinated by an infected staminate vine, and two crosses (also from a single flower) used an infected pistillate vine (a sibling of the infected staminate vine), pollinated by either of two unrelated uninfected staminate vines.Cotyledon testing of seedlings from each cross confirmed staminate transmission at high frequency (∼60%), and pistillate transmission at even higher frequency (81% and 86%, respectively).The results show ASbLV is transmitted at very high rates, whether from infected ovules or pollen. Transmission to seedlings is lower than detection in whole seeds perhaps due to ASbLV being sometimes residing on (or within) the seed coat only. The results also show RT-PCR of cotyledons allows non-destructive detection of ASbLV in very young seedlings, and could be used to screen kiwifruit plants in a nursery to avoid virus spread to orchards. Likewise, bulk testing of seed lots can quickly detect infected parent plants (fruit bearing female or male pollinator) already in an orchard.ImportanceActinidia seed-borne latent virus (ASbLV, Betaflexiviridae), was detected at high frequency in healthy seedlings grown from lines of imported seed in a New Zealand post-entry quarantine facility. However there are several technical barriers to detecting the presence of seed transmitted viruses and understanding their biology, which has significance for detection in quarantine and subsequent management under germplasm collections. To overcome this, we developed a rapid molecular protocol to detect infected progeny and to identify a reliable plant tissue appropriate to detect transmission rates from paternal and maternal parents under quarantine environment. Individual whole seeds, or single cotyledons from newly-emerged seedlings, true leaf or a root from those positive-tested seedlings, were assessed for presence of ASbLV by reverse transcription-polymerase chain reaction (RT-PCR) analysis. This was done with seed lots obtained from four separate controlled crosses between ASbLV-infected and ASbLV-uninfected Actinidia chinensis var. deliciosa parents.</jats:sec

Evolutionary dynamics of rDNA clusters on chromosomes of moths and butterflies (Lepidoptera)

We examined chromosomal distribution of major ribosomal DNAs (rDNAs), clustered in the nucleolar organizer regions (NORs), in 18 species of moths and butterflies using fluorescence in situ hybridization (FISH) with a codling moth (Cydia pomonella) 18S rDNA probe. Most species showed one or two rDNA clusters in their haploid karyotype but exceptions with four to eleven clusters also occurred. Our results in a compilation with previous data revealed dynamic evolution of rDNA distribution in Lepidoptera except Noctuoidea, which showed a highly uniform rDNA pattern. In karyotypes with one NOR, interstitial location of rDNA prevailed, whereas two-NOR karyotypes showed mostly terminally located rDNA clusters. A possible origin of the single interstitial NOR by fusion between two NOR-chromosomes with terminal rDNA clusters lacks support in available data. In some species, spreading of rDNA to new, mostly terminal chromosome regions was found. The multiplication of rDNA clusters without alteration of chromosome numbers rules out chromosome fissions as a major mechanism of rDNA expansion. Based on rDNA dynamics in Lepidoptera and considering the role of ordered nuclear architecture in karyotype evolution, we propose ectopic recombination, i.e. homologous recombination between repetitive sequences of non-homologous chromosomes, as a primary motive force in rDNA repatterning

Molecular Cytogenetics (Fluorescence In Situ Hybridization - FISH and Fluorochrome Banding): Resolving Species Relationships and Genome Organization

International audienc

Potential of environmental enrichment to prevent transgenerational effects of paternal trauma

Adverse experiences in early life are risk factors for the development of behavioral and physiological symptoms that can lead to psychiatric and cognitive disorders later in life. Some of these symptoms can be transmitted to the offspring, in some cases by non-genomic mechanisms involving germ cells. Using a mouse model of unpredictable maternal separation and maternal stress, we show that postnatal trauma alters coping behaviors in adverse conditions in exposed males when adult and in their adult male progeny. The behavioral changes are accompanied by increased glucocorticoid receptor (GR) expression and decreased DNA methylation of the GR promoter in the hippocampus. DNA methylation is also decreased in sperm cells of exposed males when adult. Transgenerational transmission of behavioral symptoms is prevented by paternal environmental enrichment, an effect associated with the reversal of alterations in GR gene expression and DNA methylation in the hippocampus of the male offspring. These findings highlight the influence of both negative and positive environmental factors on behavior across generations and the plasticity of the epigenome across life

Cytology and DNA content variation of Capsicum genomes

Chromosome data and characterization by fluorescent banding, silver nucleolar organizer region staining (AgNOR), and fluorescence in situ hybridization (FISH) are compiled in this chapter, together with estimations of nuclear DNA content of Capsicum species. To date, the diploid chromosome number of 77.8% of the species in the genus has been recorded. The chromosome number distinguishes two groups of species, one with 2n=2x= 24 and the other with 2n=2x= 26. Only two clades, Andean and Atlantic Forest, possess the chromosome number of 2n= 26.A physical chromosome map with heterochromatin distribution besides5Sand active and inactive 45S ribosomal genes (rDNA) of 12 Capsicum taxa was constructed using fluorescent banding, AgNOR and FISH. The chromosome banding pattern with fluorochromes chromomycin A3 and 4′-6-diamidino-2-phenylindole (CMA/DAPI) reveals number of bands, distribution and content of heterochromatin, and FISH reports the localization of 5Sand active and inactive 45S rDNA. Both methods are specific and, together with morphological characters, are instrumental for identifying taxa in Capsicum. AgNOR method informs the number, size, and position of just active NORs. Additionally, nuclear DNA content was estimated for nine diploid species of Capsicum by flow cytometry. Genome size displays significant variation between but not within species and contributes to their taxonomic grouping.Fil: Scaldaferro, Marisel Analía. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Córdoba. Instituto Multidisciplinario de Biología Vegetal. Universidad Nacional de Córdoba. Facultad de Ciencias Exactas Físicas y Naturales. Instituto Multidisciplinario de Biología Vegetal; ArgentinaFil: Moscone, Eduardo Alberto. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Córdoba. Instituto Multidisciplinario de Biología Vegetal. Universidad Nacional de Córdoba. Facultad de Ciencias Exactas Físicas y Naturales. Instituto Multidisciplinario de Biología Vegetal; Argentin