DNaseI-sensitive and undermethylated rDNA is preferentially expressed in a maize hybrid

Switch them off or not: selective rRNA gene repression in grasses

Nucleolar dominance (ND) is selective epigenetic silencing of 35-48S rDNA loci. In allopolyploids, it is frequently manifested at the cytogenetic level by the inactivation of nucleolar organiser region(s) (NORs) inherited from one or several evolutionary ancestors. Grasses are ecologically and economically one of the most important land plant groups, which have frequently evolved through hybridisation and polyploidisation events. Here we review common and unique features of ND phenomena in this monocot family from cytogenetic, molecular, and genomic perspectives. We highlight recent advances achieved by using an allotetraploid model grass, Brachypodium hybridum, where ND commonly occurs at a population level, and we cover modern genomic approaches that decipher structural features of core arrays of NORs.

DNA barcoding of Cymbidium by genome skimming: Call for next-generation nuclear barcodes

Cymbidium is an orchid genus that has undergone rapid radiation and has high ornamental, economic, ecological and cultural importance, but its classification based on morphology is controversial. The plastid genome (plastome), as an extension of plant standard DNA barcodes, has been widely used as a potential molecular marker for identifying recently diverged species or complicated plant groups. In this study, we newly generated 237 plastomes of 50 species (at least two individuals per species) by genome skimming, covering 71.4% of members of the genus Cymbidium. Sequence-based analyses (barcoding gaps and automatic barcode gap discovery) and tree-based analyses (maximum likelihood, Bayesian inference and multirate Poisson tree processes model) were conducted for species identification of Cymbidium. Our work provides a comprehensive DNA barcode reference library for Cymbidium species identification. The results show that compared with standard DNA barcodes (rbcL + matK) as well as the plastid trnH-psbA, the species identification rate of the plastome increased moderately from 58% to 68%. At the same time, we propose an optimized identification strategy for Cymbidium species. The plastome cannot completely resolve the species identification of Cymbidium, the main reasons being incomplete lineage sorting, artificial cultivation, natural hybridization and chloroplast capture. To further explore the potential use of nuclear data in identifying species, the Skmer method was adopted and the identification rate increased to 72%. It appears that nuclear genome data have a vital role in species identification and are expected to be used as next-generation nuclear barcodes.

Molecular evidence for asymmetric hybridization in three closely related sympatric species

Natural hybridization is common in plants and results in different evolutionary consequences to hybridizing species. Pre- and post-zygotic reproductive isolating barriers can impede hybridization between closely related species to maintain their species integrity. In Northwest Yunnan, three Ligularia species (Ligularia cyathiceps, L. duciformis and L. yunnanensis) and four types of morphologically intermediate individuals were discovered growing together in an area subject to human disturbance. In this study, we used three low-copy nuclear loci to test the natural hybridization hypothesis and the hybridization direction was ascertained by three chloroplast DNA fragments. The results indicated there were two hybridization groups at the study site, L. cyathiceps × L. duciformis and L. duciformis × L. yunnanensis, and two types of morphologically intermediate individuals were produced by L. cyathiceps and L. duciformis, and another two types were produced by L. duciformis and L. yunnanensis, while no hybrids between L. cyathiceps and L. yunnanensis were observed. Both hybridizing groups showed bidirectional but asymmetric hybridization and the factors influencing the symmetry are discussed. Most hybrids produced by the two hybridization groups seemed to be F1 generation. Hybrids with different morphologies within the same hybridization group showed similar genetic components. The results suggest that although human disturbance may promote natural hybridization among the three Ligularia species bringing them together, hybrids are limited to F1s and therefore species boundaries might be maintained.

Reprint of: using nuclear gene data for plant phylogenetics: progress and prospects

The paper reviews the current state of low and single copy nuclear markers that have been applied successfully in plant phylogenetics to date, and discusses case studies highlighting the potential of massively parallel high throughput or next-generation sequencing (NGS) approaches for molecular phylogenetic and evolutionary investigations. The current state, prospects and challenges of specific single- or low-copy plant nuclear markers as well as phylogenomic case studies are presented and evaluated.

Ribosomal DNA heterochromatin in plants

The aim of this review is to integrate earlier results and recent findings to present the current state-of-the-art vision concerning the dynamic behavior of the ribosomal DNA (rDNA) fraction in plants. The global organization and behavioral features of rDNA make it a most useful system to analyse the relationship between chromatin topology and gene expression patterns. Correlations between several heterochromatin fractions and rDNA arrays demonstrate the heterochromatic nature of the rDNA and reveal the importance of the genomic environment and of developmental controls in modulating its dynamics.

Agrobacterium T-DNA integration in Arabidopsis is correlated with DNA sequence compositions that occur frequently in gene promoter regions

Mobile insertion elements such as transposons and T-DNA generate useful genetic variation and are important tools for functional genomics studies in plants and animals. The spectrum of mutations obtained in different systems can be highly influenced by target site preferences inherent in the mechanism of DNA integration. We investigated the target site preferences of Agrobacterium T-DNA insertions in the chromosomes of the model plant Arabidopsis thaliana. The relative frequencies of insertions in genic and intergenic regions of the genome were calculated and DNA composition features associated with the insertion site flanking sequences were identified. Insertion frequencies across the genome indicate that T-strand integration is suppressed near centromeres and rDNA loci, progressively increases towards telomeres, and is highly correlated with gene density. At the gene level, T-DNA integration events show a statistically significant preference for insertion in the 5' and 3' flanking regions of protein coding sequences as well as the promoter region of RNA polymerase I transcribed rRNA gene repeats. The increased insertion frequencies in 5' upstream regions compared to coding sequences are positively correlated with gene expression activity and DNA sequence composition. Analysis of the relationship between DNA sequence composition and gene activity further demonstrates that DNA sequences with high CG-skew ratios are consistently correlated with T-DNA insertion site preference and high gene expression. The results demonstrate genomic and gene-specific preferences for T-strand integration and suggest that DNA sequences with a pronounced transition in CG- and AT-skew ratios are preferred targets for T-DNA integration.

5S rRNA genes expression is not inhibited by DNA methylation in Arabidopsis

Methylation has often been correlated with transcriptional inhibition of genes transcribed by polymerase II, but its role on polymerase III genes is less well understood. Using the genomic sequencing technique, we have analysed the methylation pattern of the different 5S-rDNA arrays of the Arabidopsis genome. Every cytosine position within the 5S sequence is highly methylated whatever the context - CpG, CpNpG or non-symmetrical. The methylation pattern of both transcribed and non-transcribed 5S units is similar, with no preferential methylated or unmethylated site. These results, taken together with 5-azacytidine treatments and in vitro transcription experiments using methylated 5S templates, demonstrate that 5S rRNA gene transcription is not inhibited by methylation. Non-transcribed 5S arrays are more subject to transition mutations resulting from deamination of 5-methylcytosines, leading to CpG depletions and an increasing A + T content. As there were no detectable differences in methylation, this implies more efficient repair and/or selection pressure in transcribed 5S-blocks.

The epigenetics of nucleolar dominance

Epigenetic phenomena are heritable, alternative states of gene activity that are not explained by mutation, changes in gene sequence or normal developmental regulation. Among the earliest examples was nucleolar dominance, a common phenomenon in interspecific hybrids in which only ribosomal RNA (rRNA) genes inherited from one parent are transcribed. Only active rRNA genes initiate formation of a nucleolus, hence the name for the phenomenon. As in other epigenetic phenomena, chromatin modifications enforce selective gene silencing in nucleolar dominance. However, the mechanisms that discriminate between parental sets of rRNA genes are unclear. Possibilities include sequence differences that affect transcription factor affinities. Other evidence suggests that chromosomal context is more important than rRNA gene sequences, implying control on a larger scale.

Nucleolar dominance and silencing of transcription

Nucleolar dominance is a phenomenon in plant and animal hybrids whereby one parental set of ribosomal RNA (rRNA) genes is transcribed, but the hundreds of rRNA genes inherited from the other parent are silent. The phenomenon gets it name because only transcriptionally active rRNA genes give rise to a nucleolus, the site of ribosome assembly. Nucleolar dominance provided the first clear example of DNA methylation and histone deacetylation acting in partnership in a gene-silencing pathway. However, the sites of chromatin modification and the ways in which one set of rRNA genes are targeted for repression remain unclear. Another unresolved question is whether the units of regulation are the individual rRNA genes or the multi-megabase chromosomal domains that encompass the rRNA gene clusters.

Gene dosage and stochastic effects determine the severity and direction of uniparental ribosomal RNA gene silencing (nucleolar dominance) in Arabidopsis allopolyploids

Nucleolar dominance is an epigenetic phenomenon in which one parental set of ribosomal RNA (rRNA) genes is silenced in an interspecific hybrid. In natural Arabidopsis suecica, an allotetraploid (amphidiploid) hybrid of Arabidopsis thaliana and Cardaminopsis arenosa, the A. thaliana rRNA genes are repressed. Interestingly, A. thaliana rRNA gene silencing is variable in synthetic Arabidopsis suecica F1 hybrids. Two generations are needed for A. thaliana rRNA genes to be silenced in all lines, revealing a species-biased direction but stochastic onset to nucleolar dominance. Backcrossing synthetic A. suecica to tetraploid A. thaliana yielded progeny with active A. thaliana rRNA genes and, in some cases, silenced C. arenosa rRNA genes, showing that the direction of dominance can be switched. The hypothesis that naturally dominant rRNA genes have a superior binding affinity for a limiting transcription factor is inconsistent with dominance switching. Inactivation of a species-specific transcription factor is argued against by showing that A. thaliana and C. arenosa rRNA genes can be expressed transiently in the other species. Transfected A. thaliana genes are also active in A. suecica protoplasts in which chromosomal A. thaliana genes are repressed. Collectively, these data suggest that nucleolar dominance is a chromosomal phenomenon that results in coordinate or cooperative silencing of rRNA genes.

Chromatin structure and methylation of rat rRNA genes studied by formaldehyde fixation and psoralen cross-linking

By using formaldehyde cross-linking of histones to DNA and gel retardation assays we show that formaldehyde fixation, similar to previously established psoralen photocross-linking, discriminates between nucleosome- packed (inactive) and nucleosome-free (active) fractions of ribosomal RNA genes. By both cross-linking techniques we were able to purify fragments from agarose gels, corresponding to coding, enhancer and promoter sequences of rRNA genes, which were further investigated with respect to DNA methylation. This approach allows us to analyse independently and in detail methylation patterns of active and inactive rRNA gene copies by the combination of Hpa II and Msp I restriction enzymes. We found CpG methylation mainly present in enhancer and promoter regions of inactive rRNA gene copies. The methylation of one single Hpa II site, located in the promoter region, showed particularly strong correlation with the transcriptional activity.

Transcriptional analysis of nucleolar dominance in polyploid plants: biased expression/silencing of progenitor rRNA genes is developmentally regulated in Brassica

Nucleolar dominance is an epigenetic phenomenon that describes the formation of nucleoli around rRNA genes inherited from only one parent in the progeny of an interspecific hybrid. Despite numerous cytogenetic studies, little is known about nucleolar dominance at the level of rRNA gene expression in plants. We used S1 nuclease protection and primer extension assays to define nucleolar dominance at a molecular level in the plant genus Brassica. rRNA transcription start sites were mapped in three diploids and in three allotetraploids (amphidiploids) and one allohexaploid species derived from these diploid progenitors. rRNA transcripts of only one progenitor were detected in vegetative tissues of each polyploid. Dominance was independent of maternal effect, ploidy, or rRNA gene dosage. Natural and newly synthesized amphidiploids yielded the same results, arguing against substantial evolutionary effects. The hypothesis that nucleolar dominance in plants is correlated with physical characteristics of rRNA gene intergenic spacers is not supported in Brassica. Furthermore, in Brassica napus, rRNA genes silenced in vegetative tissues were found to be expressed in all floral organs, including sepals and petals, arguing against the hypothesis that passage through meiosis is needed to reactivate suppressed genes. Instead, the transition of inflorescence to floral meristem appears to be a developmental stage when silenced genes can be derepressed.

Co-segregation of the maize dwarf mosaic virus resistance gene, Mdm1, with the nucleolus organizer region in maize

The mdm1 locus on the short arm of chromosome six confers resistance in maize to five strains of the maize dwarf mosaic virus (MDMV), an aphid transmitted potyvirus. The location of mdm1 in relation to RFLP and morphological loci on the short arm of chromosome six was determined using BC1 and F2 mapping populations. The following map order and distance in cM was obtained from the F2 population; jc1270-2.5-npi245-1.6-umc85/po1-0.5-mdm1/nor-0.5-bnl6.29A-0.5-npi235-0.8-npi101A-4.3-numc59. No recombination between mdm1 and the nucleolus organizer region (nor) was detected, as determined using a probe from the intergenic spacer region of the rDNA repeat. In order to resolve the relationship between mdm1 and the nor, and to recover recombinants around mdm1, a highresolution map within the polymitotic1 (po1) yellow kernel1 (y1) interval was generated using [po1 y1 tester (po1 mdm1 y1) x Pa405 (Po1 Mdm1 Y1)] F2 plants. The recessive po1 allele imparts a male-sterile phenotype when homozygous and since po1 and y1 are closely linked, the majority of fertile plants from white endosperm (y1/y1) F2 kernels will arise though a recombination event between the Pa405 Po1 allele and the y1 allele of the po1 y1 tester. Plants from 7,650 white (y1/y1) F2 kernels were examined (15,300 chromosomes) and a total of 626 F2∶3 recombinant families was recovered. Analysis of these recombinants revealed that mdm1 cosegregates with the nor. This lack of recombination between mdm1 and the nor suggests that: either (1) mdm1 is located in the region flanking the nor and recombination is suppressed within that region, or (2) mdm1 is located within the nor.

Hypomethylated sequences: characterization of the duplicate soybean genome

Soybean is believed to be a diploidized tetraploid generated from an allotetraploid ancestor. In this study, we used hypomethylated genomic DNA as a source of probes to investigate the genomic structure and methylation patterns of duplicated sequences. Forty-five genomic clones from Phaseolus vulgaris and 664 genomic clones from Glycine max were used to examine the duplicated regions in the soybean genome. Southern analysis of genomic DNA using probes from both sources revealed that greater than 15% of the hypomethylated genomic regions were only present once in the soybean genome. The remaining ca. 85% of the hypomethylated regions comprise duplicated or middle repetitive DNA sequences. If only the ratio of single to duplicate probe patterns is considered, it appears that 25% of the single-copy sequences have been lost. By using a subset of probes that only detected duplicated sequences, we examined the methylation status of the homeologous genomes with the restriction enzymes MspI and HpaII. We found that in all cases both copies of these regions were hypomethylated, although there were examples of low-level methylation. It appears that duplicate sequences are being eliminated in the diploidization process. Our data reveal no evidence that duplicated sequences are being "silenced" by inactivation correlated with methylation patterns.

The structure of the rDNA intergenic spacer of Avena sativa L.: a comparative study

The sequence of the 18S-25S ribosomal RNA gene intergenic spacer (IGS) of Avena sativa was determined. DNA was cloned after polymerase chain reaction amplification of the IGS. The spacer of 3980 bp is composed of non-repeated sequences and five tandem arrays of repeated sequences, named A to E. Homology between oats IGS and other grass species was found. Tandem arrays D and E seem to be originated by duplication from single-copy sequences in related species. A transcription initiation site and putative sites of termination, processing and methylation were detected by computer-aided search. These sites resemble motifs conserved in the IGS of plant species.