To Be or Not to Be Expressed: The First Evidence of a Nucleolar Dominance Tissue-Specificity in Brachypodium hybridum

Nucleolar dominance (ND) is an epigenetic, developmentally regulated phenomenon that describes the selective inactivation of 35S rDNA loci derived from one progenitor of a hybrid or allopolyploid. The presence of ND was documented in an allotetraploid grass, Brachypodium hybridum (genome composition DDSS), which is a polyphyletic species that arose from crosses between two putative ancestors that resembled the modern B. distachyon (DD) and B. stacei (SS). In this work, we investigated the developmental stability of ND in B. hybridum genotype 3-7-2 and compared it with the reference genotype ABR113. We addressed the question of whether the ND is established in generative tissues such as pollen mother cells (PMC). We examined condensation of rDNA chromatin by fluorescence in situ hybridization employing state-of-art confocal microscopy. The transcription of rDNA homeologs was determined by reverse-transcription cleaved amplified polymorphic sequence analysis. In ABR113, the ND was stable in all tissues analyzed (primary and adventitious root, leaf, and spikes). In contrast, the 3-7-2 individuals showed a strong upregulation of the S-genome units in adventitious roots but not in other tissues. Microscopic analysis of the 3-7-2 PMCs revealed extensive decondensation of the D-genome loci and their association with the nucleolus in meiosis. As opposed, the S-genome loci were always highly condensed and localized outside the nucleolus. These results indicate that genotype-specific loss of ND in B. hybridum occurs probably after fertilization during developmental processes. This finding supports our view that B. hybridum is an attractive model to study ND in grasses.

Chromosomal Characterization of Tripidium arundinaceum Revealed by Oligo-FISH

Sugarcane is of important economic value for producing sugar and bioethanol. Tripidium arundinaceum (old name: Erianthus arundinaceum) is an intergeneric wild species of sugarcane that has desirable resistance traits for improving sugarcane varieties. However, the scarcity of chromosome markers has hindered the cytogenetic study of T. arundinaceum. Here we applied maize chromosome painting probes (MCPs) to identify chromosomes in sorghum and T. arundinaceum using a repeated fluorescence in situ hybridization (FISH) system. Sequential FISH revealed that these MCPs can be used as reliable chromosome markers for T. arundinaceum, even though T. arundinaceum has diverged from maize over 18 MYs (million years). Using these MCPs, we identified T. arundinaceum chromosomes based on their sequence similarity compared to sorghum and labeled them 1 through 10. Then, the karyotype of T. arundinaceum was established by multiple oligo-FISH. Furthermore, FISH results revealed that 5S rDNA and 35S rDNA are localized on chromosomes 5 and 6, respectively, in T. arundinaceum. Altogether, these results represent an essential step for further cytogenetic research of T. arundinaceum in sugarcane breeding.

Ancient Origin of Two 5S rDNA Families Dominating in the Genus Rosa and Their Behavior in the Canina-Type Meiosis

The genus Rosa comprises more than 100 woody species characterized by intensive hybridization, introgression, and an overall complex evolutionary history. Besides many diploid species (2n = 2x = 14) polyploids ranging from 3x to 10x are frequently found. Here we analyzed 5S ribosomal DNA in 19 species covering two subgenera and the major sections within subg. Rosa. In addition to diploids and polyploids with regular meiosis, we focused on 5x dogroses (Rosa sect. Caninae), which exhibit an asymmetric meiosis differentiating between bivalent- and univalent-forming chromosomes. Using genomic resources, we reconstructed 5S rDNA units to reveal their phylogenetic relationships. Additionally, we designed locus-specific probes derived from intergenic spacers (IGSs) and determined the position and number of 5S rDNA families on chromosomes. Two major 5S rDNA families (termed 5S_A and 5S_B, respectively) were found at variable ratios in both diploid and polyploid species including members of the early diverging subgenera, Rosa persica and Rosa minutifolia. Within subg. Rosa species of sect. Rosa amplified the 5S_A variant only, while taxa of other sections contained both variants at variable ratios. The 5S_B family was often co-localized with 35S rDNA at the nucleolar organizer regions (NOR) chromosomes, whereas the co-localization of the 5S_A family with NOR was only exceptionally observed. The allo-pentaploid dogroses showed a distinct distribution of 5S rDNA families between bivalent- and univalent-forming chromosomes. In conclusion, two divergent 5S rDNA families dominate rose genomes. Both gene families apparently arose in the early history of the genus, already 30 myrs ago, and apparently survived numerous speciation events thereafter. These observations are consistent with a relatively slow genome turnover in the Rosa genus.

Different from tracheophytes, liverworts commonly have mixed 35S and 5S arrays

Background and Aims Unlike other nuclear genes in eukaryotes, rDNA genes (5S and 35S loci) are present in numerous copies per cell and, when stained, can therefore provide basic information about genome organization. In tracheophytes (vascular plants), they are usually located on separate chromosomes, the so-called S-type organization. An analysis of 1791 species of land plants suggested that S-type arrays might be ancestral in land plants, while linked (L-type) organization may be derived. However, no outgroup and only a handful of ferns and bryophytes were included. Methods We analysed genome sizes and the distribution of telomere, 5S and 35S rDNA FISH signals in up to 12 monoicous or dioicous species of liverworts from throughout a phylogeny that includes 287 of the 386 currently recognized genera. We also used the phylogeny to plot chromosome numbers and the occurrence of visibly distinct sex chromosomes. Key Results Chromosome numbers are newly reported for the monoicous Lejeunea cavifolia and for females of the dioicous Scapania aequiloba. We detected sex-related differences in the number of rDNA signals in the dioicous Plagiochila asplenioides and Frullania dilatata. In the latter, the presence of two UU chromosomes in females and additional 5S-35S rDNA loci result in a haploid genome 0.2082 pg larger than the male genome; sex-specific genome differences in the other dioicous species were small. Four species have S-type rDNA, while five species have mixed L-S rDNA organization, and transitions may have occurred multiple times, as suggested by rDNA loci not being conserved among closely related species of Pellia. All species shared an Arabidopsis-like telomere motif, and its detection allowed verification of the chromosome number of Radula complanata and chromosome rearrangements in Aneura pinguis and P. asplenioides, the latter also showing sex-specific interstitial telomere repeats. Conclusions The S and L rDNA arrangements appear to have evolved repeatedly within liverworts, even in the same species. Evidence for differential accumulation of rDNA between the sexes so far is limited.

Skim-Sequencing Reveals the Likely Origin of the Enigmatic Endangered Sunflower Helianthus schweinitzii

Resolving the origin of endangered taxa is an essential component of conservation. This information can be used to guide efforts of bolstering genetic diversity, and also enables species recovery and future evolutionary studies. Here, we used low-coverage whole genome sequencing to clarify the origin of Helianthus schweinitzii, an endangered tetraploid sunflower that is endemic to the Piedmont Plateau in the eastern United States. We surveyed four accessions representing four populations of H. schweinitzii and 38 accessions of six purported parental species. Using de novo approaches, we assembled 87,004 bp of the chloroplast genome and 6770 bp of the nuclear 35S rDNA. Phylogenetic reconstructions based on the chloroplast genome revealed no reciprocal monophyly of taxa. In contrast, nuclear rDNA data strongly supported the currently accepted sections of the genus Helianthus. Information from combined cpDNA and rDNA provided evidence that H. schweinitzii is likely an allo-tetraploid that formed as a result of hybridization between the diploids Helianthus giganteus and Helianthus microcephalus.

Genome size and chromosome number conservation contrasting with karyotype diversity in Hohenbergia (Bromelioideae, Bromeliaceae)

Plant evolution may be triggered by significant chromosome changes. In some plant groups, karyoevolution played an important role, influencing speciation processes. Hohenbergia comprises 48 species distributed through eastern Brazil. Previous cytological information includes few species and only chromosome counts, lacking information about genome size and more accurate karyomorphological investigation. Here, we compare cytomolecular features and genome sizes of 12 Hohenbergia spp. Besides, new measurements of genome sizes of 32 species are reported. All studied species presented 2n = 50, a number prevalent in Bromelioideae. The genome sizes (2C) varied from 0.74 to 1.52 pg. Despite the apparent homogeneity in chromosome number and genome size in Hohenbergia, significant polymorphism was observed in regard to the distribution of CMA+/DAPI0 bands and sites of 35S and 5S rDNA in metaphase chromosomes. Seven out of 12 analysed species presented heteromorphic pairs regarding 35S rDNA and/or 5S rDNA. Hohenbergia thus shows karyotypic diversity despite the conservation in chromosome number.

Allopolyploid origin and genome differentiation of the parasitic species Cuscuta veatchii (Convolvulaceae) revealed by genomic in situ hybridization

Interspecific hybridization and genome duplication to form allopolyploids are major evolutionary events in angiosperms. In the parasitic genus Cuscuta (Convolvulaceae), molecular data suggested the existence of species of hybrid origin. One of them, C. veatchii, has been proposed as a hybrid between C. denticulata and C. nevadensis, both included in sect. Denticulatae. To test this hypothesis, a cytogenetic analysis was performed with CMA/DAPI staining and fluorescent in situ hybridization using 5S and 35S rDNA and genomic probes. Chromosomes of C. denticulata were small with a well-defined centromeric region, whereas C. nevadensis had larger, densely stained chromosomes, and less CMA+ heterochromatic bands. Cuscuta veatchii had 2n = 60 chromosomes, about 30 of them similar to those of C. denticulata and the remaining to C. nevadensis. GISH analysis confirmed the presence of both subgenomes in the allotetraploid C. veatchii. However, the number of rDNA sites and the haploid karyotype length in C. veatchii were not additive. The diploid parentals had already diverged in their chromosomes structure, whereas the reduction in the number of rDNA sites more probably occurred after hybridization. As phylogenetic data suggested a recent divergence of the progenitors, these species should have a high rate of karyotype evolution.