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.

A Tandemly Arranged Pattern of Two 5S rDNA Arrays in Amolops mantzorum (Anura, Ranidae)

In an attempt to extend the knowledge of the 5S rDNA organization in anurans, the 5S rDNA sequences of Amolops mantzorum were isolated, characterized, and mapped by FISH. Two forms of 5S rDNA, type I (209 bp) and type II (about 870 bp), were found in specimens investigated from various populations. Both of them contained a 118-bp coding sequence, readily differentiated by their non-transcribed spacer (NTS) sizes and compositions. Four probes (the 5S rDNA coding sequences, the type I NTS, the type II NTS, and the entire type II 5S rDNA sequences) were respectively labeled with TAMRA or digoxigenin to hybridize with mitotic chromosomes for samples of all localities. It turned out that all probes showed the same signals that appeared in every centromeric region and in the telomeric regions of chromosome 5, without differences within or between populations. Obviously, both type I and type II of the 5S rDNA arrays arranged in tandem, which was contrasting with other frogs or fishes recorded to date. More interestingly, all the probes detected centromeric regions in all karyotypes, suggesting the presence of a satellite DNA family derived from 5S rDNA.

Evolution in the block: common elements of 5S rDNA organization and evolutionary patterns in distant fish genera

The 5S rDNA is organized in the genome as tandemly repeated copies of a structural unit composed of a coding sequence plus a nontranscribed spacer (NTS). The coding region is highly conserved in the evolution, whereas the NTS vary in both length and sequence. It has been proposed that 5S rRNA genes are members of a gene family that have arisen through concerted evolution. In this study, we describe the molecular organization and evolution of the 5S rDNA in the genera Lepidorhombus and Scophthalmus (Scophthalmidae) and compared it with already known 5S rDNA of the very different genera Merluccius (Merluccidae) and Salmo (Salmoninae), to identify common structural elements or patterns for understanding 5S rDNA evolution in fish. High intra- and interspecific diversity within the 5S rDNA family in all the genera can be explained by a combination of duplications, deletions, and transposition events. Sequence blocks with high similarity in all the 5S rDNA members across species were identified for the four studied genera, with evidences of intense gene conversion within noncoding regions. We propose a model to explain the evolution of the 5S rDNA, in which the evolutionary units are blocks of nucleotides rather than the entire sequences or single nucleotides. This model implies a “two-speed” evolution: slow within blocks (homogenized by recombination) and fast within the gene family (diversified by duplications and deletions).

Different patterns of rDNA organization at interphase in nuclei of wheat and rye

The physical location of the rDNA repeating units (25 S, 18 S and 5.8 S rRNA genes and the intergenic spacer sequences) was investigated in rye (Secale cereale L.) and wheat (Triticum aestivum L.) root tip meristematic cells by in situ hybridization using light and electron microscopy. The rDNA sequences are organized differently in the two related and intercrossable species. In rye (2n = 14, one pair of chromosomes with nucleolar organizing regions, NORs), two condensed blocks of rDNA-containing chromatin occurred in each interphase nucleus. The blocks were associated with the periphery of nucleoli and a single-labelled, decondensed rDNA fibre extended into the nucleolus from the block. We term this expression pattern terminal decondensation. In wheat (2n = 6x = 42, five pairs of chromosomes with NORs), inactive condensed labelled chromatin was found unassociated with nucleoli. Active NORs had some condensed rDNA associated with the nucleolar periphery, but, in contrast to rye, condensed rDNA was also found within the nucleolus. The condensed labelled rDNA in wheat nucleoli was visible as fluorescent foci in the light microscope and labelled condensed chromatin in the electron microscope. Its absence in rye shows that condensed rDNA need not be present in active plant nucleoli. Diffuse labelled sites of rDNA, likely to represent actively transcribed rDNA, were found in both rye and wheat. Active rDNA loci in wheat have many expressed segments separated by unexpressed, condensed, rDNA-fragmented decondensation-while each locus in rye has a single, unexpressed perinucleolar condensed block of rRNA genes. Thus the positions of actively transcribed genes within the tandem arrays of rDNA at each locus are fundamentally different in the two cereals. The NOR chromosome appeared to extend through the nucleolus, and active rDNA sequences did not loop out from chromatin into the nucleolus as is frequently described in nucleolar models.