Sequencing of the Arabidopsis NOR2 reveals its distinct organization and tissue-specific rRNA ribosomal variants

Despite vast differences between organisms, some characteristics of their genomes are conserved, such as the nucleolus organizing region (NOR). The NOR is constituted of multiple, highly repetitive rDNA genes, encoding the catalytic ribosomal core RNAs which are transcribed from 45S rDNA units. Their precise sequence information and organization remain uncharacterized. Here, using a combination of long- and short-read sequencing technologies we assemble contigs of the Arabidopsis NOR2 rDNA domain. We identify several expressed rRNA gene variants which are integrated into translating ribosomes in a tissue-specific manner. These findings support the concept of tissue specific ribosome subpopulations that differ in their rRNA composition and provide insights into the higher order organization of NOR2.

Sequencing and analysis of Arabidopsis thaliana NOR2 reveal its distinct organization and tissue-specific expression of rRNA ribosomal variants

Despite vast differences between organisms, some characteristics of their genomes are conserved, such as the nucleolus organizing region (NOR). The NOR is constituted of multiple, highly repetitive rDNA genes, encoding the catalytic ribosomal core RNAs which are transcribed from 45S rDNA units. Their precise sequence information and organization remained uncharacterized.We used a combination of long- and short-read sequencing technologies to assemble contigs of the Arabidopsis NOR2 rDNA domain providing a first map. We identified several expressed rRNA gene variants which are integrated into translating ribosomes in a tissue-specific manner. These findings support the concept of tissue specific ribosome subpopulations that differ in their rRNA composition and provide the higher order organization of NOR2.

Simultaneous Mendelian and clonal genome transmission in a sexually reproducing, all-triploid vertebrate

Meiosis in triploids faces the seemingly insuperable difficulty of dividing an odd number of chromosome sets by two. Triploid vertebrates usually circumvent this problem through either asexuality or some forms of hybridogenesis, including meiotic hybridogenesis that involve a reproductive community of different ploidy levels and genome composition. Batura toads ( Bufo baturae ; 3 n = 33 chromosomes), however, present an all-triploid sexual reproduction. This hybrid species has two genome copies carrying a nucleolus-organizing region (NOR+) on chromosome 6, and a third copy without it (NOR−). Males only produce haploid NOR+ sperm, while ova are diploid, containing one NOR+ and one NOR− set. Here, we conduct sibship analyses with co-dominant microsatellite markers so as (i) to confirm the purely clonal and maternal transmission of the NOR− set, and (ii) to demonstrate Mendelian segregation and recombination of the NOR+ sets in both sexes. This new reproductive mode in vertebrates (‘pre-equalizing hybrid meiosis’) offers an ideal opportunity to study the evolution of non-recombining genomes. Elucidating the mechanisms that allow simultaneous transmission of two genomes, one of Mendelian, the other of clonal inheritance, might shed light on the general processes that regulate meiosis in vertebrates.

Cytotaxonomic diagnosis of Trichomycterus diabolus (Teleostei: Trichomycteridae) with comments about its evolutionary relationships with co-generic species

The karyotype and the Ag-NOR location of a sample of Trichomycterus diabolus collected in the córrego Hortelã (Botucatu, São Paulo, Brazil) are described. The species exhibited 2n=56 chromosomes (42 metacentrics, 12 submetacentrics and 2 subtelocentrics) and the nucleolus organizing region located near to the centromere on the long arm of the largest metacentric pair. The presence of 2n=56 chromosomes in T. diabolus is an interesting characteristic since until now all cis-Andean species karyotyped presented 2n=54 chromosomes while almost all trans-Andean species presented different diploid numbers. The possible origin of this unexpected karyotypic form is discussed.

A Candidate Recombination Modifier Gene for Zea mays L.

Maize meiotic mutant desynaptic (dy) was tested as a candidate recombination modifier gene because its effect is manifested in prophase I. Recombination rates for desynaptic (dy) and its wild type were compared in two ways: (1) segregation analysis using six linked molecular markers on chromosome 1L and (2) cytogenetic analysis using fluorescence in situ hybridization (FISH)-aided meiotic configurations observed in metaphase I. Chromosome 1L map lengths among the six linked markers were 45–63 cM for five F2 dy/dy plants, significantly lower than the wild-type F2 map distance of 72 cM. Chromosomes 2 and 6 were marked with rDNA FISH probes, and their map lengths were estimated from FISH-adorned meiotic configurations using the expectation-maximization algorithm. Chiasma frequencies for dy/dy plants were significantly reduced for both arms of chromosome 2, for chromosome arm 6L, and for eight unidentified chromosomes. There was a notable exception for the nucleolus-organizing region-bearing arm chromosome arm 6S, where dy increased chiasma frequency. Maize meiotic mutant desynaptic is a recombination modifier gene based on cytogenetic and segregation analyses.

A possible mechanism for the inhibition of ribosomal RNA gene transcription during mitosis.

When cells enter mitosis, RNA synthesis ceases. Yet the RNA polymerase I (pol I) transcription machinery involved in the production of pre-rRNA remains bound to the nucleolus organizing region (NOR), the chromosome site harboring the tandemly repeated rRNA genes. Here we examine whether rDNA transcription units are transiently blocked or "frozen" during mitosis. By using fluorescent in situ hybridization we were unable to detect nascent pre-rRNA chains on the NORs of mouse 3T3 and rat kangaroo PtK2 cells. Appropriate controls showed that our approach was sensitive enough to visualize, at the light microscopic level, individual transcriptionally active rRNA genes both in situ after experimental unfolding of nucleoli and in chromatin spreads ("Miller spreads"). Analysis of the cell cycle-dependent redistribution of transcript-associated components also revealed that most transcripts are released from the rDNA at mitosis. Upon disintegration of the nucleolus during mitosis, U3 small nucleolar RNA (snoRNA) and the nucleolar proteins fibrillarin and nucleolin became dispersed throughout the cytoplasm and were excluded from the NORs. Together, our data rule out the presence of "frozen Christmas-trees" at the mitotic NORs but are compatible with the view that inactive pol I remains on the rDNA. We propose that expression of the rRNA genes is regulated during mitosis at the level of transcription elongation, similarly to what is known for a number of genes transcribed by pol II. Such a mechanism may explain the decondensed state of the NOR chromatin and the immediate transcriptional reactivation of the rRNA genes following mitosis.

Hybridization studies on Blattella germanica and B. asahinai (Dictyoptera: Blattellidae): species divergence and a possible influence of a major chromosome mutation

An earlier study indicated that Blattella asahinai is separated from its close relative B. germanica by a non-reciprocal translocation that apparently involved the transfer of the nucleolus organizing region from the X chromosome of B. germanica or a B. germanica like ancestor to chromosome 12 in B. asahinai. Continued study on divergence of the two species included genetic analyses of fecundity, egg case hatch, nymphal hatch, sex ratios, and segregation of X chromosomes and the segment carrying the B. asahinai nucleolar organizing region in interspecific and backcross matings. Overall, a complex of maternally related disadvantages was associated with B. asahinai. The effects of cytoplasmic factors could not generally be distinguished from possible effects of X chromosome – cytoplasmic interactions. In two crossing systems, the data fit a hypothesis of lethal effects from the presence of an X chromosome in alien cytoplasm. Cytologic differences occurred frequently in backcrosses, especially with F1 hybrid females, but were limited to chromosomes and chromosome segments affected by the translocation. The possible relationship of the chromosome mutation to traits affecting reproduction and its role in species divergence are discussed.Key words: speciation, evolution, cockroach, cytogenetics.