ALBERT

Beschreibung: Differences in expression levels are an important source of phenotypic variation within and between populations. MicroRNAs (miRNAs) are key players in post-transcriptional gene regulation that are important for plant development and stress responses. We surveyed expression variation of miRNAs and mRNAs of six accessions from two rice subspecies Oryza sativa L. ssp. indica and Oryza sativa L. ssp . japonica using deep sequencing. While more than half (53.7%) of the mature miRNAs exhibit differential expression between grains and seedlings of rice, only 11.0% show expression differences between subspecies, with an additional 2.2% differentiated for the development-by-subspecies interaction. Expression variation is greater for lowly conserved miRNAs than highly conserved miRNAs, whereas the latter show stronger negative correlation with their targets in expression changes between subspecies. Using a permutation test, we identified 51 miRNA–mRNA pairs that correlate negatively or positively in expression level among cultivated rice. Genes involved in various metabolic processes and stress responses are enriched in the differentially expressed genes between rice indica and japonica subspecies. Our results indicate that stabilizing selection is the major force governing miRNA expression in cultivated rice, albeit positive selection may be responsible for much of the between-subspecies expression divergence.

Beschreibung: Geographical variation among contiguous populations is frequently attributed to ecological divergence or historical isolation followed by secondary contact. Distinguishing between these effects is key to studies of incipient speciation and could be revealed by different genomic signatures. We used RAD-seq analyses to examine morphologically divergent populations of the endemic lizard ( Gallotia galloti ) from the volcanic island of Tenerife. Previous analyses have suggested ecological and historical causes to explain the morphological diversity. Analyses of 276,483 single nucleotide polymorphisms (SNPs) from 〉20 Mbp of the genome revealed one genetically divergent population from Anaga, a region associated with divergent mtDNA lineages in other Tenerife endemics. This population also has a high number of private alleles, and its divergence can be explained by historical isolation. Bayesian outlier analyses identified a small proportion of SNPs as candidates for selection (0.04%) which were strongly differentiated between xeric and mesic habitat types. Individual testing for specific xeric–mesic selection using an alternative approach also supported ecological divergence in a similarly small proportion of SNPs. The study indicates the roles of both historical isolation and ecological divergence in shaping genomic diversity in G. galloti . However, north–south morphological divergence appears solely associated with the latter and likely involves a relatively small proportion of the genome.

Beschreibung: Streptococcus anginosus is a member of the normal oral flora that can become a pathogen causing pyogenic infections in humans. The genome of daptomycin-resistant strain J4206, originally isolated from a patient suffering from breakthrough bacteremia and septic shock at the University of Texas Health Science Center at San Antonio, was determined. The circular genome is 2,001,352 bp long with a GC content of 38.62% and contains multiple mobile genetic elements, including the phage-like chromosomal island SanCI that mediates a mutator phenotype, transposons, and integrative conjugative elements. Daptomycin resistance involves multiple alterations in the cell membrane and cell wall, and unique features were identified in J4206 that may contribute to resistance. A cluster of capsular polysaccharide (CPS) genes for choline metabolism and transport are present that may help neutralize cell surface charges, destabilizing daptomycin binding. Further, unique J4206 genes encoding sortases and LPXTG-target proteins that are involved in cell wall modification were present. The J4206 genome is phylogenetically closely related to the recently reported vancomycin-resistant SA1 strain; however, these genomes differ with SNPs in cardiolipin synthetase, histidine kinase yycG , teichoic acid modification genes, and other genes involved in cell surface modification. Transmission electron microscopy showed that the cell walls of both strains J4206 and SA1 were significantly thicker and more electron dense than daptomycin- and vancomycin-sensitive strain J4211. This comparative genomic study has identified unique genes as well as allelic variants in the J4206 genome that are involved in cell surface modification and thus might contribute to the acquisition of daptomycin resistance.

Beschreibung: Chromosome number changes during the evolution of angiosperms are likely to have played a major role in speciation. Their study is of utmost importance, especially now, as a probabilistic model is available to study chromosome evolution within a phylogenetic framework. In the present study, likelihood models of chromosome number evolution were fitted to the largest family of flowering plants, the Asteraceae. Specifically, a phylogenetic supertree of this family was used to reconstruct the ancestral chromosome number and infer genomic events. Our approach inferred that the ancestral chromosome number of the family is n = 9. Also, according to the model that best explained our data, the evolution of haploid chromosome numbers in Asteraceae was a very dynamic process, with genome duplications and descending dysploidy being the most frequent genomic events in the evolution of this family. This model inferred more than one hundred whole genome duplication events; however, it did not find evidence for a paleopolyploidization at the base of this family, which has previously been hypothesized on the basis of sequence data from a limited number of species. The obtained results and potential causes of these discrepancies are discussed.

Beschreibung: Ribosomal RNAs (rRNAs) account for 〉60% of all RNAs in eukaryotic cells and are encoded in the ribosomal DNA (rDNA) arrays. The rRNAs are produced from two sets of loci: the 5S rDNA array resides exclusively on human chromosome 1, whereas the 45S rDNA array resides on the short arm of five human acrocentric chromosomes. The 45S rDNA gives origin to the nucleolus, the nuclear organelle that is the site of ribosome biogenesis. Intriguingly, 5S and 45S rDNA arrays exhibit correlated copy number variation in lymphoblastoid cells (LCLs). Here we examined the genomic architecture and repeat content of the 5S and 45S rDNA arrays in multiple human genome assemblies (including PacBio MHAP assembly) and ascertained contacts between the rDNA arrays and the rest of the genome using Hi-C datasets from two human cell lines (erythroleukemia K562 and lymphoblastoid cells). Our analyses revealed that 5S and 45S arrays each have thousands of contacts in the folded genome, with rDNA-associated regions and genes dispersed across all chromosomes. The rDNA contact map displayed conserved and disparate features between two cell lines, and pointed to specific chromosomes, genomic regions, and genes with evidence of spatial proximity to the rDNA arrays; the data also showed a lack of direct physical interaction between the 5S and 45S rDNA arrays. Finally, the analysis identified an intriguing organization in the 5S array with Alu and 5S elements adjacent to one another and organized in opposite orientation along the array. Portraits of genome folding centered on the ribosomal DNA array could help understand the emergence of concerted variation, the control of 5S and 45S expression, as well as provide insights into an organelle that contributes to the spatial localization of human chromosomes during interphase.

Beschreibung: Conserved non-coding sequences (CNSs) of Eukaryotes are known to be significantly enriched in regulatory sequences. CNSs of diverse lineages follow different patterns in abundance, sequence composition, and location. Here, we report a thorough analysis of CNSs in diverse groups of Eukaryotes with respect to GC content heterogeneity. We examined 24 fungi, 19 invertebrates, and 12 non-mammalian vertebrates so as to find lineage specific features of CNSs. We found that fungi and invertebrate CNSs are predominantly GC rich as in plants we previously observed, whereas vertebrate CNSs are GC poor. This result suggests that the CNS GC content transition occurred from the ancestral GC rich state of Eukaryotes to GC poor in the vertebrate lineage due to the enrollment of GC poor transcription factor binding sites that are lineage specific. CNS GC content is closely linked with the nucleosome occupancy that determines the location and structural architecture of DNAs.