How repetitive are genomes?

BACKGROUND: Genome sequences vary strongly in their repetitiveness and the causes for this are still debated. Here we propose a novel measure of genome repetitiveness, the index of repetitiveness, I(r), which can be computed in time proportional to the length of the sequences analyzed. We apply it to 336 genomes from all three domains of life. RESULTS: The expected value of I(r )is zero for random sequences of any G/C content and greater than zero for sequences with excess repeats. We find that the I(r )of archaea is significantly smaller than that of eubacteria, which in turn is smaller than that of eukaryotes. Mouse chromosomes have a significantly higher I(r )than human chromosomes and within each genome the Y chromosome is most repetitive. A sliding window analysis reveals that the human HOXA cluster and two surrounding genes are characterized by local minima in I(r). A program for calculating the I(r )is freely available at . CONCLUSION: The general measure of DNA repetitiveness proposed in this paper can be efficiently computed on a genomic scale. This reveals a broad spectrum of repetitiveness among diverse genomes which agrees qualitatively with previous studies of repeat content. A sliding window analysis helps to analyze the intragenomic distribution of repeats

Evolution, function and manipulation of methyl halide production in plants

Methyl halides (CH3Cl, CH3Br and CH3I) are a group of volatile organic compounds which contribute to natural ozone degradation in the atmosphere. Plants are important emitters of these compounds due to the activity of halide/thiol methyltransferases (HTMTs), however, the function of HTMTs or methyl halide production is not known. In Arabidopsis thaliana, one HTMT is primarily responsible for the production of methyl halides and encoded by the HARMLESS TO OZONE LAYER (HOL) gene. In this study, an A. thaliana hol mutant and 35S::HOL lines were used to investigate the function of HOL. No support was found for the hypothesis that HOL contributes to salt stress tolerance via the disposal of excessive amounts of halides. On the contrary, increased HOL activity made 35S::HOL plants more susceptible towards salt stress. Despite the toxicity of methyl halides, differences in HOL activity in hol mutant and 35S::HOL plants did not affect the performance of insect herbivores, nor did it alter the microbial diversity of the rhizosphere in these lines. Microarray analysis of WT and hol mutant plants pointed to a function of HOL in starch/carbon metabolism and stress response pathways in A. thaliana. Brassica crops are significant emitters of methyl halides. A HOL-homologous gene (BraA.HOL.a) was identified in Brassica rapa. It was confirmed that this gene contributes to methyl halide production in B. rapa since braA.hol.a mutants had significantly reduced emission levels compared to WT. HOL-homologous genes were also found in various plant species throughout the plant kingdom including the moss Physcomitrella patens, which was shown to produce CH3Br. These data show that methyl halide production is an ancient mechanism in land plants. Moreover, phylogenetic analysis revealed a clear separation between HTMTs from glucosinolate (GL)-containing plants and HTMTs from eudicots without GLs supporting the hypothesis of a novel function of HTMTs in the order Brassicales

Plant-parasitic nematodes: from genomics to functional analysis of parasitism genes

Nematodes (roundworms) belong to the largest phylum on earth. The numerous species inhabit practically all ecological niches, including plants. Plant-parasitic species live on plant roots, causing substantial damage to the plant and hampering its development. As such, they cause gigantic economical losses in crop production. We used a molecular approach to analyze the plant-parasitic nematode Radopholus similis by generating expressed sequence tags (ESTs). The most striking discovery was tags corresponding to aWolbachia-like endosymbiont, which was subsequently located in the ovaria of R. similis. Numerous tags corresponding to parasitism genes with potential roles in, amongst other things, host localisation, detoxification, cell wall modification, and even putative host transcriptional reprogramming were identified. In addition, a tool to explore all available nematode EST data is presented in this study. The ‘nematode EST exploration tool’ (NEXT) (http://zion.ugent.be/joachim/next) extends the usefulness by extracting and storing temporal and spatial information of all publicly available nematode EST libraries. Some members of the transthyretin-like gene family of R. similis were characterized. All stages except developing embryos express the analyzed genes, and expression is localized to the ventral nerve cord and tissues surrounding the vulva. Predicted secondary structure is suggestive of a binding capacity with a yet unknown ligand. Further, the annotation of the complete mitochondrial (mt) genome of R. similis is reported. The mt genome has the expected gene content, but shows many aberrant features such as: a considerably smaller 16S rRNA with reduced structures, two large repeat regions, the lack of stop codons on many genes and a unique codon reassignment UAA:Stop to UAA:Tyrosine. The aberrant features in the mt genome could be related to this codon reassignment, but results are ambiguous and require further research. A last part of the study reports on the response of the plant on nematode infection. Signaling of two plant hormones involved in plant defense is measured during early phases of parasitism. In addition, the role of flavonoid compounds produced by the plant is analyzed by infection tests on several mutants