Sunflower chlorotic mottle virus (SuCMoV), the most prevalent virus of sunflower in Argentina, was reported naturally infecting not only sunflower but also weeds. To understand SuCMoV evolution and ...improve the knowledge on its variability, the complete genomic sequences of two SuCMoV isolates collected from Dipsacus fullonum (-dip) and Ibicella lutea (-ibi) were determined from three overlapping cDNA clones and subjected to phylogenetic and recombination analyses. SuCMoV-dip and -ibi genomes were 9,953-nucleotides (nt) long; their sequences contained an open reading frame of 9,561 nucleotides, which encoded a polyprotein of 3,187 amino acids flanked by a 5′-noncoding region (NCR) of 135 nt and a 3′-NCR of 257 nt. SuCMoV-dip and -ibi genome nucleotide sequences were 90.9 identical and displayed 90 and 94.6 % identity to that of SuCMoV-C, and 90.8 and 91.4 % identity to that of SuCMoV-CRS, respectively. P1 of SuCMoV-dip and -ibi was 3-nt longer than that of SuCMoV-CRS, but 12-nt shorter than that of SuCMoV-C. Two recombination events were detected in SuCMoV genome and the analysis of dN/dS ratio among SuCMoV complete sequences showed that the genomic regions are under different evolutionary constraints, suggesting that SuCMoV evolution would be conservative. Our findings provide evidence that mutation and recombination would have played important roles in the evolutionary history of SuCMoV.
Protein folding: Looping from hydrophobic nuclei Berezovsky, Igor N.; Kirzhner, Valery M.; Kirzhner, Alla ...
Proteins, structure, function, and bioinformatics,
1 December 2001, Letnik:
45, Številka:
4
Journal Article
The Shannon information (SI) in distributions of occurrence frequency of short words in whole genomes is shown to exhibit universality. For given word length, the SI in genomes of all lengths is the ...same as that in random sequences of a universal lengths
L
r
. For the shorter words
L
r
is far shorter than the genome. For example,
L
r
∼
1000
bases for three-letter words. We further show that whole genomes are highly self-similar in the sense that any segment of the genome down to a length of
Λ
sim
, about twice
L
r
, also shares the universal property. We devise a simple genome growth model in which genome-size sequences grown by maximally stochastic segmental duplication and random mutation possess the universal and self-similar properties of genomes.
With the massive amount of sequence and structural data being produced, new avenues emerge for exploiting the information therein for applications in several fields. Fold distributions can be mapped ...onto entire genomes to learn about the nature of the protein universe and many of the interactions between proteins can now be predicted solely on the basis of the genomic context of their genes. Furthermore, by utilising the new incoming data on single nucleotide polymorphisms by mapping them onto three-dimensional structures of proteins, problems concerning population, medical and evolutionary genetics can be addressed.
It has been claimed that complete genome sequences would clarify phylogenetic relationships between organisms but, up to now, no satisfying approach has been proposed to use efficiently these data. ...For instance, if the coding of presence or absence of genes in complete genomes gives interesting results, it does not take into account the phylogenetic information contained in sequences and ignores hidden paralogy by using a similarity-based definition of orthology. Also, concatenation of sequences of different genes takes hardly in consideration the specific evolutionary rate of each gene. At last, building a consensus tree is strongly limited by the low number of genes shared among all organisms. Here, we use a new method based on supertree construction, which permits to cumulate in one supertree the information and statistical support of hundreds of trees from orthologous gene families and to build the phylogeny of 33 prokaryotes and four eukaryotes with completely sequenced genomes. This approach gives a robust supertree, which demonstrates that a phylogeny of prokaryotic species is conceivable and challenges the hypothesis of a thermophilic origin of bacteria and present-day life. The results are compatible with the hypothesis of a core of genes for which lateral transfers are rare but they raise doubts on the widely admitted “complexity hypothesis” which predicts that this core is mainly implicated in informational processes.
Annotations of complete genome sequences submitted directly from sequencing projects are diverse in terms of annotation strategies and update frequencies. These inconsistencies make comparative ...studies difficult. To allow rapid data preparation of a large number of complete genomes, automation and speed are important for genome re-annotation. Here we introduce an open-source rapid genome re-annotation software system, Restauro-G, specialized for bacterial genomes. Restauro-G re-annotates a genome by similarity searches utilizing the BLAST-Like Alignment Tool, referring to protein databases such as UniProt KB, NCBI nr, NCBI COGs, Pfam, and PSORTb. Re-annotation by Restauro-G achieved over 98% accuracy for most bacterial chromosomes in comparison with the original manually curated annotation of EMBL releases. Restauro-G was developed in the generic bioinformatics workbench G-language Genome Analysis Environment and is distributed at
http://restauro-g.iab.keio.ac.jp/under the GNU General Public License.
Avoidance of 4-, 5-, and 6-letter palindromes is observed in many prokaryotic genomes. A large fraction of such palindromes is formed by restriction sites of the species itself or a closely related ...species. One possible reason for that is the horizontal transfer of genes encoding restriction-modification systems. In organisms isolated from the action of such systems (e.g., in Mycoplasma), palindromes are not avoided. The general tendencies in preferences and avoidance of palindromes were studied for 33 available prokaryotic genomes. The results obtained provide additional insight into the relationships within and between taxonomic groups.
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