Improving the specificity of high-throughput ortholog prediction

Background  

Orthologs (genes that have diverged after a speciation event) tend to have similar function, and so their prediction has become an important component of comparative genomics and genome annotation. The gold standard phylogenetic analysis approach of comparing available organismal phylogeny to gene phylogeny is not easily automated for genome-wide analysis; therefore, ortholog prediction for large genome-scale datasets is typically performed using a reciprocal-best-BLAST-hits (RBH) approach. One problem with RBH is that it will incorrectly predict a paralog as an ortholog when incomplete genome sequences or gene loss is involved. In addition, there is an increasing interest in identifying orthologs most likely to have retained similar function.     

Chemical Composition of Essential Oil from Mosses from the Brazilian Atlantic Forest

This study aimed to report the unprecedented volatile composition of the mosses Phyllogonium viride BRID, Orthotichella rigida (MÜLL.HAL.) B. H. ALLEN & MAGILL and Schlotheimia rugifolia (HOOK.) SCHWÄGR occurring in the Brazilian Atlantic Forest, in order to elucidate the chemical composition of these species and enrich the chemotaxonomic knowledge of mosses. 28 compounds were identified, the major constituent being hexadecanoic acid, also known as palmitic acid, specifically P. viride com (38.55 %), O. rigida com (17.17 %) and S. rugifolia com (24.94 %), followed by phytol, P. viride com (3.92 %), O. rigida com (28.57 %) and S. rugifolia com (36.13 %). In addition, there was a prevalence of aliphatic hydrocarbons (25 %) and fatty acids (17.8 %) in the evaluated samples. These data contribute to the generation of new scientific information about the chemical constitution of mosses, still little studied, enriching the chemotaxonomic collection of the taxon.     

Evolution of antibiotic resistance genes: the DNA sequence of a kanamycin resistance gene from Staphylococcus aureus

The kanamycin resistance gene from Staphylococcus aureus has been sequenced and its structure compared with similar genes isolated from Streptomyces fradiae and from two transposons, Tn5 and Tn903, originally isolated from Klebsiella pneumoniae and Salmonella typhimurium, respectively. The genes are all homologous but, since their common ancestor, have undergone extensive divergence, with more than 43% divergence between the closest pair. The phylogeny of the genes cannot be made congruent to the phylogeny of the taxa from which they were isolated without requiring rather improbable differences in rates. One is therefore led to conclude that there have been multiple occurrences of gene transfer between these species. Thus, although they are homologous, they are neither orthologous nor paralogous. It is suggested that homologous genes of this type be called xenologous.