Correction: Evolutionary principles of modular gene regulation in yeasts.

[This corrects the article DOI: 10.7554/eLife.00603.

Evolutionary principles of modular gene regulation in yeasts.

Divergence in gene regulation can play a major role in evolution. Here, we used a phylogenetic framework to measure mRNA profiles in 15 yeast species from the phylum Ascomycota and reconstruct the evolution of their modular regulatory programs along a time course of growth on glucose over 300 million years [corrected]. We found that modules have diverged proportionally to phylogenetic distance, with prominent changes in gene regulation accompanying changes in lifestyle and ploidy, especially in carbon metabolism.

Arboretum: reconstruction and analysis of the evolutionary history of condition-specific transcriptional modules.

Comparative functional genomics studies the evolution of biological processes by analyzing functional data, such as gene expression profiles, across species. A major challenge is to compare profiles collected in a complex phylogeny. Here, we present Arboretum, a novel scalable computational algorithm that integrates expression data from multiple species with species and gene phylogenies to infer modules of coexpressed genes in extant species and their evolutionary histories.

Comparative functional genomics of the fission yeasts.

The fission yeast clade--comprising Schizosaccharomyces pombe, S. octosporus, S. cryophilus, and S.

Strand-specific RNA sequencing reveals extensive regulated long antisense transcripts that are conserved across yeast species.

Background: Recent studies in budding yeast have shown that antisense transcription occurs at many loci. However, the functional role of antisense transcripts has been demonstrated only in a few cases and it has been suggested that most antisense transcripts may result from promiscuous bi-directional transcription in a dense genome.

Results: Here, we use strand-specific RNA sequencing to study anti-sense transcription in Saccharomyces cerevisiae.

Gene duplication and the evolution of ribosomal protein gene regulation in yeast.

Coexpression of genes within a functional module can be conserved at great evolutionary distances, whereas the associated regulatory mechanisms can substantially diverge. For example, ribosomal protein (RP) genes are tightly coexpressed in Saccharomyces cerevisiae, but the cis and trans factors associated with them are surprisingly diverged across Ascomycota fungi. Little is known, however, about the functional impact of such changes on actual expression levels or about the selective pressures that affect them.

Ab initio construction of a eukaryotic transcriptome by massively parallel mRNA sequencing.

Defining the transcriptome, the repertoire of transcribed regions encoded in the genome, is a challenging experimental task. Current approaches, relying on sequencing of ESTs or cDNA libraries, are expensive and labor-intensive. Here, we present a general approach for ab initio discovery of the complete transcriptome of the budding yeast, based only on the unannotated genome sequence and millions of short reads from a single massively parallel sequencing run.

Development of an immunoglobulin M capture-based enzyme-linked immunosorbent assay for diagnosis of acute infections with Bartonella henselae.

We describe the development of an immunoglobulin M-specific enzyme-linked immunosorbent assay for the detection of an early antibody response to Bartonella henselae, the causative agent of cat scratch disease, bacillary angiomatosis, and endocarditis. This assay discriminates between B. henselae-positive and -negative patient samples with sensitivity and specificity values of 100% and 97.

MICROBIAL DEGRADATION OF CORRINOIDS. 3. PIGMENTS DERIVED FROM VITAMIN B12 BY PSEUDOMONAS RUBESCENS.

Burgus, R. C. (Wayne State University, Detroit, Mich.

MICROBIAL DEGRADATION OF CORRINOIDS. I. VITAMIN B12.

Scott, W. M. (Wayne State University, Detroit, Mich.