Phylogenetic reconstruction of ancestral character states for gene expression and mRNA splicing data

Characterization of an environmental strain of Bacillus thuringiensis from a hot spring in Western Himalayas

Bacillus anthracis, the etiological agent of anthrax, is responsible for a serious and often fatal disease of mammalian livestock and humans and is an important biological warfare agent. Bacillus sp. AKG was isolated from a hot spring in western Himalayas and species-specific primers targeting gyrB gene identified the strain as B. anthracis within cereus-group. Cloning, sequencing, and phylogenetic analysis of the partial gyrB sequence from strain AKG indicated a close affiliation with B. anthracis and a few recently isolated strains of B. thuringiensis (e.g., strain Al Hakam and serovar konkukian). Phylogenetic analysis of two other housekeeping genes, clpC and gdpD yielded similar results. This observation is further substantiated by phylogenetic reconstruction using concatenated sequences (1680 bases) of the three genes (gyrB, clpC, and gdpD). Phenotypic features indicated a non-anthracis affiliation for the strain AKG. A novel strategy to distinguish among strains of B. anthracis, B. cereus, and B. thuringiensis based on whole proteome comparison was developed and tested for the identification of this environmental strain. Proteome comparison was used to establish the identity of this unknown environmental strain. Group of replicate 2DE gels for whole cell proteome were generated for each of the three species and strain AKG. Protein spots unique to each group and those showing match between the groups, in a pair-wise comparison, indicated strain AKG as a member of B. thuringiensis. This strategy can be used to assign strains of B. cereus group to their respective species.

Measuring gene expression divergence: the distance to keep

Background

Gene expression divergence is a phenotypic trait reflecting evolution of gene regulation and characterizing dissimilarity between species and between cells and tissues within the same species. Several distance measures, such as Euclidean and correlation-based distances have been proposed for measuring expression divergence.

Results

We show that different distance measures identify different trends in gene expression patterns. When comparing orthologous genes in eight rat and human tissues, the Euclidean distance identified genes uniformly expressed in all tissues near the expression background as genes with the most conserved expression pattern. In contrast, correlation-based distance and generalized-average distance identified genes with concerted changes among homologous tissues as those most conserved. On the other hand, correlation-based distance, Euclidean distance and generalized-average distance highlight quite well the relatively high similarity of gene expression patterns in homologous tissues between species, compared to non-homologous tissues within species.

Conclusions

Different trends exist in the high-dimensional numeric data, and to highlight a particular trend an appropriate distance measure needs to be chosen. The choice of the distance measure for measuring expression divergence can be dictated by the expression patterns that are of interest in a particular study.

Reviewers

This article was reviewed by Mikhail Gelfand, Eugene Koonin and Subhajyoti De (nominated by Sarah Teichmann).

Coding region structural heterogeneity and turnover of transcription start sites contribute to divergence in expression between duplicate genes

BACKGROUND

Gene expression divergence is one manifestation of functional differences between duplicate genes. Although rapid accumulation of expression divergence between duplicate gene copies has been observed, the driving mechanisms behind this phenomenon have not been explored in detail.

RESULTS

We examine which factors influence expression divergence between human duplicate genes, utilizing the latest genome-wide data sets. We conclude that the turnover of transcription start sites between duplicate genes occurs rapidly after gene duplication and that gene pairs with shared transcription start sites have significantly higher expression similarity than those without shared transcription start sites. Moreover, we find that most (55%) duplicate gene pairs do not retain the same coding sequence structure between the two duplicate copies and this also contributes to divergence in their expression. Furthermore, the proportion of aligned sequences in cis-regulatory regions between the two copies is positively correlated with expression similarity. Surprisingly, we find no effect of copy-specific transposable element insertions on the divergence of duplicate gene expression.

CONCLUSIONS

Our results suggest that turnover of transcription start sites, structural heterogeneity of coding sequences, and divergence of cis-regulatory regions between copies play a pivotal role in determining the expression divergence of duplicate genes.

Strategies for reliable exploitation of evolutionary concepts in high throughput biology

The recent availability of the complete genome sequences of a large number of model organisms, together with the immense amount of data being produced by the new high-throughput technologies, means that we can now begin comparative analyses to understand the mechanisms involved in the evolution of the genome and their consequences in the study of biological systems. Phylogenetic approaches provide a unique conceptual framework for performing comparative analyses of all this data, for propagating information between different systems and for predicting or inferring new knowledge. As a result, phylogeny-based inference systems are now playing an increasingly important role in most areas of high throughput genomics, including studies of promoters (phylogenetic footprinting), interactomes (based on the presence and degree of conservation of interacting proteins), and in comparisons of transcriptomes or proteomes (phylogenetic proximity and co-regulation/co-expression). Here we review the recent developments aimed at making automatic, reliable phylogeny-based inference feasible in large-scale projects. We also discuss how evolutionary concepts and phylogeny-based inference strategies are now being exploited in order to understand the evolution and function of biological systems. Such advances will be fundamental for the success of the emerging disciplines of systems biology and synthetic biology, and will have wide-reaching effects in applied fields such as biotechnology, medicine and pharmacology.

Comparative analysis indicates regulatory neofunctionalization of yeast duplicates

Comparison of the expression profiles of S. cerevisiae duplicate pairs with that of their pre-duplication orthologs in C. albicans identified a class of genes that may present cases of regulatory neofunctionalization.

Background

Gene duplication provides raw material for the generation of new functions, but most duplicates are rapidly lost due to the initial redundancy in gene function. How gene function diversifies following duplication is largely unclear. Previous studies analyzed the diversification of duplicates by characterizing their coding sequence divergence. However, functional divergence can also be attributed to changes in regulatory properties, such as protein localization or expression, which require only minor changes in gene sequence.

Results

We developed a novel method to compare expression profiles from different organisms and applied it to analyze the expression divergence of yeast duplicated genes. The expression profiles of Saccharomyces cerevisiae duplicate pairs were compared with those of their pre-duplication orthologs in Candida albicans. Duplicate pairs were classified into two classes, corresponding to symmetric versus asymmetric rates of expression divergence. The latter class includes 43 duplicate pairs in which only one copy has a significant expression similarity to the C. albicans ortholog. These may present cases of regulatory neofunctionalization, as supported also by their dispensability and variability.

Conclusion

Duplicated genes may diversify through regulatory neofunctionalization. Notably, the asymmetry of gene sequence evolution and the asymmetry of gene expression evolution are only weakly correlated, underscoring the importance of expression analysis to elucidate the evolution of novel functions.

Ancestral state reconstructions for genomes

The recent expansion of phylogenetic analysis from the traditional field of molecular evolution, analyzing histories of genes, to the nascent field of "genomic evolution", analyzing histories of entire genomes, enables the construction of trees based on genome information, the quantification of the key processes that shape genome content and, ultimately, plausible parsimony reconstructions of ancestral genomes. Thus, when genomes are considered as phylogenetic characters, it is possible to reconstruct not only the history of species but also the ancestral states in terms of genome structure or function. In the future, we might be able to accurately reconstruct--or retrodict--a chain of events that led to the emergence of a specific genome sequence and, ultimately, to synthesize ancestral genomes at will, creating a "Jurassic database" of genomes.

Datasets for evolutionary comparative genomics

Many decisions about genome sequencing projects are directed by perceived gaps in the tree of life, or towards model organisms. With the goal of a better understanding of biology through the lens of evolution, however, there are additional genomes that are worth sequencing. One such rationale for whole-genome sequencing is discussed here, along with other important strategies for understanding the phenotypic divergence of species.

The Adaptive Evolution Database (TAED): a phylogeny based tool for comparative genomics

From 138 662 embryophyte (higher plant) and 348 142 chordate genes, 4216 embryophyte and 15 452 chordate gene families were generated. For each of these gene families, multiple sequence alignments, phylogenetic trees, ratios of non-synonymous to synonymous nucleotide substitution rates (K_a/K_s), mappings from gene trees to the NCBI taxonomy and structural links to solved three-dimensional protein structures in the Protein Data Bank (PDB) with Grantham-weighted mutational factors were all calculated. Of the ‘gene family trees’, 173 embryophyte and 505 chordate branches show K_a/K_s ≫ 1 and are candidates for functional adaptation. The calculated information is available both as a gene family database and as a phylogenetically indexed resource, called ‘The Adaptive Evolution Database’ (TAED), available at http://www.bioinfo.no/tools/TAED.