A simple method for phylogenomic inference using the information of gene content of genomes

Genome distance and phylogenetic inference accommodating gene duplication, loss and new gene input

With the rapid growth of entire genome data, phylogenomics focuses on analyzing evolutionary histories and relationships of species, i.e., the tree of life. For decades it has been realized that the genome-wide phylogenetic inference can be approached based upon the dynamic pattern of gene content (the presence/absence of gene families), or extended gene content (absence, presence as a single-copy, or duplicates). Those methods, conceptually or technically, invoked the birth-and-death process to model the evolutionary process (gene duplication or gene loss. One common drawback is that the mechanism of new gene input, including de novo origin of new genes and the lateral gene transfer, has not been explicitly considered. In this paper, the author developed a new genome distance approach for genome phylogeny inference under the origin-birth-death stochastic process. The model takes gene duplication, gene loss and new gene input into account simultaneously. Computer simulations found that the two-genome approach is statistically difficult to distinguish between two proliferation parameters, i.e., the rate of gene duplication and the rate of new gene input. Nevertheless, it has also demonstrated the statistical feasibility for using the loss-genome distance to infer the genome phylogeny, which can avoid the large sampling problem. The strategy to study the universal tree of life was discussed and exemplified by an example.

Insect phylogenomics

Phylogenomics, the integration of phylogenetics with genome data, has emerged as a powerful approach to study the evolution and systematics of species. Recently, several studies employing phylogenomic tools have provided better insights into insect evolution. Next-generation sequencing methods are now increasingly used by entomologists to generate genomic and transcript sequences of various insect species and strains. These data provide opportunities for comparative genomics and large-scale multigene phylogenies of diverse lineages of insects. Phy-logenomic investigations help us to better understand systematic and evolutionary relationships of insect species that play important roles as herbivores, predators, detritivores, pollinators and disease vectors. It is important that we critically assess the prospects and limitations of phylogenomic methods. In this review, I describe the current status, outline the major challenges and remark on potential future applications of phylogenomic tools in studying insect systematics and evolution.

Using the taxon-specific genes for the taxonomic classification of bacterial genomes

BACKGROUND

The correct taxonomic assignment of bacterial genomes is a primary and challenging task. With the availability of whole genome sequences, the gene content based approaches appear promising in inferring the bacterial taxonomy. The complete genome sequencing of a bacterial genome often reveals a substantial number of unique genes present only in that genome which can be used for its taxonomic classification.

RESULTS

In this study, we have proposed a comprehensive method which uses the taxon-specific genes for the correct taxonomic assignment of existing and new bacterial genomes. The taxon-specific genes identified at each taxonomic rank have been successfully used for the taxonomic classification of 2,342 genomes present in the NCBI genomes, 36 newly sequenced genomes, and 17 genomes for which the complete taxonomy is not yet known. This approach has been implemented for the development of a tool 'Microtaxi' which can be used for the taxonomic assignment of complete bacterial genomes.

CONCLUSION

The taxon-specific gene based approach provides an alternate valuable methodology to carry out the taxonomic classification of newly sequenced or existing bacterial genomes.

Tracing lifestyle adaptation in prokaryotic genomes

Lifestyle adaptation of microbes due to changes in their ecological niches or acquisition of new environments is a major driving force for genetic changes in their respective genomes. Moving into more specialized niches often results in the acquisition of new gene sets via horizontal gene transfer to utilize previously unavailable metabolites, while genetic ballast is shed by gene loss and/or gene inactivation. In some cases, larger genome rearrangements can be observed, such as the incorporation of whole genetic islands, providing a range of new phenotypic capabilities. Until recently these changes could not be comprehensively followed and identified due to the lack of complete microbial genome sequences. The advent of high-throughput DNA sequencing has dramatically changed the scientific landscape and today microbial genomes have become increasingly abundant. Currently, more than 2,900 genomes are published and more than 11,000 genome projects are listed in the Genomes Online Database. Although this wealth of information provides many new opportunities to assess microbial functionality, it also creates a new array of challenges when a comparison between multiple microbial genomes is required. Here, functional genome distribution (FGD) is introduced, analyzing the diversity between microbes based on their predicted ORFeome. FGD is therefore a comparative genomics approach, emphasizing the assessments of gene complements. To further facilitate the comparison between two or more genomes, degrees of amino-acid similarities between ORFeomes can be visualized in the Artemis comparison tool, graphically depicting small and large scale genome rearrangements, insertion and deletion events, and levels of similarity between individual open reading frames. FGD provides a new tool for comparative microbial genomics and the interpretation of differences in the genetic makeup of bacteria.

Phylogenetic analysis of protein sequences based on distribution of length about common sub-string

Up to now, various approaches for phylogenetic analysis have been developed. Almost all of them put stress on analyzing nucleic acid sequences or protein primary sequences. In this paper, we propose a new sequence distance for efficient reconstruction of phylogenetic trees based on the distribution of length about common sub-sequences between two sequences. We describe some applications of this method, which not only show the validity of the method, but also suggest a number of novel phylogenetic insights.