Investigation into the selective pressures behind the reductive genome evolution of the cyanobacteria Prochlorococcus

[bebatut]

Investigation into the selective pressures behind the reductive genome evolution of the cyanobacteria Prochlorococcus

Supervisor: Bérénice Batut - bebatut@informatik.uni-freiburg.de For degree: Master Status: Open Keywords: Evolution - Selection - Cyanobacteria - Conda - Data analysis - Phylogeny

Biological context

Given a popular view, evolution is an incremental process based on the increase of molecular complexity of organisms. Some organisms have however undergone massive genome reduction. It is the case of the endosymbionts whose the reduction is well explained by the Muller’s ratchet inherent to the endosymbiont lifestyle (small population and lack of recombination).

In Prochlorococcus, a marine cyanobacteria, 30% of genome reduction are observed in some lineages. Prochlorococcus is living in the open ocean in huge population where recombination is possible. It is considered as the most abundant living organism on earth. With a lifestyle totally different from the endosymbionts' one, the reductive genome evolution of Prochlorococcus remains an enigma [1]. It can not be explained using the same arguments as for the endosymbionts. Some other hypothesis has been proposed, but none can explain all the observed genomic characteristics of Prochlorococcus. The evolution of Prochlorococcus does not then fit in the scheme of the evolution of genomes. Understanding the forces behind the reductive genome evolution of Prochlorococcus is then an interesting challenge.

Project context

The forces behind the reductive genome evolution of Prochlorococcus remains unclear and they may imply changes in the selective pressures on the genes. One hypothesis proposes that reduced genomes may be under strong pressure to reduced their genomes because of the poor environment. Another hypothesis states that the selective pressures may be relaxed in some strains leading to erosion of some useless genes and the reduction of the genomes. Several analyses studied the selective pressures in Prochlorococcus genomes. But these analyses relies on estimation of the selective pressures which are taking into account the changes in GC content and codon usage. There is then a need to get reliable estimation of the selective pressures and their changes along Prochlorococcus evolution.

Moreover, genomes of new Prochlorococcus lineages and strains have been added to the databases recently, thanks to metagenomics analyses. These new genomes needs to be integrated in the selective pressure analyses.

Objectives

The idea of this project is to integrate the new available Prochlorococcus genomes and to investigate the selective pressures on these genomes using several more or less complex model of evolution.

The tools used for these analyses are command-line tools often difficult to install and to use. Usability and reproducibility of the analyses are major criteria for good science. To enhance the reproducibility of the analyses and the usability of the tools, the used tools and workflows will be integrated to BioConda and Galaxy.

Proposed agenda for the project

1. Construction of a new dataset with all available Prochlorococcus genomes
   • Identification of the available Prochlorococcus genomes
   • Identification of the gene families
   • Identification of a reliable phylogenetic tree
   • Construction of gene family concatenates
2. Integration of bio++ into Conda and Galaxy
3. Computation of the selective pressures on Prochlorococcus genomes using bio++ and several different more or less complex models (to identify the one that explain the best the data)
4. Analyses of the selective pressures and their relation with the codon usage changes

Prerequisites

• XML
• Bash
• Python

Further reading

1. Reductive genome evolution at both ends of the bacterial population size spectrum Review on reductive genome evolution patterns with a particular focus on Prochlorococcus and how to estimate the selective pressures
2. Etude de l'évolution réductive des génomes bactériens par expériences d'évolution in silico et analyses bioinformatique PhD thesis in French, useful to have an idea on possible outputs and images (Section XI)
3. Computational Molecular Evolution. Ziheng Yang. Great book to be introduced to the selective pressure estimations and more general stuff on computational molecular evolution
4. (SENCA: A Multilayered Codon Model to Study the Origins and Dynamics of Codon Usage)[http://gbe.oxfordjournals.org/content/8/8/2427] Article introducing a complex model to identify the selective pressures with taking into account the changes in GC and codon usage