On the reduction of biological complexity in Prochlorococcus

This dissertation focuses on the reduction of biological complexity using marine cyanobacteria Prochlorococcus as the model system. New computational methods have been developed for the understanding of genomic characteristics, for the exploration of environmental metagenomic data, and for the inference of evolutionary forces driving genome reduction in Prochlorococcus. The first part of the dissertation presents basic genomic characteristics in Prochlorococcus MED4. Known as the smallest and the most numerically abundant photosynthetic organism in the ocean, it shares many genomic characteristics with chloroplasts and bacterial endosymbionts. Orthologous genes from Prochlorococcus and a closely related marine cyanobacteria group Synechococcus, are profiled to show the gradients in genome sizes, GC% content, and the genome-wide acceleration of protein sequence evolution. The second part of the dissertation introduces new computational approaches for exploring environmental metagenomic data. The profiling of relative sequence abundance in the Sargasso Sea data has motivated the development of a phylogenetic focus group-based sequence filtering framework that takes into account of limitations in general purposed sequence similarity search, variations in evolutionary rates, as well as the context of phylogeny. A sequence trimming and segmentation mechanism has been proposed to facilitate downstream analysis. The integrated framework of sequence filtering and trimming performs better than general purpose methods, and benefits the exploration study of environmental metagenomic data. The third part of the dissertation tests a hypothesis about the relative strength of genetic drift vs. natural selection, formulated based on similarities between Prochlorococcus and endosymbionts. The hypothesis conjectures that Prochlorococcus has been experiencing a relative higher level of genetic drift, resulting in a relaxation in selection efficiency, leading to genome reduction and genome wide accelerated protein evolution. The evaluation of the hypothesis is performed by comparing the evolutionary profiles of Prochlorococcus with Synechococcus. Results from the complete genomes and the metagenomic data indicate that the average pairwise dN/dS ratios in the high-light adapted Prochlorococcus ecotypes are significantly lower than that in Synechococcus, i.e., Prochlorococcus is actually experiencing stronger selection genome-wide. The hypothesis is thus rejected, opening up space for constructing new hypotheses regarding the evolution of Prochlorococcus