Chapter 4.

Microbial Evolution from a Genomics PerspectiveJizhong Zhou and Dorothea K. Thompson

2011. 04. 06 Su Gyeong Woo

- Microbial Functional Genomics -

Understanding the phylogenetic relationships between extant organisms has been a great challenge to biologists for many centuries.

Organismal Relationships

Microbial Evolution from a Genomics Perspective

Because of the complicated evolutionary processes, phylogenetic relationships of species based on comparisons of single genes are rarely consistent with each other.

With the availability of whole-genome sequences for many organisms, it is hoped that comprehensive descriptions of evolutionary relationships among different organisms can be obtained.

Recent comparative genomic studies have revealed some fundamentally different and exciting insights into various evolutionary processes of biological systems.

The Evolutionary Process

Mutations- Changes in the nucleotide sequence of an organism’s genome

Gene duplication, Horizontal Gene Transfer, and Gene loss

Gene duplicated in common ancestor

Horizontal gene transfer

Loss

Loss

Mutation

Genome Perspectives on Molecular Clock

Molecular clocks use mutations to estimate evolutionary time. Mutations add up at a constant rate in related species.

This rate is the ticking of the molecular clock. As more time passes, there will be more mutations.

DNA sequence from ahypothetical ancestor

The DNA sequences from twodescendant species show mutationsthat have accumulated (black).

The mutation rate of thissequence equals one mutationper ten million years.

Mutations add up at a fairly constant rate in the DNA of species that evolved from a common ancestor.

Ten million years later—one mutation in each lineage

Another ten million years later—one more mutation in each lineage

The molecular clock hypothesis assumes that the rate of amino acid or nucleotide substitution is roughly constant among diverse lineages.

Scientists estimate mutation rates by linking molecular data and real time.

– an event known to separate species– the first appearance of a species in fossil record

Genome Perspectives on Molecular Clock

Vertical evolution Horizontal evolution

Genome Perspectives onHorizontal gene transfer

Horizontal gene transfer (HGT) or lateral gene transfer(LGT) is an evolutionary phenomenon that involves the occurrence of genetic exchanges between different evolutionary lineages.

- Thee types of horizontal gene transfer

Transduction:via bacteriophage

Transformation:integrating free DNA or plasmids

Conjugation:direct contact

Genome Perspectives on Horizontal gene transfer

Horizontal gene transfer(HGT) cause the transfer/acquisition of genes within a genome, among members of the same species, or between members of very different taxa.

Genome sequence analysis indicates that HGT is a common evolutionary event, but whether it is a major evolutionary force is still highly controversial.

Various approaches can be used to identify HGT events, but it is very difficult to identify and prove them because the evidence supporting HGT can be explained by other forces.

Genome Perspectives on Horizontal gene transfer

Gene duplication is another major force in genome evolution, because the duplication of genes and groups of genes has occurred frequently in all genomes through processes of unequal crossing-over, DNA amplification, replication slippage, etc.

The duplicated genes could have different evolutionary fates. Duplicated genes may diverge to generate different genes, or one copy may become an inactive pseudogene.

Genome Perspectives on Gene Duplication, Gene Loss

Another exciting discovery revealed by comparative genomics is that lineage-specific gene loss also plays a key role during the evolution of life.

Genome sequence comparison revealed that genes could be lost by large deletion and/or by mutational inactivation, followed by gene erosion.

Genome Perspectives on Gene Duplication, Gene Loss

While the genome size increases through gene duplications and horizontal gene transfer, it decreases via gene deletions and gene inactivation followed by gene erosion. As a consequence, the prokaryotic genomes remain relatively small and constant.

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