Gene duplication and biased functional retention of paralogs in bacterial genomes

Abstract

Gene duplication is considered an important prerequisite for gene innovation that can facilitate adaptation to changing environments. The analysis of 106 genome sequences shows a significant number of paralogs in all bacterial genomes. Analysis of the functional classification of these paralogs reveals a preferential enrichment in functional classes that are involved in transcription, metabolism and defense mechanisms. From the organization of paralogs in the genome we can conclude that duplicated genes in Bacteria seem to have mainly been created by small scale duplication events such as tandem and operon duplications.

Supplementary Data

1. The Bacterial Paranome

• Duplication Table: Detailed numerical data on prevalence of paralogs, orphans, and singletons within 106 whole genome sequences (~ Fig. 1).

• Duplication Plot: A plot showing that genome size is strongly correlated with the number of duplicated genes in a linear regression.

• Operon duplication: Examples of operon and block duplication found in E. coli K12 (MG1655) (~ Fig. 2).

2. The functional Landscape of the Paranome

• Clickable figure to explore biased functional retention of paralogs in 48 bacterial genomes (~ Fig. 3).

3. The Bacterial Core Genes

• A detailed list of the bacterial core gene families.

• A description of how gene families were constructed from the complete bacterial proteome, including an evaluation of the parameters used.

4. Downloads

• A list of Accession Numbers included in this study

• A Full Genelist of the paralogs in 48 bacterial genomes (cfr. functional landscape)