Estimation of redundancy in microbial genomes

Abstract Background Microbial genomes vary considerably both with respect to size and base composition. While the smallest genomes have less than 200,000 base pairs, or nucleotides, others can consist of millions. The same is true for genomic base composition, often summarized as genomic AT or GC content due to the similar frequencies of (A)denine and (T)hymine on one hand and (C)ytosine and (G)uanine on the other; the most extreme microbes can have genomes with AT content below 25% or above 85%. Genomic AT content influences the frequency of DNA words, or oligonucleotides, consisting of multiple nucleotides. Here we explore to what extent genome size, AT/GC content and genomic oligonucleotide usage variance (OUV) are linked to microbial genome redundancy, or compression rate, as measured using both a DNA based- (MBGC) and a general purpose (ZPAQ) compression algorithm on 4,713 RefSeq genomes. Results We find that genome size (p < 0.001) and OUV (p < 0.001) are both strongly associated with genome redundancy for both types of file compressors. The DNA based MBGC compressor managed to improve compression with approximately 3% on average with respect to ZPAQ. Moreover, MBGC detected a significant (p < 0.001) compression ratio difference between AT poor and AT rich genomes that was not detected with ZPAQ. Conclusion As lack of compressibility is equivalent to the presence of randomness, our findings suggest that small and AT rich genomes may have accumulated more random mutations on average than larger and AT poor/GC rich genomes, which, in turn, were significantly more redundant. Moreover, we find that OUV is a strong proxy for genome compressibility in microbial genomes. The ZPAQ compressor was found to agree with the MBGC compressor, albeit with a poorer performance, except for the compressibility of AT-rich and AT-poor genomes.