Insights from 20 years of bacterial genome sequencing

Abstract

Since the first two complete bacterial genome sequences were published in 1995, the science of bacteria has dramatically changed. Using third-generation DNA sequencing, it is possible to completely sequence a bacterial genome in a few hours and identify some types of methylation sites along the genome as well. Sequencing of bacterial genome sequences is now a standard procedure, and the information from tens of thousands of bacterial genomes has had a major impact on our views of the bacterial world. In this review, we explore a series of questions to highlight some insights that comparative genomics has produced. To date, there are genome sequences available from 50 different bacterial phyla and 11 different archaeal phyla. However, the distribution is quite skewed towards a few phyla that contain model organisms. But the breadth is continuing to improve, with projects dedicated to filling in less characterized taxonomic groups. The clustered regularly interspaced short palindromic repeats (CRISPR)-Cas system provides bacteria with immunity against viruses, which outnumber bacteria by tenfold. How fast can we go? Second-generation sequencing has produced a large number of draft genomes (close to 90 % of bacterial genomes in GenBank are currently not complete); third-generation sequencing can potentially produce a finished genome in a few hours, and at the same time provide methlylation sites along the entire chromosome. The diversity of bacterial communities is extensive as is evident from the genome sequences available from 50 different bacterial phyla and 11 different archaeal phyla. Genome sequencing can help in classifying an organism, and in the case where multiple genomes of the same species are available, it is possible to calculate the pan- and core genomes; comparison of more than 2000 Escherichia coli genomes finds an E. coli core genome of about 3100 gene families and a total of about 89,000 different gene families. Why do we care about bacterial genome sequencing? There are many practical applications, such as genome-scale metabolic modeling, biosurveillance, bioforensics, and infectious disease epidemiology. In the near future, high-throughput sequencing of patient metagenomic samples could revolutionize medicine in terms of speed and accuracy of finding pathogens and knowing how to treat them.

Why prokaryotes have pangenomes

“…The largest pangenome analysis for a single species to date included 2,085 E. coli genomes 11 which estimated 3,188 core gene families (which they defined as being present in 95% of genomes) and approximately 90,000 unique gene families. By contrast, the intracellular pathogen Chlamydia trachomatis has a pangenome size only slightly bigger than its core genome (974 gene pangenome, 821 gene core genome) with 67 genomes sequenced (see Table 1).…”

Genetic and biochemical characterization of arginine biosynthesis in Sinorhizobium meliloti 1021

“…By this analysis, we found 372 unique bacterial species potentially encoding both ArgE and ArgJ. This represents 14.7 % of the 2518 unique bacterial species that have been completely sequenced (Land et al, 2015). The same analysis performed with the S. meliloti HipO1 sequence as a query revealed that a HipO1 orthologue was present in 75.8 % of the unique species containing both ArgE and ArgJ.…”

Insights from Comparative Genomics of the Genus Salmonella

“…But how close are Salmonella and Escherichia, in terms of conserved proteins? To address this question, the core genes of S. enterica Typhimurium LT2 (the type strain of the species) were compared to the core genes recently deined for E. coli (using the same deinitions and parameters) [16], which we applied to the species typestrain E. coli DSM 30083. As reported in Table 1, the 95% core genome of all Salmonella comprises 3470 gene families, of which 11 are missing in Typhimurium LT2.…”