The importance of complete genome sequences

Response from Edwards et al.Although we appreciate Dr Parkhill's view that comparisons of complete genome sequences are ideal for gaining insights into point mutations that can affect gene expression or function, economic realities also limit the number of genomes that can be sequenced to a level that allows this type of comparison. Draft genome sequencing, while not providing the detailed minutiae of the complete sequence, allows comparisons between genomes to identify insertions and deletions (indels) that are undoubtedly important in the different phenotypes of strains. The smaller costs associated with draft genome sequencing, the level of information that they provide about the strains in question, and their ability to guide more detailed efforts can outweigh their inability to identify all point mutations.Dr Parkhill focuses on the point mutations that result in pseudogenes, that is, mutations that introduce frameshifts and stop codons. However, point mutations that do not interrupt the transcription of a coding sequence can also have severe effects on phenotype. For example, point mutations in fimH, the type-I fimbrial adhesin in Escherichia coli, can alter the tropism of this pathogen without interrupting translation [1xPathogenic adaptation of Escherichia coli by natural variation of the FimH adhesin. Sokurenko, E.V. et al. Proc. Natl. Acad. Sci. U. S. A. 1998; 95: 8922–8926Crossref | PubMed | Scopus (215)See all References[1]. Phenotype is not simply determined by the presence or expression of a gene; the sequence of the gene product is also critical. Although Dr Parkhill mentions that DNA–DNA hybridizations will not identify the presence of pseudogenes, comparative gene expression studies (such as microarray transcriptome analysis) will at least indicate whether the pseudogenes are expressed. Nevertheless, neither approach will indicate whether a functional protein is made.The correlation between pseudogenes and the host specificity of pathogens is based on the comparison of a limited number of complete genome sequences. At this time, it is unclear whether this is a cause or effect: are host-adapted serovars limited in their range of hosts because they have inactivated large swathes of their genomes, or are these regions inactive because they are no longer required? It is difficult to evaluate this hypothesis using the limited amount of data currently available. As more sequences become available, and the comparisons are expanded, the role of both pseudogenes and point mutations as a whole could be clarified. However, without more genome sequences it will be impossible to predict the role of these pseudogenes in determining host specificity.Beyond genome sequencing, genetic analysis is required to prove, or disprove, the role of pseudogenes in affecting the phenotype of a strain [2xSee all References[2]. Although comparative genomics can provide a great deal of information about what is present or absent in each genome it is still only one small step in understanding the biology of an organism. Genome sequencing projects must be followed up with thorough genetic investigations that will discern the contribution of each gene in the overall biology of the organism. The complete genome sequence is only the start of the biological journey.