ABSTRACT The relative ease of sequencing bacterial genomes has resulted in thousands of sequenced... more ABSTRACT The relative ease of sequencing bacterial genomes has resulted in thousands of sequenced bacterial genomes available in the public databases. This same technology now allows for using the entire genome sequence as an identifier for an organism. There are many methods available which attempt to use genome sequences to classify bacteria, and the method of choice, as always, depends on the question asked and the particular need. For example, 16S rRNA can define a bacterial species, and relate species, genera, and higher orders into groups consistent with their known biological properties. However, distinguishing between strains of the same species requires additional information. The advantage of having the whole-genome sequence is that roughly a 1,000 times as much information is available, and this information can be used for rapid classification of strains, based on DNA sequence. This chapter reviews many commonly used methods and also describes potential pitfalls if used inappropriately, as well as which questions are best addressed by particular methods. After a brief introduction to the classical methods of taxonomy, a description of the bacterial genomes currently available is given, and then whole-genome-based methods are explored using three different data sets.
Thirty-two genome sequences of various Vibrio-naceae members are compared, with emphasis on what ... more Thirty-two genome sequences of various Vibrio-naceae members are compared, with emphasis on what makes V. cholerae unique. As few as 1,000 gene families are conserved across all the Vibrionaceae genomes analysed ; this fraction roughly doubles for gene families conserved within the species V. cholerae. Of these, approximately 200 gene families that cluster on various locations of the genome are not found in other sequenced Vibrionaceae; these are possibly unique to the V. cholerae species. By comparing gene family content of the analysed genomes, the relatedness to a particular species is identified for two unspeciated genomes. Conversely, two genomes presumably belonging to the same species have suspiciously dissimilar gene family content. We are able to identify a number of genes that are conserved in, and unique to, V. cholerae. Some of these genes may be crucial to the niche adaptation of this species.
ABSTRACT The relative ease of sequencing bacterial genomes has resulted in thousands of sequenced... more ABSTRACT The relative ease of sequencing bacterial genomes has resulted in thousands of sequenced bacterial genomes available in the public databases. This same technology now allows for using the entire genome sequence as an identifier for an organism. There are many methods available which attempt to use genome sequences to classify bacteria, and the method of choice, as always, depends on the question asked and the particular need. For example, 16S rRNA can define a bacterial species, and relate species, genera, and higher orders into groups consistent with their known biological properties. However, distinguishing between strains of the same species requires additional information. The advantage of having the whole-genome sequence is that roughly a 1,000 times as much information is available, and this information can be used for rapid classification of strains, based on DNA sequence. This chapter reviews many commonly used methods and also describes potential pitfalls if used inappropriately, as well as which questions are best addressed by particular methods. After a brief introduction to the classical methods of taxonomy, a description of the bacterial genomes currently available is given, and then whole-genome-based methods are explored using three different data sets.
Thirty-two genome sequences of various Vibrio-naceae members are compared, with emphasis on what ... more Thirty-two genome sequences of various Vibrio-naceae members are compared, with emphasis on what makes V. cholerae unique. As few as 1,000 gene families are conserved across all the Vibrionaceae genomes analysed ; this fraction roughly doubles for gene families conserved within the species V. cholerae. Of these, approximately 200 gene families that cluster on various locations of the genome are not found in other sequenced Vibrionaceae; these are possibly unique to the V. cholerae species. By comparing gene family content of the analysed genomes, the relatedness to a particular species is identified for two unspeciated genomes. Conversely, two genomes presumably belonging to the same species have suspiciously dissimilar gene family content. We are able to identify a number of genes that are conserved in, and unique to, V. cholerae. Some of these genes may be crucial to the niche adaptation of this species.
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Papers by Tammi Vesth