title: Marker genes that are less conserved in their sequences are useful for predicting genome-wide similarity levels between closely related prokaryotic strains.
abstract: The 16s rRNA gene is so far the most widely used marker for taxonomical classification and separation of prokaryotes. Since it is universally conserved among prokaryotes, it is possible to use this gene to classify a broad range of prokaryotic organisms. At the same time, it has often been noted that the 16s rRNA gene is too conserved to separate between prokaryotes at finer taxonomic levels.
  
  
  
  In this paper, we examine how well levels of similarity of 16s rRNA and 73 additional universal or nearly universal marker genes correlate with genome-wide levels of gene sequence similarity. We demonstrate that the percent identity of 16s rRNA predicts genome-wide levels of similarity very well for distantly related prokaryotes, but not for closely related ones. In closely related prokaryotes, we find that there are many other marker genes for which levels of similarity are much more predictive of genome-wide levels of gene sequence similarity. Finally, we show that the identities of the markers that are most useful for predicting genome-wide levels of similarity within closely related prokaryotic lineages vary greatly between lineages. However, the most useful markers are always those that are least conserved in their sequences within each lineage.
  
  
  
  Our results show that by choosing markers that are less conserved in their sequences within a lineage of interest, it is possible to better predict genome-wide gene sequence similarity between closely related prokaryotes than is possible using the 16s rRNA gene. We point readers towards a database we have created (POGO-DB) that can be used to easily establish which markers show lowest levels of sequence conservation within different prokaryotic lineages.
authors.affiliation: School of Biomedical Engineering, Science and Health Systems, Drexel University, 3141 Chestnut Street, Philadelphia, PA, 19104, USA.
authors.forename: Yemin
authors.initials: Y
authors.lastname: Lan
authors.affiliation: Ecological and Evolutionary Signal-processing and Informatics Laboratory, Electrical & Computer Engineering Department, Drexel University, 3141 Chestnut Street, Philadelphia, PA, 19104, USA.
authors.forename: Gail
authors.initials: G
authors.lastname: Rosen
authors.affiliation: Rachel & Menachem Mendelovitch Evolutionary Processes of Mutation & Natural Selection Research Laboratory, Department of Genetics and Developmental Biology, the Ruth and Bruce Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, 31096, Haifa, Israel. ruthersh@tx.technion.ac.il.
authors.forename: Ruth
authors.initials: R
authors.lastname: Hershberg
mesh_terms: D001105:Archaea / Q000145:classification* / Q000235:genetics*; D001419:Bacteria / Q000145:classification* / Q000235:genetics*; D001483:Base Sequence; D017124:Conserved Sequence / Q000235:genetics; D030541:Databases, Genetic; D020043:Genes, Essential / Q000235:genetics*; D005819:Genetic Markers / Q000235:genetics; D020745:Genome, Archaeal / Q000235:genetics; D016680:Genome, Bacterial / Q000235:genetics; D010802:Phylogeny; D012336:RNA, Ribosomal, 16S / Q000235:genetics*; D016415:Sequence Alignment; D017422:Sequence Analysis, DNA
chemical_list: D005819:Genetic Markers; D012336:RNA, Ribosomal, 16S
keywords: Genome-wide similarity; Less-conserved genes; Lineage-specific; Marker genes