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Since all bacteria have one circular chromosome, there is no designated origin to start the systematic gene locus numbering. Therefore, what is the rule to start the numbering at a particular point (i.e. why is in the E.coli K12 strain the thrL gene given the ordered locus number b0001? If the answer is: It is the first Gene downstream of basepair-1, then why is basepair-1 at this particular position)

Why the question? Since bacteria show frequently functional synteny between genes, should I be surprised to find a gene frequently associated with the (arbitrary?) annotation origin? If the annotation origin is i.e. the origin of replication that would be an interesting case of synteny, but if no such rule exists, then such a case would most likely just reflect the historic sequence of Genome Sequencing

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  • $\begingroup$ I don't know this from experience, but since every bacterial chromosome has an origin of replication, it'd make sense to start from there $\endgroup$ – Luigi Dec 19 '14 at 15:50
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    $\begingroup$ Even I think it is the ori. But let me find a reference $\endgroup$ – WYSIWYG Dec 19 '14 at 15:51
  • $\begingroup$ Trying to find a reference has me googling ridiculous things like "numbering base pair convention circular chromosome bacteria" $\endgroup$ – Luigi Dec 19 '14 at 15:52
  • $\begingroup$ I guess it is not ori.. From E.coli genome GTF: NC_007779.1 RefSeq region 3710706 3710937 . - . ID=id233;Dbxref=GeneID:12934266;Note=ECK3735:JWS0001:b4489~origin of replication;gbkey=rep_origin;gene=oriC $\endgroup$ – WYSIWYG Dec 19 '14 at 16:07
  • $\begingroup$ I suspect it's based on some kind of linkage map generated by interrupted mating experiments a long time ago. It certainly makes sense that ThrL would be one of the first genes since it used in threonine biosynthesis, making it a good marker. Why they chose that marker could be arbitrary, possibly it happened to be downstream of the F factor integration site in whatever strain the original researchers where using. If I find some kind of literature about it, I'll post an answer. $\endgroup$ – canadianer Dec 19 '14 at 17:22
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[I'm sure we have a skilled microbiologist somewhere here, so he would correct my answer.]

The necessity to designate gene locations in classical bacterial model species predated the genomic era, so traditional maps were normally neither bound to origin of replication, nor were they necessarily expressed in base-pairs. In E. coli, for example the traditional map was created based on the F-pili-mediated DNA transfer experiments.

When whole genome sequences became available it was only natural to continue the traditionally defined numeration in terms of placing the "base-pair one". Thus, in E. coli "the traditional and physical maps ... linkage map are closely correlated".

My understanding of the current situation with bacteria without genetic prehistory is that their genomes are numerated either respective to classic closely-related species (if any) or according to the presumed location of ori. Just to give an example of how the dilemma was solved for the Buchnera genome: it was "assumed the DnaA box upstream of the gidA gene is the replication origin" and the authors decided to designate "the start of the DnaA box as base pair one".

As you see, still, even if the authors try to define "base-pair one" based on the position of ori, the problem is that this point depends on the ori-searching tool one uses and on the contemporary understanding of how ori-sites look like (direct determination of origins of replications are in many cases not easy). See e.g. this table with a revision of ori locations in a set of genomes: while most of the genomes received their numeration irrespective of ori, some of them were indeed bound to it, but the new analysis showed that these locations were inaccurate.

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