Question: Where to put start for assembled genome/plasmid
2
gravatar for mschmid
3.6 years ago by
mschmid90
Switzerland
mschmid90 wrote:

If you have a closed bacterial genome or plasmid, what are the general rules where to put the start. With start I mean where the base "1" of the finished sequence is (or you could also say with which gene the sequence starts).

I heard some rules already like putting the OriC at the beginning.

Does anyone have a good paper/source for that?

Thanks!

sequencing assembly genome • 1.2k views
ADD COMMENTlink modified 3.6 years ago by piet1.7k • written 3.6 years ago by mschmid90
2
gravatar for piet
3.6 years ago by
piet1.7k
planet earth
piet1.7k wrote:

There is no general rule, but please avoid to linearize your circular sequence within a coding sequence. There are many plasmids in Genbank where interesting genes like antibiotic resistance determinates have been cut into two halves. Its always a pain to work with such sequences. 

In most Eubacterial chromosomes the origin of replication is located between the highly conserved genes rpmH and dnaA. For Firmicutes it is a good choice to place the start codon of dnaA on position 500. In some species there may exist isolates where the orientation of the oriC region is reversed with respect to the majority of the chromosome. With such an isolate it may be appropriate to make rpmH the first gene on the linearized chromosome and dnaA the last.

ADD COMMENTlink written 3.6 years ago by piet1.7k

OK, that helps me already a lot

ADD REPLYlink written 3.6 years ago by mschmid90

Follow up question: How do you detect the exact position of origin of replication in plasmids and in genomes? I guess they are pretty much the same in general, right?

At the moment I want to do it specifically for Lactobacillus.

ADD REPLYlink modified 3.5 years ago • written 3.5 years ago by mschmid90

The chromosomal origin of replication is located between rpmH and dnaA, I would guess that Lactobacillus is not different from other Firmicutes.

With plasmids there is not such a simple rule.There exist different mechanismens of replication, especially small plasmids (sometimes called cryptic plasmids) are using rolling circle. Maybe you can blast putative rep genes and try to find an ortholog on a well annotated sequence.  

ADD REPLYlink written 3.4 years ago by piet1.7k
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