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This is a figure from a research article that I am to do a senior presentation for. It is showing bacterial replication of an enteric bacteria population. The researchers hypothesize that the number of regions near the replication origin will be the highest point (peak) on the graph and the terminus region will be the lowest point because there are least copies of this region in a dividing species. The determine that the ratio of the peak to the trough will reflect the growth rate of the species. That all being said, I don't understand their use of color. The peak has several different colors that do not seem to match any of the examples on the right. Wondering if anyone can help me decipher this? Thanks!

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The short answer is that it looks like the colors are meant to represent different, partial copies of the bacterial genome in the process of being synthesized.

When bacteria replicate, they initiate replication at the origins of their chromosomes. In fact, these origins can be replicated multiple times before it gets to the "end" of the bacterial chromosome (terminus). Looks like the stacking on the right figure shows this, with the colors just aiding in differentiating the partially replicated chromosomes. The coverage plot on the left shows how this might look based on read coverage from deep sequencing (again the colors just show different, partially replicated, chromosomes).

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I think the figure has the answer. "High copy number near the origin". This is depicted in the graph by the spike at x = 4Mbp. The graph also shows that the number of reads is lowest at a point opposite the ori (2Mbp).

Mbp stands for Mega-base pairs, or 1 million nucleotides. Mbp in the graph refers to a point on the chromosome, with 4Mbp being at '12 oclock', the origin of replication(ori), and 2Mbp being at '6 oclock' opposite the ori. The researchers are measuring the number of DNA fragments(y-axis) that map to a certain position on the chromosome (x-axis). I am slightly color blind, but it seems to me that the colors generally match up. Also note that the reads that fall within the lower-most bracket on the right side of the x-axis span the entire x-axis. This is because these fragments map completely to the chromosome, and indeed they are labelled 'original genome'.

Hope that helps.

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First, it would help if you could provide any more information on the figure (how it was made, is it data based or representative of a model?)

Given that there is little to go on, I can offer my two bits - and I hope it will help you get thinking about it - but ...

It appears to me that these data are a snapshot of the replicating bacterial genomes isolated from many cells at a given timepoint. The right side of the figure shows a model of the (circular) genome in black with a number of smaller fragments of the genome caught partway through the replication process. The left side shows the same fragments stretched out in a linear representation.

The green fragment is the largest as it is nearly finished copying. Other colors show different sized fragments at different points in the copying process. It sounds like the graph is meant to relate the number of different sized fragments to growth rate (assuming you measure fragments from the same number of cells).

So, what does this tell you? (I think it would be helpful for you to think this out yourself form here and determine if you believe this is a good measure or not.)

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  • $\begingroup$ Would you agree that "genomic location" (x axis title) shows that they are splitting the circular chromosome into 4 regions? $\endgroup$ Oct 27 '15 at 14:10
  • $\begingroup$ Bryant, I don't think they mean to break it into regions. The X - axis is a measurement (in mega-base pairs = millions of bases) according to an arbitrary start point. Replication begins at the origin and extends in both directions. Note the point of symmetry for each of the fragments around the origin. $\endgroup$
    – johntreml
    Oct 27 '15 at 20:27

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