BIRCH

TUTORIAL: Comparing genomes using Mauve


Dec. 13, 2016



References:

Mauve Web Site

This tutorial continues from the previous tutorial Comparing genomes using dotplots.

Rationale: It's pointless to do sophisticated analysis and generate large quantites of output if we can't make sense of the results. One of the big challenges in bioinformatics is presenting big data in such a way that we can explore it and understand it.  As in the previous tutorial, we will compare S. cereviseae and S. arboricola, this time using a Mauve, a genome comparison tool.

Localized Co-linear Blocks (LCB) - The key concept underlying Mauve is that as genomes diverge from an ancestral species into two or more modern species, chromosomes undergo many sorts of rearrangements, including insertions, deletions, inversions and translocations. Much of the same sequences remain even after long periods of evolutionary history, but in different arrangements from one species to the next. In Mauve, Localized Co-Linear Blocks are regions of chromosomes that appear to be conserved across all species being examined. If an entire chromosome is unchanged, then the entire chromosme would be a single LCB in all species in the alignment. Many chromosomes will be a mosiac of several LCBs. In other cases, an LCB on one chromosome will be found on a different chromosome, indicating a translocation. The purpose of Mauve, then is to calculate the LCBs shared between two or more genomes, and to display them visually.

Goal: To gain a more in-depth understanding of the chromosomal changes occurring since the divergence of S. cereviseae and S. arboricola.

1. Comparison of S. cereviseae and S. arboricola genomes

Mauve is an interactive genome viewer specialized for identifying syntenic regions between two or more genomes. It can be launched by typing

mauve

To produce a Mauve alignment, go to the File menu and run Align with progressive Mauve.

You can add as many genomes as you wish in the Align sequences window. For now, read in

GCF_000146045.2_R64_genomic.fna
GCF_000292725.1_SacArb1.0_genomic.fna

We'll use the Output name "SerArb" for this comparison.


Click the Align button to begin the alignment.

 
Progress of the alignment is shown in a popup window. This alignment will probably take several minutes.

The window will indicate "Done" when the alignment is complete. After a slight delay, the alignment will appear in a new Mauve window.





To make it easier to see the distinct LCBs conserved between the two species, choose View --> Style --> LCB outlines. In this example, Mauve read the S. arb. genome first, so that was set as the reference genome. Since S. cer. is the best characterized yeast, move the S. cer. to the top of the alignment by clicking on the up arrow (^) next to the GCF_000146045.2_R64 sequence. The alignment should now look like this:



A quick guide to the Mauve viewer

Try the following: 1. Press the Zoom (+) button and pan all the way to the right. Repeat this two more times.  You should see something like this:



The cluster of parallel red lines indicate the Unaligned Scaffolds, all of which are fairly short. The last pair of red lines denotes the mitochondrial genomes of Ser and Arb. You can see that there have been a number of rearranged LCBs since the divergence of these mitochondrial genomes. Most of the Ser mito. genome is on the reverse strand, relative to the Arb mito genome, although some LCBs in Ser are on the forward strand, relative to Arb.


Exporting images - You can export the current view of the alignment to an image file by choosing Tools --> Export Image.

In the example at right, the default format is JPEG, and the image is saved to a file called SerArbView.jpg.



Resuming a Mauve session - When creating the alignment, Mauve saves all files related to the alignment in the current working directory. In the example, we ran Mauve with the Output name 'SerArb'. All files will begin with SerArb as the basename eg. SerArb.guide_tree. You can quit Mauve and resume your session by choosing File --> Open Alignment. Click on the file named SerArb (with no extension) and the alignment files will be read back into Mauve.