Genome evolution tutorial

This section will cover a set of tools implemented in the PLAZA platform that can be used to study genome evolution. Especially in plants WGDs occurred independently in several lineages.

This tutorial will show how to use WGDotplot, Skyline plot & Multiplicon view

Here is explained how, using the Vitis (or papaya) genome, the existence of two Arabidopsis specific WGDs can be demonstrated.

Figure 1: Settings that need to be changed are highlighted

Figure 2: Output with notable regions highlighted

Figure 3: Settings that need to be changed are highlighted

Figure 4: For several vitis regions 4 colinear Arabidopsis regions are found, while for an Arabidopsis region only one is found in vitis

• How many duplications can be found in Populus trichocarpa using this appoach?
• Additional tips:
  • There is a triplication(hexaploidisation) shared between all eudicots
  • Poplar and grapevine have slowly evolving genomes and remnants of this event are still visible in the inter-species WGDotplot
  • The color coding by Ks can sometimes help discriminating old events from recent ones.
• If you figured out this one you are ready for the advanced tutorial!
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This part of the tutorial will go more into depth on how Ks and genomic homology can be used to pinpoint WGDs in different lineages. Please note that this is an advanced tutorial and you should be familiar with Ks dating, genomic homology and have a basic knowledge of the phylogeny of the species (hint: a species tree can be found on PLAZA's main page). Please ensure you're familiar with the tools in PLAZA, there is a more elaborate tutorial on the tools used here.

The goal here is to determine if the most recent WGD in Rice and Sorghum is a shared event.

• Start with generating an Rice-Rice WGDotplot. You can do this from the menu Analyze → WGDotplot , select Rice (Oryza sativa) for both organism 1 and 2. Leave other settings at their default values. Now click submit to generate the plot. Now look at the plot carefully, note that the remnants of a WGD can be seen with a Ks of ~1.
• Do the same thing for Sorghum, again remnants of a rather recent WGD can be seen with again a Ks of ~1
• Finally generate using the WGDotplot a Rice-Sorghum plot. (select Rice as organism 1 and Sorghum as organism 2 or vica versa) Now a set of long preserved colinear regions can be seen with a Ks of ~0.5 together with a set of older ones. The lowest Ks (most recent) values in an inter-species comparison will always be due to the speciation event.
• Combining the knowledge from the three plots we conclude that both Sorghum and Rice have remnants of one recent (and small hints of an older event). As the Ks for this event is in both cases higher then the speciation, we can conclude the WGD predates the speciation and therefore is an event shared by both species.

• Repeat this exercise with Poplar (Populus trichocarpa) and Arabidopsis thaliana. The intra species plots reveal a WGD in Arabidopsis with a Ks ~1 and one in Poplar with a Ks ~0.2. Though there is a big difference in Ks it's still too early to conclude these were two separate events. A difference in nucleotide substitution rate can cause this difference in Ks as well. Though the inter-species plot reveals the speciation has a Ks of >1.5. With this new evidence we can now reliably certainty conclude that the duplications are in fact independent of each other.
• Note that here there are also hints of older duplications.

• The same thing can be repeated using the Vitis and papaya genome. Though this case is much less obvious compared to the previous examples.
• View our Solution