Berkeley Lab

Desulfovibrio – Methanococcus Co-Evolution

kronaKrona Website →
Interactive display of mutations identified in evolved co-cultures.

We have determined the genetic changes that occurred during laboratory evolution of Desulfovibrio vulgaris Hildenborough and Methanococcus maripaludis S2 syntrophic community by using whole-genome re-sequencing.

Community that was evolved for 1000 generations was sequenced and variants associated with each organism were identified. Overall distribution of mutations and their impact are displayed as interactive Krona display.

VISUALIZATION HELP

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What is Krona display?
Krona is a HTML5 based visualization tool similar to pie charts for visualizing hierarchical data. It is commonly used to display taxonomical or functional abundance in metagenomics data.

Getting Around
DvH-Mmp co-culture mutation data is represented in 6 levels.

From top level to → lowest level:
Organism → Evolution Line → Mutation Effect → Mutation Impact→ Locus → Description

You can select a wedge by clicking and details about the selected category will be shown on the top right.

Count will display number of mutations assigned to particular category.

Frequency will list average frequency for top categories. At the individual gene level, frequency will show frequency of given mutation in the genome.

Small pie-charts for a given category listing percent of the category relative to its top category will be shown on the right. Clicking on the pie-chart will take you to given category.

Zooming In & Out
If arrows appear around a selected wedge, it can be zoomed in on by clicking it again or by clicking the expand button next to the wedge’s name in the upper right corner. To zoom out click on the upper level categories listed inside the circle.

Other Controls
You can use search box to find specific items. You can also control chart/font size and take snapshots by using controls on the left.