FractBias

Background

Whole genome duplications (WGDs) and genome fractionation are covered more thoroughly in other CoGepedia entries. In short, WGDs create two or more copies of a genome: which are referred to as subgenomes. The duplicate subgenomes then undergo gene loss in a process called fractionation which is part of returning to a diploid state, diploidization. All things being equal, one may assume that fractionation would occur randomly across the redundant genes created after a WGD, however bias towards gene loss on one genome, called fractionation bias, has been observed in several species including: maize , Brassica rapa , .

Overview

What goes in

1. Two assembled genomes that have annotated coding sequences (CDS)
2. A syntenic ratio set by the user (identified by empiric tests outside of the FractBias tool)
3. The full GFF of the target

FractBias Methods

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FractBias is a tool used to assess fractionation bias between genomes. This is accomplished by:

User Input

1. Select two genomes to compare in the SynMap tool.
2. Select the SynMap 'Syntenic Depth' option under 'Analysis Options.'
3. Set syntenic depth ratio between genomes (determined by empirically outside of this tool).

FractBias tool analysis

1. The coordinates for syntenic regions between the genomes are determined by the SynMap tool
2. The syntenic genes are then parsed according to the 'target' and 'query' genomes. The genome with the lower syntenic depth ratio is set as the target genome; the genome with the higher ratio is set as the query genome.
3. A list of genes present on every target genome chromosome is made and ordered according to start site (bp) in the annotation (gff/gtf file).
4. The FractBias tool then goes through the list of each target genome gene, and determines if it has a syntenic pair on one (or more) of the query chromosomes.
5. Finally, the FractBias tool runs a sliding window analysis to calculate how many genes are retained for each query chromosome.
6. A figure is generated that contains a subplot for every target genome chromosome
   1. The x-axis: target genome gene order number in sliding window according to order of start site in genome annotation (gff/gtf).
   2. The y-axis:

Example Output

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Window Iteration

X-axis Value

Genes counted in Subgenome 1

Y-axis Value Sub 1

Genes counted in Subgenome 2

Y-axis Value Sub 2

All Genes Example Data Table
1
2
3
4
5
6

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Food complements

Orange	Apple
Bread	Pie
Butter	Ice cream

Biological Examples

Sorghum and Maize Fractionation Bias

Arabidopsis and Brassica Fractionation Bias

Esox and Oncorhynchus Fractionation Bias