FractBias
Contents
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 [1], Brassica rapa [2], and rainbow trout [3].
Overview
What goes in
- Two assembled genomes that have annotated coding sequences (CDS)
- A syntenic ratio set by the user (identified by empiric tests outside of the FractBias tool)
- The genome with a lower ratio will be the target genome
- The genome with a higher ratio will be the query genome
- The full GFF of the target genome
- The syntenic blocks identified by SynMap
What comes out
- A figure containing a subplot for every target genome chromosome
- Links to the raw data used to create the subplots
FractBias Methods
FractBias is a tool used to assess fractionation bias between genomes. This is accomplished by:
User Input
- Select two genomes to compare in the SynMap tool.
- Select the SynMap 'Syntenic Depth' option under 'Analysis Options.'
- Set syntenic depth ratio between genomes (determined by empirically outside of this tool).
- Set how many target genome chromosomes should be included in the analysis. There is a maximum of 40 target chromosomes that can be included, and the longest chromosomes are selected first.
- Set how many query genome chromosomes should be included in the analysis. There is a maximum of 40 query chromosomes that can be included, and the longest chromosomes are selected first.
- Set the size of the sliding window during analysis.
FractBias tool analysis
- The coordinates for syntenic regions between the genomes are determined by the SynMap tool
- 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.
- 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).
- The FractBias tool then goes through the list of each target genome gene, and determines if it has a retained homolog on one (or more) of the query chromosomes.
- Finally, the FractBias tool runs a sliding window analysis to calculate how many genes are retained for each query chromosome.
- A figure is generated that contains a subplot for every target genome chromosome
- The x-axis: target genome gene order number in sliding window analysis according to order of start site in genome annotation (gff/gtf).
- The y-axis: percent of retained genes from the target genome present on each query chromosome within that window.
- The SynMap raw data, the FractBias data, genes identified using FractBias, and the images can be downloaded through links for further use.
Example Output
To demonstrate how the FractBias tool works, a
| All Genes Example Data Table | |||||
|---|---|---|---|---|---|
| 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 |
| 1 | 1 | 1,2,3,4 | 100 | 1, 2, 3, 4 | 50 |
| 2 | 2 | 2, 3, 4,5 | 75 | 2, 3, 4, 5 | 25 |
| 3 | 3 | 3, 4, 5, 6 | 75 | 3, 4, 5, 6 | 50 |
| 4 | 4 | 4, 5, 6, 8 | 75 | 4, 5, 6, 8 | 50 |
| Only Retained Genes Example Data Table | |||||
|---|---|---|---|---|---|
| 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 |
| 1 | 1 | 1,2,3,4 | 100 | 1, 2, 3, 4 | 50 |
| 2 | 2 | 2, 3, 4, 5 | 75 | 2, 3, 4, 6 | 25 |
| 3 | 3 | 3, 4, 5, 6 | 75 | 3, 4, 6, 8 | 50 |
| 4 | 4 | 4, 5, 6, 8 | 75 | 4, 5, 6, 8 | 50 |
Biological Examples
Sorghum and Maize Fractionation Bias
Arabidopsis and Brassica Fractionation Bias
Esox and Oncorhynchus Fractionation Bias
References
- ↑ Schnable, J.C. et al. Dose–sensitivity, conserved non-coding sequences, and duplicate gene retention through multiple tetraploidies in the grasses. Front. Plant Sci. http://dx.doi.org/10.3389/fpls.2011.00002 (2011)
- ↑ Cheng, F. et al. Biased gene fractionation and dominant gene expression among the subgenomes of Brassica rapa. PLOS ONE DOI: 10.1371/journal.pone.0036442 (2012)
- ↑ Berthelot, C. et al. The rainbow trout genome provides novel insights into evolution after whole-genome duplication in vertebrates. Nature Communications 5: DOI:10.1038/ncomms4657 (2014)
