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 , and rainbow trout .

The FractBias code and an example data set can be found on GitHub

Overview

Figure 1. A demonstration of which genes are included in the FractBias analysis of retained genes when the include "All genes" setting is selected. All genes that exist on target genome chromosomes will be used to determine the sliding window size and calculate the number of retained genes on query chromosomes.

Workflow

1. SynMap comparison is carried out between two genomes with Syntenic Depth option set
2. FractBias takes output and runs sliding window analysis
3. A figure with subplots for every target genome chromosome is created
   1. x-axis: number of genes present on the chromosome in the target genome chromosome
   2. y-axis: percentage of retained genes in each sliding window

[[File:|right|thumb|900px|Figure 2. A demonstration of which genes are included in the FractBias analysis of retained genes when the include "Only retained genes" is selected. Genes unique to either the target or to the query genome will not be considered in either the window size or in calculating the number of retained genes within in the window.]]

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)
   1. The genome with a lower ratio will be the target genome
   2. The genome with a higher ratio will be the query genome
3. The full GFF of the target genome
4. The syntenic blocks identified by SynMap
5. Parameters defined by the user
   1. Window size in number of genes
   2. How many total chromosomes should be used
      1. The maximum number of query chromosome that should be considered
      2. The maximum number of target chromosome that should be considered
   3. Whether chromosomes containing the name 'unknown' or 'random' should be removed from consideration
   4. What genes should be counted
      1. Count all genes present on the target genome
      2. Only count genes that are retained in both genomes

Data files passed in

1. SynMap DAGChainer output: comparison_name.aligncoords.gcoords
2. GFF file for target genome

What comes out

1. A figure containing a subplot for every target genome chromosome
2. Links to the raw data used to create the subplots

Fractionation Bias Examples

Sorghum and Maize Fractionation Bias

The fractionation bias in the maize genome has been previously studied independently. This analysis was rerun using the FractBias tool. Zea mays (maize) and Sorghum bicolor (sorghum) have recently diverged. Zea mays experienced a whole genome duplication (Figure 5), and so the syntenic depth ratio is sorghum 1:maize 2. Therefore, for each sorghum chromosome subplot there will be up to two chromosomes of maize present (Figure 6). Fractionation bias in maize chromosomes is present across almost all sorghum chromosomes except for sorghum chromosomes 8 and 10. Sorghum chromosomes 1, 7, 9, and 10 have more than two maize chromosomes represented. These indicate areas of the maize chromosomes that have recombined over the maize evolutionary history.

Figure 5. The fractionation bias that occurred after the maize whole genome duplication (WGD) has been studied previously by comparing maize to sorghum. The WGDs events are denoted by stars along the Poaceae lineage. This analysis used the 'only retained genes' option to remove any genes unique to maize or sorghum. Link to regenerate analysis:

Figure 6. Results from running the FractBias tool

Arabidopsis thaliana and Brassica rapa Fractionation Bias

Figure 6. Results from running the FractBias tool

Additional Examples

More examples can be found in the table below. While FractBias was designed to investigate fractionation after whole genome duplications, it can also be used to investigate chromosome composition between species.

Figure 7. A syntenic depth ratio 1:1 comparison between the first 12 chromosomes of Homo sapiens and all the chromosomes of Pan troglodytes using the 'all genes' setting.

Table 1. FractBias examples available through CoGe’s SynMap. Syntenic depth ratios range from 1:1 to 1:6 using two species of plasmodia, two mammals, and six species of plants to highlight the flexibility and ease of use of FractBias.
Target Species	Query Species	Syntenic Depth Ratio	Link to 'All Genes' Analysis	Link to 'Only Syntenic Genes' Analysis
Plasmodium falciparum	Plasmodium knowlesi	1:1	https://genomevolution.org/r/k7j6	https://genomevolution.org/r/k7km
Homo sapiens	Pan troglodytes	1:1	https://genomevolution.org/r/k813	https://genomevolution.org/r/k811
Sorghum bicolor	Zea mays	1:2	https://genomevolution.org/r/k7jx	https://genomevolution.org/r/k7j3
Brassica rapa	Brassica napus	1:2	https://genomevolution.org/r/k7mw	https://genomevolution.org/r/k7k3
Arabidopsis thaliana	Brassica rapa	1:3	https://genomevolution.org/r/k7jq	https://genomevolution.org/r/k7jg
Vitis vinifera	Arabidopsis thaliana	1:4	https://genomevolution.org/r/k7p1	https://genomevolution.org/r/k7ov
Arabidopsis thaliana	Brassica napus	1:6	https://genomevolution.org/r/k7qz	https://genomevolution.org/r/k7r6