FractBias

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Revision as of 13:26, 20 April 2016 by BJoyce (Talk | contribs) (Example Output)

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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].

The FractBias code and an example data set can be found on GitHub https://github.com/bjoyce3/SynMapFractBiasAnalysis

Overview

[[File:|right|thumb|900px|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.]] [[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. Setting defined by the user
    1. What genes should be counted
      1. Count all genes present on the target genome (refer to Figure 1)
      2. Only count genes that are retained in both genomes (refer to Figure 2)
    2. Target chromosome number
    3. Query chromosome number
    4. Window size

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



Example Output

Biological Examples

Sorghum and Maize Fractionation Bias

Figure 5. The fractionation bias that occurred after the maize whole genome duplication (WGD) has been studied previously[4] 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:

The fractionation bias in the maize genome has been previously studied[4] independently. This analysis was rerun using the FractBias tool.


Figure 6. Results from running the FractBias tool


Arabidopsis thaliana and Brassica rapa Fractionation Bias

Figure 6. Results from running the FractBias tool
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


References