FractBias

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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

Overview

Figure 1. Setting the SynMap syntenic depth and Run FractBias options (https://genomevolution.org/CoGe/SynMap.pl).

Workflow

  1. SynMap comparison is carried out between two genomes with Syntenic Depth option set (Figure 1)
  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


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[4] 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 2. 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:
Figure 3. Results from running the FractBias tool. Areas of underfractionation (black arrows), intermediate fractionation (blue arrows), and overfractionation (red arrows) can be observed. .

Arabidopsis thaliana and Brassica rapa Fractionation Bias

Figure 4. Results from running the FractBias tool comparing Arabidopsis thaliana (target genome) to Brassica rapa (query genome). Areas of underfractionation (black arrows), intermediate fractionation (blue arrows), and overfractionation (red arrows) can be observed. Results can be regenerated https://genomevolution.org/r/k7jg.

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 5. 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

References