Fig 1.
Evolution after WGD and identification of ohnologs.
Evolution after WGD and identification of ohnologs using content-based synteny comparison. The genomes of three lineages sharing a common ancestor are shown. Orthologs and paralogs have been depicted by the same color. The WGD lineage (A) underwent whole genome duplication (B) followed by non-functionalization (C) and genome rearrangements (D) leading to the current intragenomic content-based synteny (I). By contrast, the two outgroup genomes without WGD (E, G) experienced lineage specific genome rearrangements (F, H) leading to 1-to-2 content-based synteny pattern with the WGD lineage (J, K). Note, that some ohnolog pairs (D) are only identified by one of the two outgroups (J or K) due to lineage specific rearrangements.
Fig 2.
Flowchart of the algorithm to identify ohnologs.
Flowchart of the algorithm to identify ohnolog pairs and construct ohnolog families for a single vertebrate genome using content-based synteny comparison with multiple outgroup genomes (left panel) and self-comparison (right panel), see main text and S1 Text for details.
Table 1.
Individual ohnologs, pairs and families for different quantitative criteria in the human genome (see text).
Fig 3.
Venn diagram of distribution of human ohnologs with respect to outgroups.
A six-way Venn diagram showing the distribution in percentages of the 7,715 of the total 8,178 human ohnolog pairs that are identified by at least one outgroup and predicted from the relaxed criteria. Only 3.8% of human ohnolog pairs are identified by all outgroup. Each of the shaded sectors in green contributes to more than 2% of all ohnolog pairs (numbers of ohnolog pairs are given in S8 Fig).
Fig 4.
Venn diagram of the distribution of amniote ohnologs.
A six-way Venn diagram showing the distribution in percentages of the ohnologs identified in at least one amniote and predicted from the relaxed criteria. 36.6% of ohnologs are found in all six amniotes. Each shaded sectors in red contributes to more than 2% of all consensus ohnologs in amniotes (numbers of ohnologs are given in S10 Fig).
Fig 5.
Ohnolog association to cancer and diseases in human.
(A) Gene Ontology enrichment for four amniote ohnolog datasets from the relaxed criteria. From top to bottom, the top 25 enriched GO terms, sorted on the basis of average rank across the four genomes. Bubble sizes are proportional to the rank (p-value) of the term for each genome. (B) Ohnolog association to cancer and genetic diseases in human. Ohnolog enrichment is especially significant for core cancer genes, autosomal dominant disease genes and genes with autoinhibitory protein folds, see text, in agreement with earlier reports [5, 6, 15].