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. 2017 May 1;9(5):1312-1319.
doi: 10.1093/gbe/evx069.

DeCoSTAR: Reconstructing the Ancestral Organization of Genes or Genomes Using Reconciled Phylogenies

Wandrille Duchemin  1   2 , Yoann Anselmetti  2   3 , Murray Patterson  2   4 , Yann Ponty  5   6 , Sèverine Bérard  3   7 , Cedric Chauve  8 , Celine Scornavacca  3 , Vincent Daubin  2 , Eric Tannier  1   2
Affiliations

DeCoSTAR: Reconstructing the Ancestral Organization of Genes or Genomes Using Reconciled Phylogenies

Wandrille Duchemin et al. Genome Biol Evol. .

Abstract

http://pbil.univ-lyon1.fr/software/DeCoSTAR (Last accessed April 24, 2017).

Keywords: evolution; gene fusion/fission; gene order; protein domain; rearrangements; reconciliation; software.

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Figures

F<sc>ig</sc>. 1.—
Fig. 1.—
A species tree (light blue), three reconciled gene trees (black, red, and green) (losses are orange squares; duplications are green squares) and a set of extant and ancestral adjacencies linking genes (white). (A) An adjacency is inherited by both sister species after a speciation occurs. (B) An adjacency between the red and green gene is transferred, and so are both extremities of this adjacency. (C) The red gene undergoes gene loss and thus both adjacencies it was a part of disappear. (D) The adjacency between the red and black genes disappears due to an adjacency break on the branch leading to the leaf. (E) An adjacency is gained between the black gene and the newly acquired red gene.
F<sc>ig</sc>. 2.—
Fig. 2.—
Density of the distribution of the degree of all genes inferred by DeCoSTAR on the 18 Anopheles data set. The degree of an extant or ancestral gene is the sum of the weights of all adjacencies containing this gene. For extant genomes in the input (black line), this value can only be 0, 1, or 2. For genomes in the output, extant (red line) or ancestral (green line), all values are possible because adjacencies have scores between 0 and 1, and a gene can belong to an arbitrary number of adjacencies. The difference between the black and red lines are due to the scaffolding: genes with 0 or 1 neighbor are linked to other genes as an output of DeCoSTAR. In ancestral genomes, some genes have degree three or slightly more.
F<sc>ig</sc>. 3.—
Fig. 3.—
A schematic representation of the results obtained for the fusion–fission data set, following the schema described in figure 1, and with adjacency gain marked by an upper G. Family A and B are represented as reconciled gene trees, respectively, in red and green. The presence of an adjacency denotes the fusion of A and B to form the family C.
See this image and copyright information in PMC

References

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