Research ArticlePLANT SCIENCES

Early genome duplications in conifers and other seed plants

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Science Advances  20 Nov 2015:
Vol. 1, no. 10, e1501084
DOI: 10.1126/sciadv.1501084
  • Fig. 1 MAPS results on the associated phylogeny.

    Percentage of subtrees that contained a gene duplication (red line) shared by descendant species at each node. Ovals correspond to inferred locations of WGD events. (A) Seed plant analysis: black oval, seed plant WGD. (B) Pinaceae analysis: black oval, seed plant WGD; green oval, Pinaceae WGD. (C) Cupressophyte analysis: black oval, seed plant WGD; red oval, cupressophyte WGD.

  • Fig. 2 Phylogenetic placement of WGDs in seed plant and gymnosperm history.

    Ovals correspond to inferred locations of WGD events; black, seed plant WGD; gray, angiosperm WGD; purple, Welwitschia WGD; green, Pinaceae WGD; red, cupressophyte WGD. All botanical illustrations are in the public domain. Amborella image adopted from Amborella Genome Project, 2013 (46). Other botanical illustrations are in the public domain (5975).

  • Fig. 3 Pinaceae-Cupressaceae ortholog divergence and independent WGDs.

    Combined Ks plot of the gene age distributions of P. glauca (Pinaceae; green), C. japonica (Cupressaceae; orange), and their ortholog divergences (blue). The median peaks for these plots are highlighted. Analyses of ortholog divergence indicated that these two taxa diverged before their most recent WGDs.

Supplementary Materials

  • Supplementary material for this article is available at http://advances.sciencemag.org/cgi/content/full/1/10/e1501084/DC1

    Fig. S1. Example topologies processed by MAPS to identify a gene duplication (red star) or not (black dot) in a given gene family phylogeny.

    Fig. S2. Example MAPS summary results for a four-taxon phylogeny.

    Fig. S3. Histograms of the age distribution of gene duplications from 24 gymnosperm transcriptomes.

    Fig. S4. Numerical summary of MAPS results.

    Table S1. Assembly statistics and accession numbers for 25 transcriptomes and 2 genomes.

    Table S2. Number of gene subtrees that fit the expected species tree support shared duplication in seed plant analysis.

    Table S3. Number of gene subtrees that fit the expected species tree support shared duplication in Pinaceae analysis.

    Table S4. Number of gene subtrees that fit the expected species tree support shared duplication in cupressophyte analysis.

    Table S5. Number of gene subtrees that fit the expected species tree support shared duplication in cupressophyte analysis using only trees with >50% bootstrap support for each branch.

  • Supplementary Materials

    This PDF file includes:

    • Fig. S1. Example topologies processed by MAPS to identify a gene duplication (red star) or not (black dot) in a given gene family phylogeny.
    • Fig. S2. Example MAPS summary results for a four-taxon phylogeny.
    • Fig. S3. Histograms of the age distribution of gene duplications from 24 gymnosperm transcriptomes.
    • Fig. S4. Numerical summary of MAPS results.
    • Table S1. Assembly statistics and accession numbers for 25 transcriptomes and 2 genomes.
    • Table S2. Number of gene subtrees that fit the expected species tree support shared duplication in seed plant analysis.
    • Table S3. Number of gene subtrees that fit the expected species tree support shared duplication in Pinaceae analysis.
    • Table S4. Number of gene subtrees that fit the expected species tree support shared duplication in cupressophyte analysis.
    • Table S5. Number of gene subtrees that fit the expected species tree support shared duplication in cupressophyte analysis using only trees with >50% bootstrap support for each branch.

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