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EDF 7. TANDEM DUPLICATIONS Phylogenetic trees of the mix/bix cluster. Nucleotide sequences were aligned using MUSCLE, and a phylogenetic diagram was generated by the ML method with 1,000 bootstraps (MEGA6). Circles with different colors represent X. laevis L genes (magenta), X. laevis S genes (blue), and X. tropicalis genes (green). The table shows the correspondence of bix gene names proposed in this study and previously used (synonyms).FISH analysis showing XLA3S-specific deletion of the nodal5 gene cluster. One unit of the nodal5 gene region, including exons, introns, and an intergenic region was used as a probe for FISH (counterstained with Hoechst). Arrows indicate the hybridization signals of nodal5s. Scale bar indicates 5 um.Comparison of the nodal5 gene cluster. Genome sequencing revealed that nodal5.e1.L~.e5.L (in pink) and nodal6.L are clustered. Amplification of nodal5 gene in XLA3L and loss of this cluster in XLA3S were confirmed. Pseudogenes (nodal5p1.L~p4.L and nodal5p1.S) are indicated in black. The nodal5 cluster of X. tropicails does not contain any pseudogene.X. laevis L chromosome has four complete copies of nodal3 (nodal3.e1.L~.e4.L), whereas the gene cluster is lost from the X. laevis S chromosome. A truncated nodal3 gene (nodal3p1.L) is likely to be a pseudogene, and highly degenerate pseudogenes (nodal3p2.L and nodal3p3.L) also exist on the L chromosome.Like nodal3, vg1 is lost from the S chromosome although there is a pseudogene (vg1p.S). vg1 is specifically amplified on the X. laevis L chromosome (vg1.e1.L~.e3.L) in comparison with X. tropicalis. An amino acid change (Ser20 to Pro20) in Vg1 protein has been shown to result in functional differences (Supplementary Note 13.9). vg1 and derrière are orthologous to mammalian gdf1.Fraction of all genes duplicated and retained to present epoch per 1 expected 4DTV(four-fold degenerate transversions) at different epochs (semi-log scale). Shown also are linear fits, which would be consistent with constant birth- and death rate models (first epoch is omitted from both fitted data sets, as is second epoch from X. laevis). See Supplemental Note 11 for a more detailed discussion.Same, but for “short genes” (CDS < 600 bp) and “long genes” (CDS > 1200 bp) separately. The loss rate of new duplicates appears to be similar. If the extra copy of a newly duplicated gene were lost when the first 100% disabling mutation occurred, we would expect, on average, the longer genes to be lost.

Image published in: Session AM et al. (2016)

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