Science Advances

Supplementary Materials

The PDF file includes:

  • Supplementary Methods and Analysis
  • Table S1. PacBio read statistics.
  • Table S2. Assembly statistics for different coverage groups.
  • Table S3. Repeated DNA statistics.
  • Table S4. Core eukaryotic genes using BUSCOs.
  • Table S5. Statistics of exon gain/loss.
  • Table S6. Statistics of CNE gain/loss.
  • Table S7. Triplets with different number of coexpressed tissues.
  • Table S8. Number and percentage of ohnolog clusters in evolutionary fate categories.
  • Table S9. Comparison of features between ZF-GF1 and ZF-GF2, where “Mean1” and “Mean2” are the mean of features between ZF-GF1 and ZF-GF2, respectively.
  • Table S10. Comparison of features between different gene evolutionary fate.
  • Fig. S1. Twenty-five–nucleotide oligomer occurrence distribution from 2 × 125 bp Illumina paired-end reads.
  • Fig. S2. Screenshot of the UCSC Genome Browser implementation of the carAur01 assembly.
  • Fig. S3. Distribution of exon and intron lengths.
  • Fig. S4. RBH gene counts between zebrafish and common carp chromosomes.
  • Fig. S5. RBH gene counts between grass carp and goldfish chromosomes.
  • Fig. S6. RBH gene counts between goldfish whole-genome duplicated chromosomes.
  • Fig. S7. Chain-net alignment between each zebrafish chromosome (middle light blue bars) and two corresponding whole-genome duplicated goldfish chromosomes (green bars), and goldfish to common carp (blue bars).
  • Fig. S8. GO terms prone to retaining both gene copies (blue rectangle) or losing one copy (blue rectangle) after WGD in goldfish.
  • Fig. S9. GO molecular function comparison among zebrafish (ZF), grass carp (GC), common carp (CC), goldfish (GF).
  • Fig. S10. Example of neo-F.
  • Fig. S11. Expression of ohnolog gene pairs in seven tissues.
  • Fig. S12. Number of ohnolog gene pairs in the same cluster (diagonal) or between each of the 20 clusters (top triangle).
  • Fig. S13. Function enrichment and reduction in divergent expressed gene pairs.
  • Fig. S14. Sequence divergence among zebrafish-goldfish triplets.
  • Fig. S15. Pearson’s correlation coefficient between zebrafish ortholog (ZF)–goldfish ohnolog (GF) and goldfish ohnolog-ohnolog (GF1-GF2).
  • Fig. S16. Definition of neo-F, sub-F, and neo-F.
  • Fig. S17. Correlation between different classes of gene expression changes and gain/loss of CNEs.
  • Fig. S18. Function enrichment (red) or reduction (blue) of genes in coexpressed groups.
  • Fig. S19. Function enrichment (red) or reduction (blue) of genes in nonfunctionalized groups.
  • Fig. S20. Function enrichment (red) or reduction (blue) of genes in subfunctionalized groups.
  • Fig. S21. Function enrichment (red) or reduction (blue) of genes in neofunctionalized groups.
  • References (6179)

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