The impact of local genomic properties on the evolutionary fate of genes
- Research Center for Genome & Medical Sciences, Tokyo Metropolitan Institute of Medical Science, Japan
- Molecular Life History Laboratory, Department of Genomics and Evolutionary Biology, National Institute of Genetics, Japan
- Department of Genetics, Sokendai (Graduate University for Advanced Studies), Japan
- RIKEN Center for Biosystems Dynamics Research, Japan
Figures
Figure 1
Detection of ‘elusive’ genes.
(a) Pipeline of ortholog group clustering and gene loss detection. (b) Definition of an elusive gene schematized with ortholog presence/absence pattern referring to a taxonomic hierarchy. Red and …
Figure 2 with 1 supplement
Genomic and evolutionary characteristics of elusive genes.
Distributions of non-synonymous, synonymous, and intronic nucleotide substitution rates, namely KA (a), KS (b), and KI (c) values, respectively, between the human–chimpanzee orthologs of the elusive …
Figure 2—figure supplement 1
Comparison of KA and KS values between orthologs of the elusive and non-elusive genes.
Distributions of KA and KS values between the orthologs of human elusive and non-elusive genes of closely related vertebrates. Correction for multiple testing was performed for comparison in each …
Figure 3 with 2 supplements
Long-standing characteristics of elusive genes.
Retention of the genomic and evolutionary characteristics of the human elusive genes across vertebrates. The individual round squares with arrows indicate significant increases or decreases of the …
Figure 3—figure supplement 1
Asymmetric ortholog retention across the vertebrates.
(a) Number of retained orthologs of the human elusive and non-elusive genes that originated in the common ancestors of the gnathostomes or older age. (b) Intersections of the retained orthologs …
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Figure 3—figure supplement 1—source data 1
A 2×2 contingency table in Figure 3—figure supplement 1.
- https://cdn.elifesciences.org/articles/82290/elife-82290-fig3-figsupp1-data1-v1.xlsx
Figure 3—figure supplement 2
Genomic characteristics of the orthologs of elusive and non-elusive genes.
Distribution of (a) gene length and (b) GC content of the orthologs of the human elusive and non-elusive genes and (c) distribution of the gene density of the genomic regions where the orthologs of …
Figure 4
Genetic variations of the elusive and non-elusive genes within human populations.
Comparison of the density of rare single-nucleotide variants (SNVs) (a), deletion copy number variants (CNVs) (b), duplication CNVs (c), and Z-scores of synonymous (d), missense (e), and …
Figure 5 with 1 supplement
Expression profiles of elusive and non-elusive genes.
The figure shows density scatter plots of the expression quantity and divergence of elusive and non-elusive genes. The numbers of the elusive/non-elusive genes and those for which the expression …
Figure 5—figure supplement 1
Expression profiles of the orthologs of the elusive and non-elusive genes for non-mammalian vertebrates.
Density scatter plots of the expression quantity and divergence of elusive and non-elusive genes. The total numbers of the elusive/non-elusive genes and the number of them for which expression data …
Figure 6 with 5 supplements
Epigenetic features of the elusive genes.
Comparison of the distribution of ATAC-seq peak density (a), length of the topologically associating domains (TADs) including the elusive or non-elusive genes (b), the replication timing indicator …
Figure 6—figure supplement 1
ATAC-seq peak density of the elusive and non-elusive gene regions.
Comparison of the distribution of ATAC-seq peak density between the elusive and non-elusive genes across multiple cell types. In the elusive gene panels (orange bar), purple bar indicates the …
Figure 6—figure supplement 2
Sequence lengths of the topologically associating domains (TADs) containing elusive or non-elusive genes.
Comparison of the distribution of length of TADs including the elusive or non-elusive genes across multiple cell types. In the elusive gene panels (orange bar), purple bar indicates the elusive …
Figure 6—figure supplement 3
Comparison of the replication timing indicator based on Repli-seq between the elusive and non-elusive genes.
Comparison of the distribution of replication timing indicator based on Repli-seq between the elusive and non-elusive genes across multiple cell types. In the elusive gene panels (orange bar), …
Figure 6—figure supplement 4
The fraction of elusive and non-elusive genes that overlap with lamina-associated domains (LADs).
Comparison of frequency of overlap with LADs computed from Lamin B1 ChIP-seq data between the elusive and non-elusive genes across multiple data. In the elusive gene panels (orange bar), purple bar …
Figure 6—figure supplement 5
ATAC-seq peak density of the chicken orthologs of the elusive and non-elusive gene regions.
Comparison of the distribution of ATAC-seq peak density between the orthologs of elusive (210) and non-elusive (7218) genes in the chicken genome. Correction for multiple testing was performed for …
Figure 7 with 1 supplement
Chromosomal distribution of human elusive genes.
Red and dark blue horizontal bars beside the chromosome ideogram represent the location of elusive genes with restricted expression (Shannon’s H′ < 1) and the other elusive genes, respectively. (a) …
Figure 7—figure supplement 1
Distribution of elusive genes across human chromosomes.
Red and dark blue horizontal bars on the side of the chromosome diagram represent the location of elusive genes with restricted expression (Shannon’s H′ < 1) and the other elusive genes, …
Tables
Author response table 1
Difference in statistical significances across different elusive gene sets.
| Features | Non-significant in theinitial gene set(1,081 elusive genes) | Non-significant in thecurrent gene set(813) | Non-significant in the current gene setexcluding chr19(669) |
|---|---|---|---|
| Gene density in the turkey genome | ✓ | ✓ | ✓ |
| Gene density in the green anole genome | ✓ | ||
| Gene density in the bamboo shark genome | ✓ | ||
| Gene density in the whale shark genome | ✓ | ✓ | ✓ |
| KS in avians | ✓ | ✓ | |
| KA in avians | ✓ | ✓ | ✓ |
| KA in sharks | ✓ | ✓ | ✓ |
| ATAC-seq peak density for GM23338 | ✓ | ||
| Lamin B1 ChIP-seq peak density for K562 | ✓ |
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The other features showed significantly different trends between the elusive and non-elusive genes for all of the elusive gene sets and thus are not included in this table.
Author response table 2
Number of chicken orthologs of elusive and non-elusive genes locating in macro- and microchromosomes.
| Elusive | Non-elusive | |
|---|---|---|
| Macrochromosome (chr1-10, Z) | 93 | 4211 |
| Microchromosome (chr11-, W) | 68 | 2078 |
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Genes in non-chromosome scaffolds and mitochondrial genome were excluded Fisher's exact test p=0.0175, odds ratio=1.48
Author response table 3
Number of elusive and non-elusive genes locating in the genomic regions derived from ancestral macro- and microchromosomes.
| Elusive | Non-elusive | |
|---|---|---|
| Ancestral macrochromosome | 395 | 5950 |
| Ancestral microchromosome | 296 | 1929 |
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Genes in the genomic regions that did not correspond to the ancestral macro/microchromsomes were excluded. Fisher's exact test p=9.50x10-24, odds ratio=2.31.
Additional files
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Supplementary file 1
Supplementary Tables S1, S3, S4.
(a) Supplementary Table S1. Vertebrate species used for creating gene phylogenies. (b) Supplementary Table S3. ENCODE accession ID list used for epigenomic analyses. (c) Supplementary Table S4. RNA-seq and ATAC-seq samples of non-mammalian vertebrates.
- https://cdn.elifesciences.org/articles/82290/elife-82290-supp1-v1.xlsx
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Supplementary file 2
Supplementary Table S2.
Characteristics of the elusive and non-elusive genes in the human genome.
- https://cdn.elifesciences.org/articles/82290/elife-82290-supp2-v1.zip
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MDAR checklist
- https://cdn.elifesciences.org/articles/82290/elife-82290-mdarchecklist1-v1.docx
