Alternative splicing across the tree of life
- Foundation for the Promotion of Sanitary and Biomedical Research of the Valencian Community (FISABIO), Spain
- Institute of Integrative Systems Biology (I2Sysbio), University of Valencia and Spanish National Research Council (CSIC), Spain
- Center for Biomedical Research in Epidemiology and Public Health Network (CIBEResp), Spain
Figures
Figure 1
Schematic representation of the compositional structure of a gene and alternative splicing.
The selective combination of exons and introns in a gene of 33 nucleotides gives rise to three distinct mRNA isoforms: mRNA1 (16 nucleotides), mRNA2 (9 nucleotides), and mRNA3 (19 nucleotides). When these coding DNA sequences (CDSs) are mapped onto the genome, the coding DNA—defined as the DNA sequences that are transcribed into a mRNA—is found to be composed of 25 nucleotides. The ASR is then computed as the ratio of the total number of nucleotides in mRNA isoforms to the number of nucleotides composing coding DNA: .
Figure 2
Comparative analysis of (A) alternative splicing ratio (ASR) and (B) normalized ASR (ASR*) distributions across taxonomic groups, including mammals, birds, fish, arthropods, plants, fungi, unicellular eukaryotes, bacteria, and archaea.
Box plots represent the median (horizontal line), interquartile range (IQR, box), and whiskers extending to 1.5× IQR. A yellow diamond-shaped point represents the mean, and outliers are shown as individual red points. Colors in the box plots correspond to taxonomic classifications.
Figure 3 with 5 supplements
Normalized alternative splicing ratio vs genome size across taxonomic groups.
(A–I) Phylogenetic generalized least squares (PGLS) regression between the genome size and the normalized alternative splicing ratio (ASR*) across different taxonomic groups. Each panel represents a distinct taxonomic group. The regression lines represent the estimated evolutionary relationship between the two variables while accounting for phylogenetic dependence. (J) Global relationship across all taxonomic groups. The inset provides a logarithmic representation of the x-axis.
Figure 3—figure supplement 1
Alternative splicing ratio vs genome size across taxonomic groups.
(A–I) Phylogenetic generalized least squares (PGLS) regression between genome size and alternative splicing ratio (ASR). (J) Global relationship. The inset provides a logarithmic representation of the x-axis.
Figure 3—figure supplement 2
Normalized alternative splicing ratio vs gene content across taxonomic groups.
(A–I) Phylogenetic generalized least squares (PGLS) regression between gene content and alternative splicing ratio (ASR*). (J) Global relationship. The inset provides a logarithmic representation of the x-axis.
Figure 3—figure supplement 3
Alternative splicing ratio vs gene content across taxonomic groups.
(A–I) Phylogenetic generalized least squares (PGLS) regression between gene content and alternative splicing ratio (ASR). (J) Global relationship. The inset provides a logarithmic representation of the x-axis.
Figure 3—figure supplement 4
Normalized alternative splicing ratio vs coding DNA across taxonomic groups.
(A–I) Phylogenetic generalized least squares (PGLS) regression between coding content and alternative splicing ratio (ASR*). (J) Global relationship.
Figure 3—figure supplement 5
Alternative splicing ratio vs coding DNA across taxonomic groups.
(A–I) Phylogenetic generalized least squares (PGLS) regression between coding content and alternative splicing ratio (ASR). (J) Global relationship.
Figure 4 with 1 supplement
Normalized alternative splicing ratio vs the percentage of coding DNA across taxonomic groups.
(A–I) Phylogenetic generalized least squares (PGLS) regression between the proportion of coding relative to gene content and the normalized alternative splicing ratio (ASR*) across different taxonomic groups.
Each panel represents a distinct taxonomic group. The regression lines represent the estimated evolutionary relationship between the two variables while accounting for phylogenetic dependence. (J) Global relationship across all taxonomic groups.
Figure 4—figure supplement 1
Alternative splicing ratio vs the percentage of coding DNA across taxonomic groups.
(A–I) Phylogenetic generalized least squares (PGLS) regression between the proportion of coding relative to gene content and alternative splicing ratio (ASR). (J) Global relationship.
Figure 5 with 1 supplement
Normalized alternative splicing ratio vs the percentage of gene content across taxonomic groups.
(A–I) Phylogenetic generalized least squares (PGLS) regression between the proportion of gene content relative to genome size and the normalized alternative splicing ratio (ASR*) across different taxonomic groups.
Each panel represents a distinct taxonomic group. The regression lines represent the estimated evolutionary relationship between the two variables while accounting for phylogenetic dependence. (J) Global relationship across all taxonomic groups.
Figure 5—figure supplement 1
Alternative splicing ratio vs the percentage of gene content across taxonomic groups.
(A–I) Phylogenetic generalized least squares (PGLS) regression between the proportion of gene content relative to genome size and alternative splicing ratio (ASR). (J) Global relationship.
Figure 6
Normalized alternative splicing ratio (ASR*) is represented as a color gradient across different genomic profiles.
The x-axis spans the gene-to-genome proportion, while the y-axis spans the coding-to-gene proportion.
Figure 7
Organisms were classified into taxonomic groups based on the hierarchical structure provided by the NCBI Taxonomy Database, using annotation data from NCBI that meet conditions (i) and (ii) described in ‘NCBI RefSeq dataset’.
Tables
Table 1
Summary statistics for the percentage of gene content relative to genome size (Gene Content/Genome Size (%)),the percentage of coding relative to gene size (Coding Size / Gene Content (%)),the percentage of coding relative to genome size (Coding Size / Genome Size(%)), the alternative splicing ratio (ASR),and the normalized alternative splicing ratio (ASR*) across different taxonomic groups.
The table includes the mean (), the interpercentile range between the 5th and 95th percentiles , and standard deviation (σ) for each group.
| Group | Gene Content / Genome Size (%) | Coding Size / Gene Content (%) | Coding Size / Genome Size (%) | ASR | ASR* | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Mammals | 44.7 | [35.5,55.6] | 6.27 | 3.05 | [2.47,3.76] | 0.42 | 1.35 | [1.09,1.60] | 0.15 | 3.09 | [1.78,4.60] | 0.92 | 2.81 | [2.11,3.50] | 0.59 |
| Birds | 52.6 | [41.8,62.5] | 6.05 | 4.79 | [4.18,5.53] | 0.45 | 2.5 | [2.21,2.83] | 0.2 | 2.71 | [1.76,3.62] | 0.64 | 2.48 | [1.96,2.96] | 0.31 |
| Fish | 61.9 | [49.4,74.3] | 7.50 | 8.65 | [5.23,13.4] | 2.52 | 5.39 | [2.69,8.57] | 1.77 | 2.26 | [1.55,2.92] | 0.41 | 2.02 | [1.57,2.50] | 0.29 |
| Arthropods | 60.3 | [33.1,79.9] | 14.0 | 11.3 | [2.15,25.1] | 7.15 | 6.92 | [0.910,15.1] | 4.36 | 2.16 | [1.34,3.14] | 0.54 | 2.3 | [1.59,2.90] | 0.39 |
| Plants | 24.7 | [7.04,40.4] | 11.0 | 27.3 | [14.3,38.5] | 7.50 | 6.80 | [1.69,13.6] | 3.68 | 1.56 | [1.30,1.87] | 0.2 | 2.1 | [1.61,2.46] | 0.24 |
| Fungi | 63.2 | [41.2,85.9] | 13.8 | 86.9 | [67.6,99.2] | 11.5 | 55.3 | [33.2,82.7] | 15.4 | 1.01 | [1,1.09] | 0.05 | 1.01 | [1,1.09] | 0.05 |
| Unicellular Eukaryotes | 60.9 | [42.5,88.1] | 16.2 | 88.6 | [69.2,99.9] | 12 | 53.6 | [33.0,76.3] | 14.9 | 1.00 | [1,1.01] | 2.56 × 10−3 | 1.00 | [1,1.01] | 2.56 × 10−3 |
| Bacteria | 85.7 | [76.8,92.2] | 5.06 | 98.8 | [97.7,99.5] | 0.57 | 84.6 | [75.6,91.2] | 5.07 | 1.00 | [1.00,1.00] | 8.21 × 10−4 | 1.00 | [1.00,1.00] | 8.21 × 10−4 |
| Archaea | 86.1 | [74.5,92.4] | 5.21 | 99.1 | [98.7,99.4] | 0.22 | 85.3 | [73.9,91.5] | 5.10 | 1.00 | [1.00,1.01] | 1.72 × 10−3 | 1.00 | [1.00,1.01] | 1.72 × 10−3 |
Additional files
-
MDAR checklist
- https://cdn.elifesciences.org/articles/94802/elife-94802-mdarchecklist1-v1.pdf
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Supplementary file 1
Comparisons of alternative splicing ratio across taxonomic groups.
- https://cdn.elifesciences.org/articles/94802/elife-94802-supp1-v1.docx
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Supplementary file 2
Comparisons of genomic variables across taxonomic groups.
- https://cdn.elifesciences.org/articles/94802/elife-94802-supp2-v1.docx
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Supplementary file 3
PGLS analyses.
- https://cdn.elifesciences.org/articles/94802/elife-94802-supp3-v1.docx
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Supplementary file 4
Coefficient of variation across taxonomic groups.
- https://cdn.elifesciences.org/articles/94802/elife-94802-supp4-v1.docx
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Supplementary file 5
Relative variability among genomic features.
- https://cdn.elifesciences.org/articles/94802/elife-94802-supp5-v1.docx
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Alternative splicing across the tree of life
eLife 13:RP94802.
https://doi.org/10.7554/eLife.94802.3
