Little skate genome provides insights into genetic programs essential for limb-based locomotion
- Interdisciplinary Program in Bioinformatics, Seoul National University, Republic of Korea
- Department of Brain Sciences, DGIST, Republic of Korea
- Department of Biology, Graduate School of Arts and Science, NYU, United States
- Genome Technology Center, Division for Advanced Research Technologies, and Department of Pathology, NYU School of Medicine, United States
- Department of Agricultural Biotechnology, Seoul National University, Republic of Korea
- Neuroscience Institute, Department of Neuroscience and Physiology, New York University School of Medicine, United States
- Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, Seoul National University, Republic of Korea
- eGnome, Inc, Republic of Korea
Figures
Figure 1 with 6 supplements
Assembly and comparison of little skate genomes across diverse phylogenetic lineages.
(A) Top 49 scaffolds ranked by the length. Gene density in the scaffolds is color coded. (B) Assembly statistics of the skate genome. (C). Comparison of BUSCO gene synteny across diverse …
Figure 1—figure supplement 1
Genome size estimation via Genome Scope 2.
K-mer spectrum with K=31 and the fitted model of little skate genome. (‘len’: estimated genome size, ‘uniq’: proportion of the unique sequence, ‘aa’: homozygosity, ‘ab’: heterozygosity, ‘kcov’: …
Figure 1—figure supplement 2
Genome assembly process.
Improvement of the new genome assembly throughout the assembly process in terms of contiguity (contig N50), duplications and BUSCO gene contents. Y-axis on the BUSCO gene contents summary represents …
Figure 1—figure supplement 3
BUSCO genes and repetitive elements of little skate genome.
(A) BUSCO gene contents summarizing the completeness of the new little skate genome. Y-axis represents different classes of BUSCO genes as follows: M, missing; F, fragmented; D, complete and …
Figure 1—figure supplement 4
Limitation of previous transcriptome data.
(A) The Alignment coverage distribution when the alignment was performed using the predicted genes of new skate genome (blue) and old transcriptome (yellow) as the reference. (B) The example of the …
Figure 1—figure supplement 5
Qualitative assessment of genome assembly of Hoxa cluster.
(A) Pairwise-alignment of Hoxa cluster. (B) Hoxa genes of previous BAC clone (top) and the new genome (bottom).
Figure 1—figure supplement 6
Comparison of Hoxc clusters.
(A) The majority of ortholog genes highly conserved in multiple species near Hoxc cluster are mapped to s41 of little skate genome. (B) The repeat and gene contents near the orthologous genes. The Ho…
Figure 2
Differentially expressed genes of Pec-MNs and Tail-SC.
(A) Volcano plot of gene expression. Each dot represents individual genes, and each gene is color-coded according to its fold difference and significance: Red dots: FD ≥2, adjusted p-value (adj. p)<0…
Figure 3 with 3 supplements
Potential MN marker genes commonly or divergently expressed in different species.
(A) Venn diagram and heatmap of MN-expressed genes (percentile expression >70) of little skate, mouse and chick. In the heatmap, expression levels are color coded according to percentile expression …
Figure 3—figure supplement 1
Validation of chick MN RNA-seq.
(A) volcano plot of DEG analysis of chick br-MNs compared to ce-SC. Each dot represents individual genes. Left side: enriched genes in ce-SC; right side: enriched genes in br-MNs. Dashed lines …
Figure 3—figure supplement 2
Validation of MN gene expression.
Gene expression pattern in tissue sections is revealed by in situ RNA hybridization. Common MN-expressed genes: expression levels ranked above 70th percentile in all species; Mouse MN-specific …
Figure 3—figure supplement 3
Common and species-specific genes.
(A) Similarity index between the three species based on the number of shared and specific MN-expressed genes. The heatmap of the genes associated with the ion channel and neurotransmitter …
Figure 4 with 3 supplements
Overview of ATAC-seq data.
(A) Heatmap of 61997 ACRs. Fin-MN ACRs on the left and tail-SC ACRs on the right. The number of ACRs: shared-ACRs, 7869; fin-MNs- specific ACRs, 35741; tail-SC-specific ACRs, 18387. Higher intensity …
Figure 4—figure supplement 1
ATAC-seq data quality control.
Fraction of signal plot showing ATAC-seq read depth nearby TSS sites of (A) fin-MN and (B) tail-SC. The heatmap of 1 kb up and downstream regions of TSS sites in (C) fin-MN and in (D) tail-SC. …
Figure 4—figure supplement 2
Chromatin accessibility of constitutively expressed genes and example genes with different peak types.
The gene expression and chromatin accessibility of constitutively expressed genes (including shared ACRs), (A) Actb, (B) Tomm70, and example genes with fin-MN and tail-SC ACRs, (C) Anxa1, (D) Trappc1…
Figure 4—figure supplement 3
Correlation between promoter accessibility with gene expression.
No peak indicates genes without any ACR located in promoters and low, medium and high are those genes with ATAC-seq read depth <Q10, Q10 <x < Q90 and Q90 <. Center line represents median and the box …
Figure 5 with 2 supplements
Predicted gene regulatory modules in MNs.
(A) TF motif predictions (adj.p <0.05) identified in skate fin MN and mouse limb-level MN ACRs of MN-expressed genes (percentile >70 in either skate MNs or mouse MNs; around 10 Kb up- and downstream …
Figure 5—figure supplement 1
Differential regulation of Foxp1 expression in MNs of different species.
(A) The identity of PGC neurons is defined by immunofluorescence staining of marker proteins. Left: pectoral sections showing the axons (NFAP) and putative sympathetic chain ganglia (Isl1/2); middle …
Figure 5—figure supplement 2
Comparison of intergenic size and number of ACRs between mouse and little skate.
(A) Comparison of intergenic size of orthologous genes of mouse and little skate. (B) Distribution of the number of ACRs in all and neuronal genes. (C) Proportion of genic and intergenic ACRs for …
Additional files
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Supplementary file 1
Ortholog gene cluster.
Ortholog genes defined by the OrthoVenn2.
- https://cdn.elifesciences.org/articles/78345/elife-78345-supp1-v1.xlsx
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Supplementary file 2
DEG results.
The DEG results for little skate (pec-MN vs tail-SC) and chick (br-MN vs ce-SC) MNs.
- https://cdn.elifesciences.org/articles/78345/elife-78345-supp2-v1.xlsx
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Supplementary file 3
Comparison with previous RNA-seq data.
The percentile expression level and p-values of previous MN marker genes.
- https://cdn.elifesciences.org/articles/78345/elife-78345-supp3-v1.xlsx
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Supplementary file 4
Multiple species RNA.
The percentile expression of genes displayed in Figure 3.
- https://cdn.elifesciences.org/articles/78345/elife-78345-supp4-v1.xlsx
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Supplementary file 5
eggNOG ortholog groups.
The ortholog group information predicted by eggNOG.
- https://cdn.elifesciences.org/articles/78345/elife-78345-supp5-v1.xlsx
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Supplementary file 6
Species-specific Paralogs.
The list of additional paralog genes which are species-specific.
- https://cdn.elifesciences.org/articles/78345/elife-78345-supp6-v1.xlsx
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Supplementary file 7
Specific genes without common gene paralogs.
The list of species-specific genes which do not share the same ortholog groups with common genes.
- https://cdn.elifesciences.org/articles/78345/elife-78345-supp7-v1.xlsx
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Supplementary file 8
Oligonucleotide sequences used in generating in situ probes.
T7 promoter sequence is indicated in blue
- https://cdn.elifesciences.org/articles/78345/elife-78345-supp8-v1.docx
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Transparent reporting form
- https://cdn.elifesciences.org/articles/78345/elife-78345-transrepform1-v1.pdf
