Additional file 1: of Genome sequence of walking catfish (Clarias batrachus) provides insights into terrestrial adaptation

Figure S1. Multiple sequence alignment of myoglobin genes in the genomes of Clarias batrachus, Danio rerio, Ictalurus punctatus and Astyanax mexicanus. Figure S2. Detailed phylogenetic tree of olfactory receptor related to class A G protein-coupled receptor (ora) with species names and sequence names for Figure 3b. Figure S3. Multiple sequence alignment of olfactory receptor related to class A G protein-coupled receptor 1 (ora1) in the genomes of Clarias batrachus, Danio rerio, Ictalurus punctatus and Astyanax mexicanus. Figure S4. Syntenic analysis of myoglobin gene (mb) using genomic information of Danio rerio, Ictalurus punctatus and Clarias batrachus. Figure S5. Comparison of relative fold changes between air-breathing organ and gill in Clarias batrachus after normalization to 28S rRNA using RNA-Seq datasets and qRT-PCR. Table S1. Completeness of genome assembly assessed by CEGMA and BUSCO. Table S2. Mapping of five longest ABySS scaffolds to genome assembly. Table S3. Repetitive elements in the Clarias batrachus genome. Table S4. Orthogroups shared between species by OrthoFinder. Table S5. Specific genes in the Clarias batrachus genome compared with that of channel catfish (Ictalurus punctatus). Table S6. GO terms significantly enriched in the specific genes in the Clarias batrachus genome compared with that of channel catfish (Ictalurus punctatus). Table S7. Positively selected genes in the Clarias batrachus genome compared with those of 11 non-air-breathing teleost fish. Table S8. GO terms significantly enriched in the positively selected genes in the Clarias batrachus genome. Table S9. Expanded genes in the Clarias batrachus genome. Table S10. Summary of transcriptome sequencing data. Table S11. Expression values (RPKM) of all the genes in the transcriptomes of the gill and the air-breathing organ. Table S12. Differentially expressed genes in the transcriptome of the air-breathing organ compared with that of the gill. Table S13. GO terms significantly enriched in the differentially expressed genes comparing the transcriptome of the air-breathing organ with that of the gill. Table S14. Pathways significantly enriched in the differentially expressed genes comparing the transcriptome of the air-breathing organs with that of the gill. Table S15. Accession numbers of protein sequences and models used in the construction of phylogenetic trees of expanded genes. Table S16. Primer sequences used for qRT-PCR. (ZIP 5238 kb)