Statistics of the Epinephelus malabaricus chromosome-scale genome assembly, scaffolding and gene annotation.

Additional statistics can be found in Supp. Table S2.

Transcriptomic results of E. malabaricus larval development.

A) Principal component analysis of different larval stages using variance stabilizing transformed complete transcriptome. B) Cluster analysis using the coseq R package, focusing on genes that are upregulated on days 3 and/or 32. The number of genes in each cluster are shown above each graph. Adjusted p-values and functional annotations for the four gene clusters in this figure can be found in the supplementary data file. Gene expression data was generated from whole larvae.

Expression levels of TH signaling pathway genes in E. malabaricus.

A) TRH: thyroid releasing hormone, TSH: thyroid stimulating hormone. B), DUOX: dual oxidase, TG: thyroglobulin, TPO: thyroperoxidase, SIS: sodium iodine symporter. C) DIO: deiodinase. D) TR: thyroid hormone receptor. Colored lines join the average values of each stage. Biochemical pathways adapted from Roux et al.15. E) T4 and T3 levels (in ng/g of larvae) during early larval development. # indicates that the value is below the quantification limit, and different letters indicate significant differences (one-way ANOVA followed by a Tukey HSD test for T4 levels only as no significant differences were observed after ANOVA for T3 levels). Gene expression data was generated from whole fish. Expression levels were derived from DESeq2 normalised gene counts.

Biological processes likely to be under TH control during E. malabaricus metamorphosis.

A) Expression patterns of key genes involved in ossification process and known to be regulated by TH in teleosts. Bglap: bone gamma carboxyglutamate protein, mgp: matrix gla protein, postna: periostin a, postnb: periostine b, phex: phosphate regulating endopeptidase homolog X linked. B) Pictures of E. malabaricus at D03, D10, D32, D60 illustrate the elongation of the dorsal and pelvic floating spines (green arrow heads at D10 and D32) and their regression (red arrow heads at D60). C) Expression patterns of genes involved in pigmentation. Three areas of interest were chosen to illustrate the appearance of melanophores (C6 to C8: at the top of the head, C11 to C13: above internal organs and, C20 to C25: close to the caudal peduncle,) and xanthophores (C7 to C8 at the top of the head, C14 to C16 above internal organs and C26: close to the caudal peduncle). D) Expression patterns of genes encoding for the rhodopsins (rh1) and the visual cone opsins (rh2A, rh2B, rh2C, opnlw, opnsw1, opnsw2A-1, opnsw2A-2, opnsw2B). Gene expression data was generated from whole fish. Expression levels were derived from DESeq2 normalised gene counts.

Metabolic transition and corticoids expression levels of E. malabaricus.

A) Schematization of the metabolic transition occuring during E. malabaricus larval development showing that young larvae rely on aerobic metabolism whereas older larvae rely on anaerobic metabolism. Expression levels of genes involved in glycolysis (pfkma, pfkmb), krebs cycle (idh3, dlstb). Gene expression data was generated from whole fish. Expression levels were derived from DESeq2 normalised gene counts.

Expression levels of genes involved in the Hypothalamo-Pituitary-Interranal axis (HPI) and corticoids synthesis.

A) Expression levels of genes involved in Hypothalamo-Pituitary-Interenal axis (HPI): crha (corticotropin releasing hormone a), crhb (corticotropin releasing hormone b), crhr1a (corticotropin releasing hormone receptor 1a), crhr1b (corticotropin release hormone receptor 1b), crhr2 (cortico release hormone receptor 2), pomc-a1 (propiomelanocortin a1), pomc-a2 (propiomelanocortin a2), pomc-b (propiomelanocortin b), mr (mineralocorticoid receptor), gr1 (glucocorticoid receptor 1), gr2 (glucocorticoid receptor 2). B) Expression levels of genes involved in corticoids synthesis: star (steroidogenic acute regulatory protein), fdx1 (ferredoxine 1), fdx2 (ferredoxine 2), fdxr (ferredoxine reductase), cyp11a1 (Cytochrome P450 Family 11 Subfamily A Member 1), hsd3b1 (Hydroxysteroid dehydrogenases 3β1), cyp17a1 (Cytochrome P450 Family 17 Subfamily A Member 1), cyp21a2 (Cytochrome P450 Family 21 Subfamily A Member 2), cyp11c1 (Cytochrome P450 Family 11 Subfamily C Member 1), hsdllbl, hsd11b2 (Hydroxysteroid dehydrogenase 11 3α1&2). C) Cortisol levels (in ng/g of larvae) during early larval development. # indicates that the value is below the quantification limit, and different letters indicate significant differences (one-way ANOVA followed by a Tukey HSD test). Gene expression data was generated from whole fish. Expression levels were derived from DESeq2 normalised gene counts.

Morphological description of the larval and juvenile stages sampled for the transcriptomic analysis.

D01: 1 day post hatching (dph), D03: 3 dph, D10: 10 dph, D:13 1315 dph, D18: 18–20 dph, D32: 32–34 dph, D60: ca. 60 dph, J: ca. 60 dph with juvenile phenotype. NL is “notochord length” for preflexion and flexion larvae, SL is “standard length” for postflexion and older stages, and TL is “total length” for all stages.

Hi-C contact map after scaffolding.

E. malabaricus genome contig contact matrix using Hi-C data. The color bar indicates contact density from dark red (high) to white (low).

Metabolic shift during grouper metamorphosis.

Expression levels of genes involved in glycolysis, lactic fermentation, and citric acid cycle at each developmental stage (D01, D03, D06, D10, D13, D18, D60, J) extracted from transcriptomic data. Enzyme highlighted in red represents rate limiting steps for each metabolic pathway.

Complete cluster analysis of differentially expressed genes.

Cluster analysis of differentially expressed genes (n = 22,135, LRT analysis (full model: design = ~ dph, reduced model: reduced = ~ 1, adjusted p-value threshold: 0.001). Genes contained in clusters: 1) 925, 2) 382, 3) 548, 4) 1,193, 5) 804, 6) 1,503, 7) 2,025, 8) 786, 9) 2,399, 10) 570, 11) 801, 12) 1,141, 13) 2,439, 14) 1,471, 15) 681, 16) 1,702, 17) 2,765.

PacBio HiFi data generated for E. malabaricus genome assembly based on three SMRT cells.

Additional genome assembly, scaffolding and annotation statistics.

Detailed repeat annotation results using the DFAM repeat database.

Differentially expressed, upregulated and downregulated genes between consecutive time points.

Origin of protein sequences used for genome annotation in braker2.