1. Chromosomes and Gene Expression
  2. Developmental Biology

The transcriptional landscape underlying larval development and metamorphosis in the Malabar grouper (Epinephelus malabaricus)

  1. Roger Huerlimann  Is a corresponding author
  2. Natacha Roux
  3. Ken Maeda
  4. Polina Pilieva
  5. Saori Miura
  6. Hsiao-chian Chen
  7. Michael Izumiyama
  8. Vincent Laudet
  9. Timothy Ravasi
  1. Marine Climate Change Unit, Okinawa Institute of Science and Technology Graduate University, Japan
  2. Centre for Sustainable Tropical Fisheries and Aquaculture, College of Science and Engineering, James Cook University, Australia
  3. Computational Neuroethology Unit, Okinawa Institute of Science and Technology Graduate University, Japan
  4. Marine Eco-Evo-Devo Unit, Okinawa Institute of Science and Technology Graduate University, Japan
  5. Marine Research Station, Institute of Cellular and Organismic Biology, Academia Sinica, Taiwan
  6. Australian Research Council Centre of Excellence for Coral Reef Studies, James Cook University, Australia
https://doi.org/10.7554/eLife.94573.3
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Cite this article
  1. Roger Huerlimann
  2. Natacha Roux
  3. Ken Maeda
  4. Polina Pilieva
  5. Saori Miura
  6. Hsiao-chian Chen
  7. Michael Izumiyama
  8. Vincent Laudet
  9. Timothy Ravasi
(2024)
The transcriptional landscape underlying larval development and metamorphosis in the Malabar grouper (Epinephelus malabaricus)
eLife 13:RP94573.
https://doi.org/10.7554/eLife.94573.3
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6 figures, 5 tables and 4 additional files

Figures

Figure 1
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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).

Figure 2 with 1 supplement
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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 …

Figure 2—figure supplement 1
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Complete cluster analysis of differentially expressed genes.

Cluster analysis of differentially expressed genes n=22,135, likelihood ratio test (LRT) analysis (full model: design = ~dph, reduced model: reduced = ~1, adjusted p-value threshold: 0.001). Genes …

Figure 3
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Expression levels of thyroid hormones (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: …

Figure 3—source data 1

Raw thyroid hormone and cortisol measurements.

https://cdn.elifesciences.org/articles/94573/elife-94573-fig3-data1-v2.xlsx
Figure 4
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Biological processes likely to be under thyroid hormones (TH) control during E. malabaricus metamorphosis.

(A) Expression patterns of key genes involved in the ossification process and known to be regulated by TH in teleosts. Bglap: bone gamma carboxyglutamate protein, mgp: matrix gla protein, postna: …

Figure 5 with 1 supplement
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Metabolic transition and corticoid 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 …

Figure 5—figure supplement 1
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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. …

Figure 6
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Expression levels of genes involved in the hypothalamo-pituitary-interrenal axis (HPI) and corticoid synthesis.

(A) Expression levels of genes involved in HPI: crha (corticotropin releasing hormone a), crhb (corticotropin releasing hormone b), crhr1a (corticotropin releasing hormone receptor 1 a), crhr1b …

Tables

Table 1
PacBio HiFi data generated for E. malabaricus genome assembly based on three SMRT cells.
SMRT cell 1SMRT cell 2SMRT cell 3Total
≥Q20 Reads322,103442,2051,373,6622,137,970
≥Q20 Yield (bp)8,468,697,81011,690,872,68726,355,056,21046,514,626,707
≥Q20 Read Length
(mean, bp)		26,29126,43719,185-
Table 2
Statistics of the Epinephelus malabaricus chromosome-scale genome assembly, scaffolding and gene annotation.
Contig assembly size1,092,599,927 bp
Number of contigs298
Contig N507,396,124 bp
Largest contig26,202,351 bp
Mean base-level coverage PacBio HiFi43 X
Contig length contained in scaffolds92.8%
Contigs contained in scaffolds90.5%
Scaffolded assembly size1,027,628,325 bp
Number of scaffolds24
Scaffold N5043,313,630 bp
Largest Scaffold50,623,973 bp
Smallest Scaffold22,540,365 bp
Non-ATGC characters36,700  bp (0.003%)
GC contents41.3%
Genome: BUSCO completeness3,406 (93.6%)
Genome: Complete and single copy3,359 (92.3%)
Genome: Complete and duplicated47 (1.3%)
Genome: Fragmented48 (1.3%)
Genome: Missing186 (5.1%)
Number of protein-coding genes26,140
Average gene length20,718 bp
Average CDS length1,750 bp
Average exons per gene11.2
Repeat contents (DFAM)56.4 %
Number of protein-coding genes26,140
Gene annotation: BUSCO completeness3476 (95.5%)
Gene annotation: Complete and single copy3,429 (94.2%)
Gene annotation: Complete and duplicated47 (1.3%)
Gene annotation: Fragmented31 (0.9%)
Gene annotation: Missing133 (3.6%)
Table 3
Detailed repeat annotation results using the DFAM repeat database.
Total Genome length1,027,628,325 bp
Bases masked579,515,295 bp (56.4 %)
number of elementslength occupiedpercentage of sequence
Retroelements660,880123,046,85611.97%
SINEs:74,0497,798,0000.76%
Penelope25,4763,705,0710.36%
LINEs:422,59786,199,6688.39%
CRE/SLACS11000.00%
L2/CR1/Rex266,32053,565,1065.21%
R1/LOA/Jockey10,9182,170,6940.21%
R2/R4/NeSL11,2863,660,2040.36%
RTE/Bov-B47,45110,563,8881.03%
L1/CIN435,2508,411,0190.82%
LTR elements:164,23429,049,1882.83%
BEL/Pao10,1862,183,6970.21%
Ty1/Copia4,658823,2280.08%
Gypsy/DIRS176,31913,796,1051.34%
Retroviral32,3175,441,5300.53%
DNA transposons1,604,009296,558,27228.86%
hobo-Activator799,713138,795,60913.51%
Tc1-IS630-Pogo138,97524,805,2982.41%
PiggyBac22,6053,909,9120.38%
Tourist/Harbinger161,21638,134,3533.71%
Other (Mirage, P-element, Transib)52,80210,665,1831.04%
Rolling-circles101,57430,491,6122.97%
Unclassified:669,818111,877,70110.89%
Total interspersed repeats:531,482,82951.72%
Small RNA:26,4052,780,0640.27%
Satellites:11,5802,523,0820.25%
Simple repeats:277,90412,099,4471.18%
Low complexity:29,1101,563,8100.15%
Table 4
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 13–15 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 …

Age (dph)Timpoint/StageMorphological description
12.5 mm NL/2.7 mm TLD01Newly hatched larva with a yolk sac; mouth unopened; eyes not pigmented;
no pectoral fin
32.7 mm NL/2.9 mm TLD03Yolk sac remains; the mouth is opened; eyes are pigmented; pectoral fins are formed;
large melanophores appear on the ventral cavity and on the second half of the body
62.9 mm NL/3.1 mm TLD06Yolk sac has been resorbed;
dorsal-fin spine starts to form within the fin fold
103.8 mm NL/4.0 mm TLD10Embryonic fin fold start differentiating in anal and dorsal fin while second spine of dorsal fin and spines of pelvic fins begin to extend with some melanophores colonizing the
tips and xanthophores start covering the ventral cavity
13–156.0 mm NL/6.4 mm TLD13Spines of dorsal and pelvic fins grow. First spine of dorsal fin appears, second spine of dorsal fin and spines of pelvic fins become serrated; head spines appear, caudal-fin rays start to form, tip of the notochord begins to flex; xanthophores continue their expansion
18–206.8 mm SL/8.3 mm TLD18Notochord post-flexed; hypural bones are formed and in perpendicular position; caudal-fin rays are segmented; soft rays of dorsal and anal fins start to form and both fins start to form their final shape; fin rays are forming on upper part of the pectoral fin; soft rays of pelvic fins began to form; melanophores appeared on the top of the head and on the caudal peduncle
30–3210.0 mm SL/12.8 mm TLD32Second spine of dorsal fin and spines of pelvic fins start to regress; soft rays in dorsal, anal, and pectoral fins are weakly segmented, caudal fin becomes truncated shape; melanophores are appearing at the basis of dorsal spines and along the notochord, melanophores ventrally on the caudal peduncle disappears; xanthophores start colonizing the caudal peduncle
6014.7 mm SL/19.1 mm TLD60Second spine of dorsal fin and spines of pelvic fins
continue their regression. Soft rays in pectoral and pelvic fins segmented; caudal-fin rays branched; anterior two bands of melanophores start appearing in some individuals: xanthophores are disappearing from the ventral cavity
6027.6 mm SL/34.6 mm TLJJuvenile stage; scales cover the body surface; second spine of dorsal fin and spines of pelvic fins fully regressed and became plain without hooks; caudal fin reached its final round
shape; adult pigmentation pattern is more visible with alternate light and brownish vertical bands making lateral line system fully visible
Table 5
Origin of protein sequences used for genome annotation in braker2.
SpeciesCommon nameNumber of proteinsSource
Amphiprion ocellarisOcellaris clownfish48,668https://www.ncbi.nlm.nih.gov/protein
Danio reriozebrafish88,631https://www.ncbi.nlm.nih.gov/protein
Acanthochromis polyacanthusspiny chromis damselfish36,648https://www.ncbi.nlm.nih.gov/protein
Oreochromis niloticusNile tilapia36,648https://www.ncbi.nlm.nih.gov/protein
Oryzias latipesJapanese medaka47,623https://www.ncbi.nlm.nih.gov/protein
Poecilia reticulataguppy45,692https://www.ncbi.nlm.nih.gov/protein
Salmo salarAtlantic salmon112,302https://www.ncbi.nlm.nih.gov/protein
Stegastes partitusbicolor damselfish31,760https://www.ncbi.nlm.nih.gov/protein
Takifugu rubripesJapanese puffer49,529https://www.ncbi.nlm.nih.gov/protein
Epinephelus lanceolatusGiant grouper42,970GCA_005281545.1, RefSeq
Epinephelus akaaraRed-spotted grouper23,9234398b9f, Dryad
Total aa sequences1,155,478

Additional files

Supplementary file 1

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

https://cdn.elifesciences.org/articles/94573/elife-94573-supp1-v2.xlsx
MDAR checklist
https://cdn.elifesciences.org/articles/94573/elife-94573-mdarchecklist1-v2.pdf
Source data 1

Raw gene count matrix of larval stages mapped against the malabar grouper genome.

https://cdn.elifesciences.org/articles/94573/elife-94573-data1-v2.xlsx
Source data 2

Annotation of significantly differentially expressed genes which are upregulated at both D03 an D32.

https://cdn.elifesciences.org/articles/94573/elife-94573-data2-v2.xlsx

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