Epinephelus Tukula Research Articles

Comparative Transcriptome Analysis of the Hypothalamic-Pituitary-Gonadal Axis of Jinhu Grouper (Epinephelus fuscoguttatus ♀ × Epinephelus tukula ♂) and Tiger Grouper (Epinephelus fuscoguttatus).

Jinhu groupers, the hybrid offspring of tiger groupers (Epinephelus fuscoguttatus) and potato groupers (Epinephelus tukula), have excellent heterosis in fast growth and strong stress resistance. However, compared with the maternal tiger grouper, Jinhu groupers show delayed gonadal development. To explore the interspecific difference in gonadal development, we compared the transcriptomes of brain, pituitary, and gonadal tissues between Jinhu groupers and tiger groupers at 24-months old. In total, 3034 differentially expressed genes (DEGs) were obtained. KEGG (Kyoto Encyclopedia of Genes and Genomes) enrichment analyses showed that the osteoclast differentiation, oocyte meiosis, and ovarian steroidogenesis may be involved in the difference in gonadal development. Trend analysis showed that the DEGs were mainly related to signal transduction and cell growth and death. Additionally, differences in expression levels of nr4a1, pgr, dmrta2, tbx19, and cyp19a1 may be related to gonadal retardation in Jinhu groupers. A weighted gene co-expression network analysis revealed three modules (i.e., saddlebrown, paleturquoise, and greenyellow) that were significantly related to gonadal development in the brain, pituitary, and gonadal tissues, respectively, of Jinhu groupers and tiger groupers. Network diagrams of the target modules were constructed and the respective hub genes were determined (i.e., cdh6, col18a1, and hat1). This study provides additional insight into the molecular mechanism underlying ovarian stunting in grouper hybrids.

A chromosome-level genome assembly of the potato grouper (Epinephelus tukula)

The potato grouper, Epinephelus tukula, is one of the largest coral reef teleost, and it is an important germplasm resource for selection and cross breeding. Here we report a potato grouper genome assembly generated using PacBio long-read sequencing, Illumina sequencing and high-throughput chromatin conformation capture (Hi-C) technology. The genome size was 1.13 Gb, with a total of 508 contigs anchored into 24 chromosomes. The scaffold N50 was 42.65 Mb. For the genome models, our assembled genome contained 98.11% complete BUSCO with the vertebrata_odb9 database. One more copies of Gh and Hsp90b1 were identified in the E. tukula genome, which might contribute to its fast growth and high resistance to stress. In addition, 435 putative antimicrobial peptide (AMP) genes were identified in the potato grouper. This study provides a good reference for whole genome selective breeding of the potato grouper and for future development of novel marine drugs.

Construction of a high-density genetic linkage map and QTL mapping for growth traits in hybrid Epinephelus fuscoguttatus (♀) and Epinephelus tukula (♂) progeny

QTL mapping is an effective method for marker assisted selection (MAS) in animal breeding, and high-density linkage genetic maps are necessary for fine mapping of QTLs. In this study, high-density genetic maps of hybrid Epinephelus fuscoguttatus (♀) and Epinephelus tukula (♂) progeny (which demonstrated improved growth rates compared with the female parent) were constructed using RAD technology. Sex-average, female-specific, and male-specific linkage maps were composed of 24 linkage groups (LGs). The genetic map developed in this study had the highest number of SNPs among reported genetic maps for groupers. The sex-average linkage map contained 2759 bin makers (150,468 SNPs) and spanned 1627.28 cM, with an average marker interval of 0.59 cM. The female-specific (E. fuscoguttatus) linkage map contained 648 bin makers (38,269 SNPs) and spanned 1414.68 cM, with an average marker interval of 2.22 cM. The male-specific (E. tukula) linkage map contained 2126 bin makers (112,015 SNPs) and spanned 1839.88 cM, with an average marker interval of 0.86 cM. In total, 45 QTLs comprising 318 SNPs for growth-related traits were identified, including 10 QTLs for body weight, 6 QTLs for full length, 7 QTLs for body length, 14 QTLs for head length, 5 QTLs for body height, and 3 QTLs for body thickness. In addition, 56 candidate genes related to growth, metabolism, bone formation, muscle development, and neural regulation were identified, including eight genes associated with growth in other fish. Among these, gpr126, fam20a, fam20c, sox9b, foxm1, foxl1, myf6, zbtb38, and sl should be a focus of further research. These results provide a foundation for fine QTL mapping in grouper, and theoretical guidance for exploring the causes of heterosis, which is of great significance for MAS in the breeding of hybrids and male and female parents.

Characterization of the complete mitochondrial genome of the hybrid grouper (Cromileptes altivelis♀ × Epinephelus tukula♂) with phylogenetic consideration

Here we isolated and characterized the complete mitochondrial genome of the hybrid grouper (Cromileptes altivelis♀ × Epinephelus tukula♂). It is 16,503 bp long and contains 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes, and a control region. The nucleotide composition is 29.08% of A, 29.03% of C, 15.66% of G and 26.23% of T, with 55.31% A + T. The phylogenetic analysis by neighbor-joining (NJ) method reveals that the hybrid offspring has a closer relationship to C. altivelis.

Development of EST-Molecular Markers from RNA Sequencing for Genetic Management and Identification of Growth Traits in Potato Grouper (Epinephelus tukula)

Simple SummaryThe potato grouper is a novel aquaculture species in Taiwan. Due to the lack of genetic information concerning this species, we have developed molecular markers based on transcriptome sequencing and further characterized their association with gene diversity and growth traits of this species. Ultimately, these markers could be utilized as accurate and efficient tools for genetic management and marker-assisted selection of potato grouper with distinct growth traits.The accuracy and efficiency of marker-assisted selection (MAS) has been proven for economically critical aquaculture species. The potato grouper (Epinephelus tukula), a novel cultured grouper species in Taiwan, shows large potential in aquaculture because of its fast growth rate among other groupers. Because of the lack of genetic information for the potato grouper, the first transcriptome and expressed sequence tag (EST)-derived simple sequence repeat (SSR) and single nucleotide polymorphism (SNP) markers were developed. Initially, the transcriptome was obtained from seven cDNA libraries by using the Illumina platform. De novo transcriptome of the potato grouper yielded 51.34 Gb and 111,490 unigenes. The EST-derived SSR and SNP markers were applied in genetic management, in parentage analysis, and to discover the functional markers of economic traits. The F1 juveniles were identified as siblings from one pair of parents (80 broodstocks). Fast- and slow-growth individuals were analyzed using functional molecular markers and through their association with growth performance. The results revealed that two SNPs were correlated with growth traits. The transcriptome database obtained in this study and its derived SSR and SNP markers may be applied not only for MAS but also to maintain functional gene diversity in the novel cultured grouper.

The complete mitochondrial genome of the hybrid grouper Epinephelus moara (♀)×Epinephelus tukula (♂), and phylogenetic analysis in subfamily Epinephelinae

The mitochondrial genome (mitogenome) of hybrid grouper Epinephelus moara (♀)×Epinephelus tukula (♂), a new hybrid progeny, can provide valuable information for analyzing phylogeny and molecular evolution. In this study, the mitogenome was analyzed using PCR amplification and sequenced, then the phylogenetic relationship of E. moara (♀)×E. tukula (♂) and 35 other species were constructed using Maximum Likelihood and Neighbor-Joining methods with the nucleotide sequences of 13 conserved protein-coding genes (PCGs). The complete mitogenome of E. moara (♀)×E. tukula (♂) was 16 695 bp in length, which contained 13 PCGs, 2 rRNA genes, 22 tRNA genes, a replication origin and a control region. The composition and order of these genes were consistent with most other vertebrates. Of the 13 PCGs, 12 PCGs were encoded on the heavy strand, and ND6 was encoded on the light strand. The mitogenome of the E. moara (♀)×E. tukula (♂) had a higher AT nucleotide content, a positive AT-skew and a negative GC-skew. All protein initiation codons were ATG, except for COX and ND4 (GTG), ATP6 (CTG), and ND3 (ATA). ND2, COXII, ND3, ND4 and Cytb had T as the terminating codon, COXIII’s termination codon was TA, and the remaining PCGs of that were TAA. All tRNA genes, except for the lacking DHU-arm of tRNASer(AGN), were predicted to form a typical cloverleaf secondary structure. In addition, sequence similarity analysis (99% identity) and phylogenetic analysis (100% bootstrap value) indicated that the mitochondrial genome was maternally inherited. This study provides mitogenome data for studying genetic, phylogenetic relationships and breeding of grouper.

Metamorphosis and skeletal development of hybrid Epinephelus awoara (♀) and Epinephelus tukula (♂) progenies

Here, we explored the metamorphosis and skeletal development of hybrids between Epinephelus awoara (♀) and Epinephelus tukula (♂) (EAT). Currently, many varieties with good characters have been produced by cross breeding, which plays an important role in the development of aquaculture. However, few basic studies have focused on the developmental biology of hybrid progeny. We studied the morphological characteristics and body structure of larvae and juveniles of the hybrid and measured their body length. The results showed that the metamorphosis process of the hybrid grouper was comparable to that of other groupers. Moreover, using whole-mount bone-staining technology, the ontogeny and ossification of the cranium, appendage skeleton and vertebral column were observed and described in the larvae and juveniles. Newly hatched larvae did not have a skeleton. Head cartilage and the pectoral fin developed at 3 days after hatching (DAH), and the total length (TL) was 2.74 ± 0.06 mm. Cartilage of the dorsal fin and pelvic fin developed at 15 DAH (3.90 ± 0.97 mm TL). The vertebral column and caudal fin cartilage appeared at 18 DAH (4.69 ± 0.58 mm TL). Cartilage was observed in the anal fin at 22 DAH (6.16 ± 1.76 mm TL). The second dorsal fin spine and pelvic fin spine were fully ossified between 24 and 26 DAH (8.01 ± 1.41–9.29 ± 1.64 mm TL). The first skeletal part that completed ossification was the pelvic fin, which occurred at the 44 DAH (24.64 ± 3.63 mm TL). The vertebral column was fully ossified at 47 DAH (29.70 ± 1.97 mm TL). The dorsal fin and anal fin were ossified at 51 DAH (34.64 ± 1.92 mm TL) and the cephalic skeleton, caudal fin and pectoral fin were fully ossified at 68 DAH (41.89 ± 2.16 mm TL). These results provide abundant biological data on the metamorphosis and skeletal development of larvae and juvenile groupers, as well as analysis of the growth and survival rate advantage of hybrid offspring.

Characterization of the complete mitochondrial genome of the hybrid grouper Epinephelus akaara ♀ × Epinephelus tukula ♂, with its phylogenetic analysis

Epinephelus akaara ♀ × Epinephelus tukula ♂ is an economically important fish. The mitochondrial genome of the hybrid grouper had a double-stranded DNA molecule with the length of 16,928 bp and consists of 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes, and a control region. The gene composition of the hybrid grouper mitochondrial genome was similar to that of most other vertebrates. Furthermore, phylogenetic analysis by maximum-likelihood (ML) method, based on the nucleotide sequences of 13 protein-coding genes, showed that the hybrid grouper has the closer relationship to Epinephelus akaara and confirmed that the mitochondrial genome is maternally inherited.

Review of the Japanese records of an endangered grouper, Epinephelus tukula, with comments on its population status (Teleostei, Serranidae).

The Potato Grouper, Epinephelus tukula, is relatively rare worldwide. Records from the northernmost part of its range (Japan) have been few, resulting in a “Critically Endangered” listing on the Red List for Japan. The Japanese records were revised by examining literature, new specimens, photographs, and the internet, and a continuous distribution pattern from the tropical Ryukyu Islands (including adult individuals) to temperate regions affected by the Kuroshio Current were delineated; this suggests the species inhabits tropical Japan and can spread to temperate regions via the warm current. The species possibly reproduces in Japanese waters but further reproductive ecology research is required.

The complete mitochondrial genome of the Epinephelus moara (Osteichthyes: Ephippidae)

We presented the complete mitochondrial genome of the Epinephelus moara in this study. The mitochondrial genome is 16,696 bp long and consists of 13 protein-coding genes, two rRNA genes, 22 tRNA genes and a control region. The gene order and composition of Epinephelus tukula mitochondrial genome was similar to that of most other vertebrates. The nucleotide compositions of the light strand are 26.45% of A, 16.09% of C, 28.60% of T and 28.86% of G. With the exception of the NADH dehydrogenase subunit 6 (ND6) and eight tRNA genes, all other mitochondrial genes are encoded on the heavy strand.

The complete mitochondrial genome of the Platax teira (Osteichthyes: Ephippidae)

We presented the complete mitochondrial genome of the Platax teira in this study. The mitochondrial genome is 16,561 bp long and consists of 13 protein-coding genes, two rRNA genes, 22 tRNA genes and a control region. The gene order and composition of Epinephelus tukula mitochondrial genome was similar to that of most other vertebrates. The nucleotide compositions of the light strand are 28.80% of A, 31.16% of C, 24.44% of T and 15.60% of G. With the exception of the NADH dehydrogenase subunit 6 (ND6) and seven tRNA genes, all other mitochondrial genes are encoded on the heavy strand.

The complete mitochondrial genome of the Epinephelus tukula (Perciformes, Serranidae)

The complete mitochondrial genome of the Epinephelus tukula was presented in this study. The mitochondrial genome is 16,503 bp long and consists of 13 protein-coding genes, two rRNA genes, 22 tRNA genes and a control region. The gene order and composition of Epinephelus tukula mitochondrial genome was similar to that of most other vertebrates. The nucleotide compositions of the light strand are 28.37% of A, 29.00% of C, 26.36% of T and 16.26% of G. With the exception of the NADH dehydrogenase subunit 6 (ND6) and seven tRNA genes, all other mitochondrial genes are encoded on the heavy strand.

Coexistence of Low Coral Cover and High Fish Biomass at Farquhar Atoll, Seychelles

We report a reef ecosystem where corals may have lost their role as major reef engineering species but fish biomass and assemblage structure is comparable to unfished reefs elsewhere around the world. This scenario is based on an extensive assessment of the coral reefs of Farquhar Atoll, the most southern of the Seychelles Islands. Coral cover and overall benthic community condition at Farquhar was poor, likely due to a combination of limited habitat, localized upwelling, past coral bleaching, and cyclones. Farquhar Atoll harbors a relatively intact reef fish assemblage with very large biomass (3.2 t ha−1) reflecting natural ecological processes that are not influenced by fishing or other local anthropogenic factors. The most striking feature of the reef fish assemblage is the dominance by large groupers, snappers, and jacks with large (>1 m) potato cod (Epinephelus tukula) and marbled grouper (E. polyphekadion), commonly observed at many locations. Napoleon wrasse (Cheilinus undulatus) and bumphead parrotfish (Bolbometopon muricatum) are listed as endangered and vulnerable, respectively, but were frequently encountered at Farquhar. The high abundance and large sizes of parrotfishes at Farquhar also appears to regulate macroalgal abundance and enhance the dominance of crustose corallines, which are a necessary condition for maintenance of healthy reef communities. Overall fish biomass and biomass of large predators at Farquhar are substantially higher than other areas within the Seychelles, and are some of the highest recorded in the Indian Ocean. Remote islands like Farquhar Atoll with low human populations and limited fishing pressure offer ideal opportunities for understanding whether reefs can be resilient from global threats if local threats are minimized.

Vaccination of grouper broodfish (Epinephelus tukula) reduces the risk of vertical transmission by nervous necrosis virus

Nervous necrosis virus (NNV) has caused mass mortality in many species of cultured fish at larval stage. Strong evidence of vertical transmission of NNV has been reported in the carrier broodstock of striped jack and sea bass. An effective immunization program was developed and monitored in adult groupers (Epinephelus coioides) with average body weight of 1.35kg. The highest neutralizing antibody titers were found in the fish intramuscularly injected with adjuvanted NNV vaccine at 109TCID50kg−1, and the enhanced 2-fold neutralization activity could sustain up to 17 months post-vaccination (mpv). An immunization program was applied in the broodstocks of grouper (Epinephelus tukula) with body weight of 35–60kg. The levels of NNV-specific antibodies detected, from 1 to 5 mpi, in the homogenates of the eggs from the vaccinated broodfish were elevated than that from non-vaccinated fish. By nested RT-PCR, NNV was detectable in the eggs from the non-vaccinated fish at Month 5, but not in the eggs from vaccinated fish. It is therefore suggested that vaccination will be a potentially practical measure to reduce the risk of vertical transmission of NNV of grouper broodfish under stress of repeated spawning.

Induced sex change, spawning and larviculture of potato grouper, Epinephelus tukula

The potato grouper ( Epinephelus tukula) is a new aquaculture species with high economic potential. This is the first report of induced sex change, reproduction and larval rearing in this species. The smallest body size at which mature females were observed was 90 cm in total length and 16 kg in body weight. The diameter of tertiary yolk globule stage of oocytes was 505±10 μm for 16–24 kg individuals. Larger oocytes (552±13 μm) were obtained from individuals at 24 kg body weight. Implantation with an androgen mixture (1000 μg/kg body weight) containing testosterone, 17α-methyltestosterone, and testosterone propionate in equal ratios, was applied to female groupers for the induction of sex change in March. Sex change had occurred by 30 days after androgen implantation, and the male ratio reached 66.7% by day 70. Natural mating and spawning activity were found in females and sex-changed males in April. The fertilized eggs were hatched and reared successfully with a series of live foods. Metamorphosis occurred and larvae became juveniles with spots and skin pigmentation by 29.3 mm body length, with complete reduction in the pelvic and dorsal fins by 33 days after hatch.