Molecular cloning of GnRH1 gene and GTH cDNAs of the protogynous longtooth grouper, Epinephelus bruneus

In teleosts, gonadotropin-releasing hormone (GnRH) and gonadotropin hormone (GTH) play important roles in regulating gonadal development and maturation. In Southeast Asia, the longtooth grouper, Epinephelus bruneus, is a commercially important aquaculture fish. In this study, we cloned and characterized the longtooth grouper GnRH1 gene and cDNAs of three gonadotropin subunits (GTHα, FSHβ, LHβ). The GnRH1 gene of longtooth grouper was 4, 032 bp long, and contained four exons, 61, 151, 99, and 423 bp long. GTHα, FSHβ, and LHβ cDNAs were 509, 576, and 579 bp, respectively. Phylogenetic and Southern hybridization analyses revealed that the longtooth grouper GTH subunits were evolutionarily close to those of groupers and are one-copy genes. RT-PCR analyses showed that GTH subunit mRNAs were expressed at a higher level in the pituitary glands of immature fish than in those of mature fish, suggesting a role in gonadal maturation.     

Complete mitochondrial genome of Trypauchen vagina (Perciformes, Gobioidei)

The complete mitochondrial genome of Trypauchen vagina was determined first. The genome is 16,686 bp in length and consists of 13 protein-coding genes, 22 tRNA genes, 2 ribosomal RNA genes, and 2 main non-coding regions [the control region (CR) and the origin of the light strand replication], the gene composition and order of which was similar to most other vertebrates. The overall base composition of T. vagina is T 27.6%, C 27.6%, A 29.5%, and G 15.3%, with a slight A+T bias of 57.1%. In addition to the discrete and conserved sequence blocks, an incomplete tandem repeat unit is detected within the CR. This mitogenome sequence data would play an important role in population genetics and phylogenetic analysis of the Gobioidei.     

Complete mitochondrial genome of Oxuderces dentatus (Perciformes, Gobioidei)

The complete mitochondrial genome (mitogenome) of Oxuderces dentatus was determined first. The genome was 17,116?bp in length and consisted of 13 protein-coding genes, 22 tRNA genes, 2 ribosomal RNA genes, and 2 main non-coding regions [the control region (CR) and the origin of the light strand replication], the gene composition and order of which was similar to most other vertebrates. The overall base composition of the heavy strand was T 27.9%, C 26.8%, A 30.2%, and G 15.1%, with a slight A+T bias of 58.1%. In addition to the discrete and conserved sequence blocks, unusual long tandem repeat unit (three 150-bp tandem repeat units and an incomplete copy of 146?bp) was also detected within CR. This mitogenome sequence data would play an important role in population genetics and phylogenetic analysis of the Gobioidei.     

Complete mitochondrial genome of blackchin tilapia Sarotherodon melanotheron (Perciformes, Cichlidae)

Blackchin tilapia, Sarotherodon melanotheron, is a highly salt-tolerant species in tilapias. In this paper, the complete mitochondrial genome of S. melanotheron was determined first. The mitogenome (16,627 bp) had the typical vertebrate mitochondrial gene arrangement, including 13 protein-coding, 22 tRNA, 2 rRNA genes, and 1 putative control region. It shared 95.1%, 93.2%, and 92.2% mitogenome sequence with Oreochromis aureus, Oreochromis niloticus, and Oreochromis mossambicus, respectively.     

Complete mitochondrial genome of black porgy Acanthopagrus schlegelii (Perciformes, Sparidae)

Black porgy, Acanthopagrus schlegelii, is a marine protandrous hermaphrodite and belongs to one of the most important species commercialized for food in various areas of Asia. In this study, the complete mitochondrial genome of A. schlegelii has been determined. The mitogenome was 16,649 bp in length and contained 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes and 2 non-coding regions. It shared 90.2%, 82.3%, and 82.1% mitogenome sequence with Acanthopagrus latus, Parargyrops edita, and Pagrus major, respectively.     

Four species of Pseudorhabdosynochus (Monogenea: Diplectanidae) from the camouflage grouper Epinephelus polyphekadion (Perciformes: Serranidae) off New Caledonia

Gill diplectanid monogeneans from the camouflage grouper Epinephelus polyphekadion (Bleeker) collected in the coral reef lagoon of New Caledonia, South Pacific, comprise four species. Very few monogeneans were found in most fish examined. Pseudorhabdosynochus dionysos n. sp. has a sclerotised vagina with a robust trumpet, a robust primary canal and two chambers of similar size; it is close to P. bacchus Sigura, Chauvet & Justine, 2007. P. viscosus n. sp. has a sclerotised vagina with a robust trumpet, long primary canal with an extremely thin wall and two small chambers, and a male quadriloculate organ with a characteristic thickening at the extremity of its cone. P. crassus n. sp., the most abundant species, has a sclerotised vagina with a thin-walled trumpet, thin-walled primary canal which is always coiled anteriorly and two small chambers. P. huitoe Justine, 2007, P. manifestus Justine & Sigura, 2007 and P. crassus have very similar sclerotised vaginae; however, species of this 'huitoe complex' can be distinguished by measurements of the haptoral hard parts. A few diplectanid specimens found in a single specimen of E. polyphekadion were attributed to P. huitoe, a species originally described from E. maculatus (Bloch) and also rarely found in E. cyanopodus Richardson in New Caledonia; specimens from these three fish species are morphologically indistinguishable.     

Early development of dorsal and pelvic fins and their supports in hatchery-reared red-spotted grouper, Epinephelus akaara (Perciformes: Serranidae)

Early morphogenesis of dorsal and pelvic fins and their supports in the larval and juvenile red-spotted grouper, Epinephelus akaara, was examined using a hatchery-reared series. The dorsal spine anlage first appeared suspended in the middle part of the finfold at ca. 2.5 mm TL. Dorsal and pelvic supports appeared by the time the fish reached ca. 3 mm and started to ossify at ca. 3.5 mm. Elongated spines and their supports developed synchronously in both dorsal and pelvic fins. The formation of dorsal fin supports proceeded from anterior to posterior. The ossification of supports was completed by ca. 33 mm. Spinelets on the second dorsal spine and pelvic spine appeared by ca. 3 mm. In specimens larger than 36 mm, all spinelets on the second dorsal spine and pelvic spine had disappeared. The maximum size of the second dorsal spine and pelvic spine lengths relative to TL were ca. 45% and 44% at 3.3 mm in fish size, respectively. Thereafter, their proportions decreased gradually. Considering the order of development of the elongated spines and mucous cells in the early life stages, the elongated spines might function as antipredator devices. Received: June 20, 2000 / Revised: April 28, 2001 / Accepted: June 11, 2001     

Subtle population genetic structure in the Hawaiian grouper, Epinephelus quernus (Serranidae) as revealed by mitochondrial DNA analyses

The endemic Hawaiian grouper, Epinephelus quernus , is a commercially important species experiencing intense fishing pressure in part of its distributional range. We examined population genetic structure with 398 base pairs of the mitochondrial control region across a large portion of the range of E. quernus , spanning approximately 2000 km of the Hawaiian archipelago. Examination of genetic diversity shows that Gardner Island, situated midway along the island chain, harbours the most diverse haplotypes. F -statistics and Bayesian estimates of migration also reveal the mid-archipelago as genetically differentiated, where the first significant break among adjacent pairs of populations lies between the islands of Nihoa and Necker. Most island comparisons beyond Necker and Gardner to the north-west and among the lower five islands to the south-east show little to no genetic differences. Evidence of historical population expansion across the islands was also found by Maximum Likelihood analyses. The results suggest that management should be structured to reflect the genetic differentiation and diversity in the mid-archipelago, the patterns of which may be associated with oceanic current patterns.  © 2004 The Linnean Society of London, Biological Journal of the Linnean Society, 2004, 81 , 449–468.     

Complete mitochondrial genome of the rabbitfish Siganus fuscescens (Perciformes, Siganidae).

We determined the complete nucleotide sequence of the mitochondrial genome for the rabbitfish Siganus fuscescens (Perciformes, Siganidae). This mitochondrial genome, consisting of 16,491 base pairs (bp), included 13 protein-coding genes, 2 ribosomal RNAs, 22 transfer RNAs, and a noncoding control region similar those found in other vertebrates; the gene order was identical to that of typical vertebrates. Most of the genes of S. fuscescens were encoded on the H-strand, while the ND6 and eight tRNA (Gln, Ala, Asn, Cys, Tyr, Ser [UCN], Glu, and Pro) genes were encoded on the L-strand. The reading frames of ATPase 8 and 6 and those of ND4L and ND4 overlapped by ten and seven nucleotides, respectively. All mitochondrial protein-coding genes began with an ATG start codon, except for CO1, which started with GTG. Open reading frames of S. fuscescens ended with TAA (ND1, CO1, ATPase 8, ND4L, ND5 and ND6), and the remainder had incomplete stop codons, either TA (ATPase 6 and CO3) or T (ND2, CO2, ND3, ND4, and Cytb). The origin of L-strand replication in S. fuscescens was located in a cluster of five tRNA genes (WANCY) and was 34 nucleotides in length. A major noncoding region between the tRNA-Pro and tRNA-Phe genes (828 bp) was considered to be the control region (D-loop). Within this sequence, we identified a conserved sequence block characteristic of this region. The rabbitfish was grouped with Siganus canaliculatus in most parsimony analyses, which showed 100% bootstrap support for their divergence. These findings are useful for inferring phylogenetic relationships and identification within the suborder Acanthuroidei.     

Complete mitochondrial genome of three Branchiostegus (Perciformes, Malacanthidae) species: genome description and phylogenetic considerations

We cloned and sequenced the complete mitochondrial DNA (mtDNA) of three tilefishes (Branchiostegus albus, Branchiostegus argentatus, and Branchiostegus japonicus) to characterize and compare their mitochondrial genomes (mitogenomes). The mitogenomes of B. albus, B. argentatus, and B. japonicus were 16,532, 16,550, and 16,541 bp long, respectively, and all consisted of 37 genes (13 protein-coding genes, 2 ribosomal RNA, and 22 transfer RNA (tRNAs)), which are typical for vertebrate mtDNA. As in other bony fishes, most genes were encoded on the H-strand, except for the nad6 and eight tRNA genes that were encoded on the L-strand. Among the 13 protein-coding genes of all three tilefishes, 2 reading-frame overlaps were found on the same strand: atp8 and atp6 overlapped by 10 nucleotides, and nad4L and nad4 overlapped by 7 nucleotides. The identity of the nad4 gene between B. albus and B. argentatus was the lowest at 87%. Conversely, the identity of the nad6 gene between B. albus and B. japonicus was the highest at 99%. Most tRNA genes were similar in length among the three species, while the tRNA-Ser((AGY)) of B. japonicus was 9 bp longer than those of B. albus and B. argentatus. The control region of the mitogenome spanned 853, 862, and 856 bp in B. albus, B. argentatus, and B. japonicus, respectively. A maximum likelihood tree constructed using 11,035 sites contained five independent groups with bootstrap values of 100% in support of their divergence. All three tilefishes examined were clustered with the Pomacanthidae species in Group II.     

Long-term effects of passive integrated transponder (PIT) tagging on the kelp grouper Epinephelus bruneus

The effects of passive integrated transponder (PIT) tagging on the growth and survival of kelp grouper Epinephelus bruneus was examined over 1 year. The overall average mass gain for the 1 year period of the abdominal cavity tagged group was higher than the dorsal muscle tagged group. No significant differences were found in overall specific growth rate and food conversion between control and treatment groups.     

Cytogenetic examination of early embryonic development in the white grouper Epinephelus aeneus (Pisces, Serranidae)

Cytogenetic examination of early embryogenesis of the white grouper Epinephelus aeneus (Pisces, Serranidae) was conducted. All progeny from different spawnings showed various types of chromosomal aberration. Proportions of genetically abnormal embryos carrying different types of chromosomal aberrations varied significantly with specific spawning of parental fish, and ranged between 35.5 and 79%. Although the data can only be regarded as suggestive, we do, however, propose that chromosomal disorders might be considered as one of the particular genetic factors affecting survival during embryonic and early developmental stages.     

Characterization of 10 novel microsatellite loci for the brown marbled grouper, Epinephelus fuscoguttatus (Serranidae)

Epinephelus fuscoguttatus is a commercially important marine fish species in southeast Asia. Due to overfishing and water pollution, this species has been declared as near-threatened. Thus, to provide information to help maintain and preserve the species, microsatellites were developed, using an enriched genomic library method. Thirty individuals were collected from the hatchery of the Fishery Research Institute, Terengganu, Malaysia. These individuals, from four to six years old, originated from Sabah and are maintained in captive culture as broodstock. Genomic DNA was extracted from the fins of selected individuals that weighed 3-8 kg. Ten microsatellite loci were found to be polymorphic in this population, with 5 to 21 alleles per locus. Observed and expected heterozygosities ranged from 0.53 to 0.97 and 0.59 to 0.95, respectively. Only one locus deviated significantly from Hardy-Weinberg equilibrium and no significant linkage disequilibrium was found among the pairs of loci. These polymorphic microsatellite loci will be used by the Malaysian Fishery Research Institute for investigating genetic diversity and for developing breeding strategies.     

Complete mitochondrial genome of the miiuy croaker Miichthys miiuy (Perciformes, Sciaenidae) with phylogenetic consideration

The complete sequence of the 16,493 nucleotide mitochondrial genome from the single species of the family Sciaenidae, the miiuy croaker, Miichthys miiuy, was determined. The nucleotide sequences of M. miiuy mitochondrial DNA have been compared with those of three other Sciaenidae fishes. The contents of the M. miiuy mitochondrial genome are 13 protein-coding genes, two ribosomal RNA genes and 22 transfer RNA genes, and two non-coding regions (L-strand replication origin and control region), the gene order of which is identical to that observed in most vertebrates. The L-strand replication origin of M. miiuy is not pyrimidine-rich compared to those of most bony fishes. Within the control region, we identified the extended termination associated sequence domain, the central conserved sequence block domain and the conserved sequence block domain, while the typical central conserved blocks CSB-D, -E and -F could not be detected in the three other Sciaenidae species. In the ML phylogenetic analyses, the monophyly of Pseudosciaeniae was not supported, which is against with the morphological results. Collichthys niveatus is most closely related to Larimichthys polyactis, and Collichthys and Larimichthys may be merged into one genus, based on the current datasets.     

Complete mitochondrial genome of spined sleeper Eleotris oxycephala (Perciformes,Eleotridae) and phylogenetic consideration

The complete mitochondrial genome of Eleotris oxycephala was determined to be 16,527 bp in length with (A + T) content of 53%, and it consists of 13 protein-coding genes, 22 tRNAs, 2 ribosomal RNAs, and a control region. The gene composition and the structural arrangement of the E. oxycephala complete mtDNA were identical to most of other vertebrates. Phylogenetic analysis based on different sequences of species of the Gobioidei suborder and different methods showed that E. oxycephala formed a cluster with Eleotris acanthopoma and Eleotridae were divided into two clades. Furthermore, extensive taxon sampling and more molecular information are needed to confirm the phylogenetic relationships among the Gobioidei.     

Two new species of Pseudorhabdosynochus Yamaguti, 1958 (Monogenea: Diplectanidae) from the deep-sea grouper Epinephelus morrhua (Val.) (Perciformes: Serranidae) off New Caledonia

Three species of monogeneans were collected from Epinephelus morrhua, a deep-sea grouper from the external slope of the coral reef, off New Caledonia, South Pacific, and are the first parasites recorded from this fish species. Pseudorhabdosynochus morrhua n. sp. is characterised by: a sclerotised vagina with small sclerotised chambers and a short secondary canal; squamodiscs with central rows of rodlets which form closed ovals; and a scaly tegument. P. variabilis n. sp. has: a male quadriloculate organ with a characteristic structure; a sclerotised vagina in which the primary canal, secondary canal and accessory structure are very long and the different parts have various arrangements in different specimens; its squamodiscs have central rows of rodlets which form closed circles; and a smooth tegument. A prominent vaginal structure, comparable to that of P. variabilis, has been found only in P. dolicocolpos Neifar & Euzet, 2007, but the species can be distinguished by details of the vagina and other structures. A species of Haliotrema Johnson & Tiegs, 1922 (Ancyrocephalidae) is reported but not described. Specimens of each of the three species were present in similar numbers.     

Development and characterization of 32 microsatellite loci in the giant grouper Epinephelus lanceolatus (Serranidae)

An economically important marine fish species, the giant grouper Epinephelus lanceolatus (Serranidae) is widely cultured in Taiwan and costal areas of China. We isolated and characterized 32 polymorphic microsatellite loci from a CA-enriched genomic library of giant grouper. The number of alleles per locus ranged from 3 to 7, with a mean of 4.69. Observed and expected heterozygosities per locus varied from 0.387 to 1.000 and from 0.377 to 0.843, respectively. Six loci significantly deviated from Hardy-Weinberg equilibrium. After sequential Bonferroni's correction, only two loci showed deviation from Hardy-Weinberg equilibrium, and no linkage disequilibrium was found between any pair of loci. These microsatellites can be useful tools for the study of population genetics in the giant grouper.     

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.