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Norethindrone (NET) is a widely used synthetic progestin, which appears in water environments and threatens aquatic organisms. In this study, marine medaka (Oryzias melastigma) larvae were exposed to 7.6 and 80.1 ng/L NET for 190 days. The effects of NET on growth, sex differentiation, gonad histology and transcriptional expression profiles of hypothalamic-pituitary-gonadal (HPG) axis-related genes were determined. The results showed that exposure to 80.1 ng/L NET caused an all-male marine medaka population and significantly decreased the growth of males. Exposure to 7.6 ng/L NET increased the ratio of males/females in the marine medaka population, decreased the growth of males and delayed the ovary maturation in females. However, the sperm maturation was accelerated by 7.6 or 80.1 ng/L NET. In females, the transcription levels of cytochrome P450 aromatase (cyp19a1a) and progesterone receptor (pgr) in ovaries, glucocorticoid receptor (gr) and vitellogenin (vtg) in livers were suppressed after exposure to 7.6 ng/L NET, which may cause delayed ovary maturation. In males, NET significantly decreased the transcription levels of follicle stimulating hormone β (fshβ) and Luteinizing hormone β (lhβ)in the brain, Estrogen receptor β (erβ)，gr and pgr in the liver, and vitellogenin receptor (vtgr) in the testes, while NET of 80.1 ng/L led to a significant up-regulation of steroidogenic acute regulatory protein (star) in the testes of males. These results showed that NET could influence growth, sex differentiation and gonadal maturation and significantly alter the transcriptional expression levels of HPG axis-related genes.

To understand the left-right asymmetry of vertebrate eyes, this study measured the central corneal thickness (CCT) of

Norethisterone (NET) is one of the earliest synthetic progestins. Its widespread and long-term use means that NET is often detected on the surface and in groundwater samples, which may cause harm t...

Zebrafish have emerged as an attractive animal model for studying nonalcoholic fatty liver disease (NAFLD). However, little is known about the cell types and intercellular interactions in zebrafish liver. Here, we established a liver atlas that consists of 10 cell types using single-cell RNA sequencing. By examining the heterogeneity of hepatocytes and analyzing the expression of NAFLD-associated genes in the specific cluster, we provide a potential target cell model to study NAFLD. Additionally, our analysis identified two distinct resident macrophages with inflammatory and noninflammatory functions and characterized the successive stepwise development of T cell subtypes in the liver. Importantly, we uncovered possible molecular mechanisms and revealed the central regulation of macrophages on target cells of fatty liver by analyzing the cellular interaction between hepatocytes and immune cells. Our data provide valuable information for future research on NAFLD in zebrafish.

Norethisterone (NET), one of the synthetic progestins, is detected with increasing frequency in the water environment and distributed in the ocean, with a potential toxicity risk to marine organisms. However, current studies on the adverse effects of progestins (including NET) in aquatic environments have focused on freshwater organisms, mainly fish. In the present, marine medaka (Oryzias melastigma) larvae were exposed to 91.31 ng/L NET for 10 days, and then the swimming behavior, oxidation-antioxidant-related enzyme activities, sex and thyroid hormone levels, and the gene transcription patterns of the larvae were measured. After NET treatment, medaka larvae were raised in artificial seawater until 5 months of age, and the sex ratio was counted. Ten-day exposure to 91.31 ng/L NET inhibited swimming behavior, of marine medaka larvae, which showed that the time in the resting state was significantly prolonged, while the time in the large motor state was significantly reduced; disrupted oxidative-antioxidant system, significantly up-regulated the enzymatic activities of reactive oxygen species (ROS), malondialdehyde (MDA), and glutathione peroxidase (GSH-Px); affected the hormone levels of larvae, lowered 11- keto testosterone (11-KT) and triiodothyronine (T3) concentrations. RNA-seq results showed that 91.31 ng/L NET exposure for 10 days changed the transcript levels of 275 genes, of which 28 were up-regulated and 247 were down-regulated. Differentially expressed genes (DEGs) were mainly significantly enriched in piwi interacting RNA (piRNA), gonadal development, gametogenesis, and steroidogenesis biological processes, etc. After removing NET exposure and returning to breeding for 140 days, a significant increase in male proportions (69.67%) was observed in sexually mature medaka populations in the NET-treated group. These results show that exposure to 91.31 ng/L NET for 10 days can lead to various adverse effects on marine medaka larvae. These findings shed light on the potential ecological risks of synthetic progestins to marine organisms.

Ghana’s waters are biologically diverse with different fish species due to different ecological habitats and niches harboring several cryptic fish species. However, the fish production has reduced over the past decade; hence an urgent conservation and management strategies are required to save Ghanaian fishery such as accurate identification of species to formulate species-specific conservation and management strategies. Molecular method of fish identification, DNA barcoding, has proven its efficacy in species identification for both freshwater and marine species. In recent years, DNA barcoding has been accepted as a bio-identification system for living organisms globally. This system is fast and produces accurate species identification by using a short DNA sequence marker from a standard region of the DNA sequence of an organism’s genome to identify it as belonging to a particular individual or species based on Cytochrome C Oxidase type I (COI/ Cox 1) gene instead of the whole genome. Unfortunately, unlike the developed countries, this molecular method of fish identification is new in Ghana. This review article aims to examine the issues regarding fish identification and the need for DNA barcoding as a tool for taxonomic identification, grouping, and naming of fish species in Ghana. Also, this review takes a look at the current status and future direction of DNA barcoding fisheries in Ghana. In addition, the benefits of DNA Barcoding in fishery management and conservation are discussed. Key words: DNA barcoding, Ghana, marine species, current status, management, conservation.

Bisphenol AF (BPAF) is one of the substitutes for bisphenol A (BPA), which has endocrine-disrupting, reproductive and neurological toxicity. BPAF has frequently been detected in the aquatic environment, which has been a long-term threat to the health of aquatic organisms. In this study, female marine medaka (Oryzias melastigma) were exposed to 6.7 μg/L, 73.4 μg/L, and 367.0 μg/L BPAF for 120 d. The effects of BPAF on behavior, growth, liver and ovarian histology, gene transcriptional profiles, and reproduction of marine medaka were determined. The results showed that with the increase of BPAF concentration, the swimming speed of female marine medaka showed an increasing trend and then decreasing trend. BPAF (367.0 μg/L) significantly increased body weight and condition factors in females. BPAF (73.4 μg/L and 367.0 μg/L) significantly delayed oocyte maturation. Exposure to 367.0 μg/L BPAF showed an increasing trend in the transcript levels of lipid synthesis and transport-related genes such as fatty acid synthase (fasn), sterol regulatory element binding protein (srebf), diacylglycerol acyltransferase (dgat), solute carrier family 27 member 4 (slc27a4), fatty acid-binding protein (fabp), and peroxisome proliferator-activated receptor gamma (pparγ) in the liver. In addition, 6.7 μg/L BPAF significantly down-regulated the expression levels of antioxidant-related genes [superoxide dismutase (sod), glutathione peroxidase (gpx), and catalase (cat)], and complement system-related genes [complement component 5 (c5), complement component 7a (c7a), mannan-binding lectin serine peptidase 1 (masp1), and tumor necrosis factor (tnf)] were significantly up-regulated in the 73.4 and 367.0 μg/L groups, which implies the effect of BPAF on the immune system in the liver. In the hypothalamic-pituitary-ovarian axis (HPG) results, the transcription levels of estrogen receptor α (erα), estrogen receptor β (erβ), androgen receptor (arα), gonadotropin-releasing hormone 2 (gnrh2), cytochrome P450 19b (cyp19b), aromatase (cyp19a), and luteinizing hormone receptor (lhr) in the brain and ovary, and vitellogenin (vtg) and choriogenin (chg) in the liver of 367.0 μg/L BPAF group showed a downward trend. In addition, exposure to 367.0 μg/L BPAF for 120 d inhibited the spawning behavior of marine medaka. Our results showed that long-term BPAF treatment influenced growth (body weight and condition factors), lipid metabolism, and ovarian maturation, and significantly altered the immune response and the transcriptional expression levels of HPG axis-related genes.

Bisphenols (BPA, BPF, and BPAF) are widely present in the aquatic environment and have various adverse effects on aquatic organisms. However, their hepatic toxicity in marine fish is not fully understood. Hence, we examined the growth parameters, histological features, antioxidant defense mechanisms, and gene expression profiles in the livers of marine medaka after exposure to single and combined bisphenols for 70 days. The final body weight and final body length of males exposed to BPAF were significantly higher than those in the control group, and the survival rate was significantly lower. Bisphenol exposure led to vacuolization and local lesions in the liver, especially in the BPAF group, and altered antioxidant enzyme activity in the liver, leading to oxidative stress. In addition, after bisphenol exposure, marine medaka showed anxiolytic effects and a significant reduction in swimming distance compared with that in the control group. As determined by RNA-seq, bisphenol exposure altered multiple biological pathways in the liver, such as fatty acid biosynthesis, fatty acid metabolism, and ribosome biogenesis pathways, with significant changes in gene expression levels. In particular, chgs and vtgs were significantly up-regulated after BPAF exposure, suggesting an estrogenic effect. Overall, bisphenols can adversely affect the growth and metabolism of marine medaka. BPF and BPAF may not be ideal substitutes for BPA.

In this study, combining the liver transcripts from both sexes by RNA-Seq with DNA sequences by conventional PCRs, we have determined the complete mitogenome of Hainan medaka Oryzias curvinotus collected from the mangrove seawater of the Leizhou Peninsula in tropical South China (Accession no.: KY364884). The mitochondrial genome is 16,676 bp, and its content and structure are highly homologous to those of other teleostean fishes, including 13 protein-coding genes (PCGs), 2 rRNAs, 22 tRNA and 1 control region. Among the PCGs, ATG is used as the initiation codon, except for GTG in COI gene. There are 7 overlapping genes with overlap lengths ranging from 1 to 10 nucleotides (nt), while ten intergenic regions with a total of 66 nt and a maximum interval of 37 nt between tRNAAsn and tRNACys. Moreover, the data from RNA-Seq shows that the significant differences exist in the expression patterns of mitogenomes between male and female.

Quantitative real-time PCR (qRT-PCR) is a powerful and sensitive methodology to analyze expression of target genes. qRT-PCRs rely on selecting suitable reference gene. In the present study, 17 candidate reference genes in Hainan medaka, Oryzias curvinotus, were selected, and candidate genes were studied for mRNA expression levels and stabilities in different tissues and at different stages of embryonic development. Expression patterns were analyzed using RefFinder and geNorm to test for suitability of the gene as a reference gene. RefFinder analysis ranked the stability of the reference genes in the following order (Top 5): rps4x > eef1b > 60srp > dcakd > eef1a in different tissues, and mrp13 > rps20 > actb > sbds > adp in embryonic development. Similarly, geNorm selected eef1b and rps4x as the two optimal reference genes for normalizing target genes expression in Hainan medaka. The results demonstrated that the expression of reference genes is variable under different experimental conditions, highlighting the importance of validating the stability and optimal number of reference genes before doing the qRT-PCR experiment.

The effect of estrogens on Oryzias curvinotus juveniles were investigated by sequencing the transcriptome of O. curvinotus juveniles exposed to 17 β - estradiol for 24 h. A total of 69,071,524 and 71,210,528 raw reads were obtained for the control group (NC) and 17 β - estradiol exposure group (E2), respectively. After de novo assembly, total 133,210 unigenes were identified, and 85,837 unigenes (64.44% of 133,210) were annotated. Analysis of the transcriptome showed that exposure to 2 μg/L 17 β - estradiol led to the up-regulation of 19 genes and down-regulation of 18 genes. The eef1b and rps4x was most suitable as controls for quantitative real-time PCR (qPCR) using Reffinder. Different expression genes enrichment analysis found that exposed to 2 μg/L 17 β - estradiol affected various physiological processes, including spliceosome, phototransduction, amino sugar and nuclear sugar metabolism, hypotaurine metabolism, and renin-angiotensin system, etc. Exposing O. curvinotus juveniles to increasing concentrations of 17 β - estradiol (2 ng/L, 20 ng/L, 200 ng/L and 2 μg/L) led to significant up-regulation of vitellogenins (vtgs) and choriogenins (chgs) mRNA expression. The present study is the first high-throughput transcriptome sequencing of O. curvinotus juveniles, which will be useful for future functional analysis of genes related to environmental estrogen exposed, and development of biomarkers.

Opsin is a fellow of the G protein-coupled receptors (GPCRs) superfamily. It can be divided into visual and non-visual opsin according to whether it is directly involved in visual imaging. Opsin plays an important role in visual image formation and the regulation of non-image forming functions such as circadian entrainment in the growth, development and evolution of fish. Crimson snapper belongs to Perciforme mainly found in the Indo-West Pacific and the South China Sea. It is one of the most influential economic fishes in the South China Sea. In order to study the existence and expression of opsin gene in Crimson snapper, we sequenced the genome and tissue sample transcriptome of Crimson snapper. In this study, 32 opsin genes were identified from the genome of Crimson snapper. The length of these genes ranged from 1061 bp to 86203 bp and were distributed on 15 different chromosomes. The analysis of opsin gene family of Crimson snapper showed that the sws2 had two extra copies as compared with that of Zebrafish. Domain and motif analysis revealed that all the 32 opsin genes have seven-(pass)-transmembrane domain receptors (7TM receptors) each, and the opsin family contained 10 common motifs. The expression level of opsin gene, confirmed by RT-qPCR, was analyzed by using nine tissues transcriptome databases of Crimson snapper. The results showed that almost all opsin genes were highly expressed in the retina and brain, except opn7a and opn7b which were expressed in intestine and red skin, and almost no expression in other tissues. Our results provide a comprehensive basic knowledge for the opsin gene family of Crimson snapper, which has significance for the study of the function of opsin in Lutjanidaes.

In our recent survey, the transparent small Lacustrine goby, Gobiopterus lacustris had reported as the endemic species of Luzon, Philippines, was identified as an abundant species in mangroves of Leizhou Peninsula, China. Here, high diversity and significant differentiation of five sites of samples representing the west and east populations were revealed by mitochondrial DNA sequences. Five haplotypes of 56 cytochrome oxidase subunit I (Cox1) with the lengths of 623 base pairs (bp) have the high pairwise identity (>98.8%). Moreover, a total of 31 haplotypes for 129 partial D-loop regions were clustered into two clades corresponding to the east and west sampling sites. The strong population structure was confirmed (ΦST = 0.43017, p h = 0.880 ± 0.017) and low nucleotide diversity (p=.00484). Moreover, both the mismatch distribution analysis and neutral test of D-loop revealed that the west group might experience a recent demographic expansion. Lastly, the isolation-with-migration analysis supported the expansion and indicated that the east–west split happened at approximately 7.1 kyr ago. Given the distribution and diversity, G. lacustris could be a good model for the study of the sea-level fluctuations and coast evolution of the South China Sea.

Background Bluespotted seabream, Pagrus caeruleostictus is a benthopelagic marine species found in tropical regions and a member of the family Sparidae and genus Pagrus . In this article, a mitochondrial DNA sequence by high-throughput technique, Illumina Hiseq, was carried out on muscle of the above species and determined the complete mitogenome. Samples were obtained from species collected from the coast of Ghana, West Africa.Results The complete mitochondrial DNA sequence was 16,653 bases pairs in length (GenBank Accession number: MN319701) and comprises of 37 genes; 22 transfer RNA genes, 2 ribosomal RNA genes, 13 protein-coding genes as well as a control region as in a typical vertebrate mitochondrial DNA gene. The phylogenetic analysis showed P. caeruleostictus clustered with the clade of P. auriga. Conclusion This research will serve as the foundation for molecular genetic studies of Ghanaian fish species. Moreover, it will contribute to the phylogenetics of class Actinopterygii, order Spariformes, family Sparidae and genus Pagrus.

ABSTRCTLacustrine goby (Gobiopterus lacustris) belongs to a genus of gobies that are small in size and endemic to freshwater, brackish waters or coastal environments around the Indian and Pacific oceans. To date, there are no genomic or transcriptomic studies on G. lacustris. Here, we constructed gonadal transcriptomes of G. lacustris for the first time and identified genes that may be involved in gonadal development and reproduction. In total, 60,657,644 and 52,016,136 clean reads were obtained from ovary and testis, respectively, using Illumina sequencing. Reads were assembled into 62,573 unigenes with N50 value of 3,082 bp and a mean length of 1,869 bp. A total of 47,891 (76.53%) unigenes were annotated in at least one of the seven databases that were used in this study. In addition, 38,550 SSRs (simple sequence repeat, microsatellite) were identified from 20,517 SSR containing sequences. Gene expression patterns in the testis and ovary were compared, and 10,954 DEGs (differentially expressed genes) were identified. Of these genes, 2,383 were up-regulated in the testis and 8,571 were up-regulated in the ovary. RT-qPCR analysis of 14 selected genes showed patterns consistent with the transcriptome results. Numerous DEGs involved in gonadal development and gametogenesis were identified, including foxl2, dmrt1, cyp19a1a, inha, inhb, sycp2, zglp1, tdrp, zps and esra. Using GO and KEGG enrichment analyses, pathways involving regulation of gonadal development and gametogenesis also identified. This work represents the first gonadal transcriptomic analysis of G. lacustris and provides a valuable dataset for future research on the genes involved in reproduction of G. lacustris.

Background Seven in absentia homologs (SIAHs) comprise a family of highly conserved E3 ubiquitin ligases that play an important role in regulating signalling pathways in tumorigenesis, including the DNA damage repair and hypoxia response pathways. SIAH1 and SIAH2 have been found to function as a tumour repressor and a proto-oncogene, respectively, despite the high sequence identity of their substrate binding domains (SBDs). Ubiquitin-specific protease USP19 is a deubiquitinase that forms a complex with SIAHs and counteracts the ligase function. Much effort has been made to find selective inhibitors of the SIAHs E3 ligases. Menadione was reported to inhibit SIAH2 specifically. Methods We used X-ray crystallography, peptide array, bioinformatic analysis, and biophysical techniques to characterize the structure and interaction of SIAHs with deubiquitinases and literature reported compounds. Results We solved the crystal structures of SIAH1 in complex with a USP19 peptide and of the apo form SIAH2. Phylogenetic analysis revealed the SIAH/USP19 complex is conserved in evolution. We demonstrated that menadione destabilizes both SIAH1 and SIAH2 non-specifically through covalent modification. Conclusions The SBDs of SIAH E3 ligases are structurally similar with a subtle stability difference. USP19 is the only deubiquitinase that directly binds to SIAHs through the substrate binding pocket. Menadione is not a specific inhibitor for SIAH2. General significance The crystallographic models provide structural insights into the substrate binding of the SIAH family E3 ubiquitin ligases that are critically involved in regulating cancer-related pathways. Our results suggest caution should be taken when using menadione as a specific SIAH2 inhibitor.

In this study, combining the gonad transcripts of the both sexes by RNA-Seq with the DNA sequences by conventional PCRs, we have determined the complete mitogenome of Gobiopterus lacustris collected from the mangrove waters of the Leizhou Peninsula in tropical South China. This mitochondrial genome is 16593 bp in length and consists of 37 genes in the typical vertebrate mitochondrial gene arrangement. This study will contribute on the phylogenetics of genus Gobiopterus and the other genera of Gobiidae.

In this study, morphology observation and illumina sequencing were performed on two different coloration skins of crimson snapper (Lutjanus erythropterus), the black zone and the red zone. Three types of chromatophores, melanophores, iridophores and xanthophores, were organized in the skins. The main differences between the two colorations were in the amount and distribution of the three chromatophores. After comparing the two transcriptomes, 9200 unigenes with significantly different expressions (ratio change ≥ 2 and q-value ≤ 0.05) were found, of which 5972 were up-regulated in black skin and 3228 were up-regulated in red skin. Through the function annotation, Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis of the differentially transcribed genes, we excavated a number of uncharacterized candidate pigment genes as well as found the conserved genes affecting pigmentation in crimson snapper. The patterns of expression of 14 pigment genes were confirmed by the Quantitative real-time PCR analysis between the two color skins. Overall, this study shows a global survey of the morphological characters and transcriptome analysis of the different coloration skins in crimson snapper, and provides valuable cellular and genetic information to uncover the mechanism of the formation of pigment patterns in snappers.

High-throughput RNA-Seq affords a cost and time effective means of obtaining large numbers of genetic markers for aquatic genomics. Here, we present thousands of novel microsatellite loci developed for the pearl oyster, Pinctada martensii from the Illumina HiSeq™ 2000 library of the pearl sac. Free user-friendly bioinformatics tools were employed to screen for microsatellite loci and design appropriate primers in 102,762 unigenes with 7216 microsatellite loci identified in total, 4862 of which had flanking sequences suitable for polymerase chain reaction primer design. The 50 randomly chosen primer pairs were tested in two populations of pearl oyster (base population (POP1) and selected population (POP2), with 30 individuals of each population). All the primer pairs were amplified successfully in two populations. All loci were polymorphic in POP1, while there were 3 loci showing monomorphism in POP2. In POP1 and POP2, observed heterozygosity from 0.033 to 1.000 and 0.000 to 1.000, 19 and 16 microsatellite loci deviated significantly from Hardy–Weinberg expectations including a Bonferroni correction (P

WD40 repeat (WDR) domains are protein interaction scaffolds that represent one of the largest protein families in human, and a first WDR inhibitor—an allosteric antagonist of polycomb repressive complex 2—just entered the clinic. A systematic analysis of the CORUM database of protein complexes shows that WDR is the most represented domain in transcriptional regulation and one of the most prevalent in the ubiquitin proteasome system, two pathways of high relevance to drug discovery. Parsing the literature and the vulnerability of cancer cell lines to CRISPR knockout indicates that WDR proteins are targets of interest in oncology and other disease areas. A quantitative analysis of WDR structures reveals that druggable binding pockets can be found on multiple surfaces of these multifaceted protein interaction platforms. These data support the development of chemical probes to further interrogate WDR proteins as an emerging therapeutic target class.

Nacre, the iridescent material found in pearls and shells of molluscs, is formed through an extraordinary process of matrix-assisted biomineralization. Despite recent advances, many aspects of the biomineralization process and its evolutionary origin remain unknown. The pearl oyster Pinctada fucata martensii is a well-known master of biomineralization, but the molecular mechanisms that underlie its production of shells and pearls are not fully understood. We sequenced the highly polymorphic genome of the pearl oyster and conducted multi-omic and biochemical studies to probe nacre formation. We identified a large set of novel proteins participating in matrix-framework formation, many in expanded families, including components similar to that found in vertebrate bones such as collagen-related VWA-containing proteins, chondroitin sulfotransferases, and regulatory elements. Considering that there are only collagen-based matrices in vertebrate bones and chitin-based matrices in most invertebrate skeletons, the presence of both chitin and elements of collagen-based matrices in nacre suggests that elements of chitin- and collagen-based matrices have deep roots and might be part of an ancient biomineralizing matrix. Our results expand the current shell matrix-framework model and provide new insights into the evolution of diverse biomineralization systems.

As a highly successful mariculture candidate endemic to China, the wild genetic resource of Large yellow croaker (Larimichthys crocea) have collapsed in the northern and central East China Seas, which has impeded the wild sampling and assessment. Meanwhile, the wild population in South China Sea away from restocking and massive aquaculture is seldom reported. In this study, the complete mitochondrial control regions (CR) of 98 individuals of Naozhou stock were determined and the data indicated that the haplotype diversity of Naozhou stock (Hd ＞ 98%) is higher than all the reported values. Inconsistent with previous conclusion by traditional methods, the non-significant Snn and FST owing to the strong gene flows (Nm), as well as the cluster tree without substructure reflected the lack of population differentiation in Large yellow croaker of Naozhou stock. Moreover, the demographic history was examined by using neutrality tests and mismatch distribution analysis, which revealed that the species obey the sudden expansion model. This result should be basic file for fisheries management and assessment of croaker.

The Naihai cutlassfish (Trichiurus nanhaiensis) is an important commercial fish species. In this study, we report 25 microsatellite DNA markers for T. nanhaiensis. The number of alleles per locus ranged from 2 to 10 in a sample of 37 individuals. Observed and expected heterozygosities per locus varied from 0.300 to 1.000 and from 0.403 to 0.845, respectively. Thirteen of 25 loci showed significant departure from Hardy–Weinberg equilibrium (HWE) after sequential Bonferroni correction (P < 0.002). No significant linkage disequilibrium between pairs of loci was found. These microsatellite markers will provide powerful tools for investigating population genetic structure, population history and conservation management of T. nanhaiensis. The family Trichiuridae, including 32 species in nine genera, is generally benthopelagic on continental shelves and slopes from tropical to warm temperate waters (Nakamura and Parin 1993). Three species of genus Trichiurus were identified in South China Sea based on morphological characteristics and results of isozyme electrophoresis (Wang et al. 1992, 1993). T. nanhaiensis ranks second only behind T. haumela in tonnage of fish caught and both are important commercial species in South China Sea. So far, the fisheries biology, growth or mortality parameters and genetic structure of T. haumela have been studied, but few studies on T. nanhaiensis have been reported (Zhang et al. 1998; Chakraborty et al. 2005; Zhu and Qiu 2005; Hsu et al. 2007; Yang et al. 2007). In the present study, we developed 25 microsatellite loci isolated from a dinucleotide-enriched genomic library of T. nanhaiensis using the fast isolation by AFLP of sequences containing repeats (FIASCO) according to previous report (Zane et al. 2002). These markers should provide a tool for

The silver sillago, Sillago sihama Forsskal is naturally distributed in Indo–West Pacific: Red Sea and Knysna, South Africa to Japan and south to Australia (Wantiez 1993), and is common along beaches, sandbars, mangrove creeks and estuaries. Adults bury themselves in the sand when disturbed (McKay 1992), and feed mainly on polychaete worms, small prawns (Penaeus), shrimps and amphipods (Allen et al. 2002). This fish is found in all Chinese waters including East China Sea, Yellow Sea, Bohai Sea, South China Sea, and the Northern Bay. In China, it is a common marine food fish species, and the supply of this fish relies on capture from the wild. So far, studies of this species have focussed on ecology (Lee et al. 1981; Lu et al. 2008), morphology of early development (Wan 1996), discrimination of the genus Sillago with sagittal otolith shape (Pan and Gao 2010), and phylogenetic relationships of the genus Sillago (Xue et al. 2010; Gao et al. 2011). In the present study, we developed 66 microsatellite loci isolated from a dinucleotide-enriched genomic library of S. sihama using the fast isolation by AFLP of sequences containing repeats (FIASCO) protocol of Zane et al. (2002). These markers should provide a tool for assessing genetic diversity and population structure of wild stocks.

The phylogenetic relationships of 13 snapper species from the South China Sea have been established using the combined DNA sequences of three full-length mitochondrial genes (COI, COII and CYTB) and two partial nuclear genes (RAG1, RAG2). The 13 species (genus Lutjanus) were selected after DNA barcoding 72 individuals, representing 20 species. Our study suggests that although DNA barcoding aims to develop species identification systems, it may also be useful in the construction of phylogenies by aiding the selection of taxa. Combined mitochondrial and nuclear gene data has an advantage over an individual dataset because of its higher resolving power.

The entire mitochondrial DNA sequence (mitogenome) of Russell’s snapper (Lutjanus russellii) was determined using long PCR and primer-walking methodology, representing the first complete mitogenome accessioned for Lutjanid fishes (16,505 bp, GenBank Accession No. EF514208). The mitogenome was similar in gene composition and order to those of other vertebrates, having 37 structural genes, i.e., two ribosomal RNAs, 22 transfer RNAs, and 13 protein-coding genes. Phylogenetic analyses based on the mtDNA sequence of Russell’s snapper supported a close relationship between Lutjaninae and Caesioninae, consistent with taxonomic hypotheses based on morphology. More studies utilizing mitogenomes are needed to resolve high-level relationships among snappers. 2008 National Natural Science Foundation of China and Chinese Academy of Sciences. Published by Elsevier Limited and Science in China Press. All rights reserved.

Phylogenetic relationships of intra- and interspecies were elucidated based on complete cytochrome b (cyt b) and cytochrome c oxidase subunit II (COII) gene sequences from 12 recognized species of genus Lutjanus Bloch in the South China Sea (SCS). Using the combined data set of consensus cyt b and COII gene sequences, interspecific relationships for all 12 recognized species in SCS were consistent with Allen's morphology-based identifications, with strong correlation between the molecular and morphological characteristics. Monophyly of eight species (L. malabaricus, L. russellii, L. stellatus, L. bohar, L. johnii, L. sebae, L. fulvus, and L. fulviflamma) was strongly supported; however, the pairs L. vitta/L. ophuysenii and L. erythropterus/L. argentimaculatus were more similar than expected We inferred that L. malabaricus exists in SCS, and the introgression caused by hybridization is the reason for the unexpectedly high homogeneity.

A total of 37 microsatellite loci from the Russell’s snapper, Lutjanus russellii , were successfully isolated and characterized. Thirty-four loci were polymorphic in L. russellii samples. Twenty of the 37 markers did not differ significantly from Hardy–Weinberg expected genotype proportions. Significant linkage disequilibrium was detected in one pairwise comparison. The numbers of alleles and observed heterozygosities in polymorphic loci ranged from two to 16 and from 0.41 to 0.95, respectively. These markers will be useful for studying the population genetic structure of this species.

The experiment was conducted to assess the genetic diversity of genetically improved farmed tilapia (GIFT) in order to evaluate and preserve this strain as a germplasm resource. The experiment study focused on the genetic diversity of the newly bred F16 population of GIFT tilapia obtained from Guanghui Farm Limited Company, Huazhou (Guangdong, China) was analyzed using AFLP. 187 bands were detected with 5 pairs of AFLP primers (E-AGG/M-CTT, E-AGG/M-CTG, E-AAC/M-CAG, E-ACA/M-CTG, E-ACA/M-CAG) based on 27 individuals, and among them 163 (87.17%) were polymorphic with an average of 32.6 bands for per AFLP primer. Average Nei’s gene diversity was 0.288,6, average Shannon’s information index was 0.433,9. These results showed that the experiment group deposit had rich genetic diversity and maintained a high genetic heterozygosity, had further breeding and development value.