First Report of Chromosome-Level Genome Assembly for Flathead Grey Mullet, Mugil cephalus (Linnaeus, 1758).
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ABSTRACT:
SUBMITTER: Shekhar MS
PROVIDER: S-EPMC9247318 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:Background: Treatment with recombinant gonadotropin hormones (rGths), follicle-stimulating hormone (rFsh) and luteinizing hormone (rLh), was shown to induce and complete vitellogenesis to finally obtain viable eggs and larvae in the flathead grey mullet (Mugil cephalus), a teleost arrested at early stages of gametogenesis in intensive captivity conditions. This study aimed to investigate the transcriptomic changes that occur in the ovary of females during the rGths-induced vitellogenesis. Methods: Ovarian samples were collected through biopsies from the same five females at four stages of ovarian development. RNASeq libraries were constructed for all stages studied, sequenced on an Illumina HiSeq4000, and a de novo transcriptome was constructed. Differentially expressed genes (DEGs) were identified between stages and the functional properties of DEGs were characterized by comparison with the gene ontology and Kyoto Encyclopedia. An enrichment analysis of molecular pathways was performed. Results: The de novo transcriptome comprised 287,089 transcripts after filtering. As vitellogenesis progressed, more genes were significantly upregulated than downregulated. The rFsh application induced ovarian development from previtellogenesis to early-to-mid-vitellogenesis with associated pathways enriched from upregulated DEGs related to ovarian steroidogenesis and reproductive development, cholesterol metabolism, ovarian growth and differentiation, lipid accumulation, and cell-to-cell adhesion pathways. The application of rFsh and rLh at early-to-mid-vitellogenesis induced the growth of oocytes to late-vitellogenesis and, with it, the enrichment of pathways from upregulated DEGs related to the production of energy, such as the lysosomes activity. The application of rLh at late-vitellogenesis induced the completion of vitellogenesis with the enrichment of pathways linked with the switch from vitellogenesis to oocyte maturation. Conclusion: The DEGs and enriched molecular pathways described during the induced vitellogenesis of flathead grey mullet with rGths were typical of natural oogenesis reported for other fish species. Present results add new knowledge to the rGths action to further raise the possibility of using rGths in species that present similar reproductive disorders in aquaculture, the aquarium industry as well as the conservation of endangered species.
| S-EPMC9664002 | biostudies-literature
Project description:The sustainable expansion of aquaculture relies on a sufficient supply of eggs and larvae, which are the first step of life cycle management. However, marine fish larval rearing generally depends on live feed production, which needs additional facilities and labor. The flathead grey mullet (Mugil cephalus), a promising species for aquaculture diversification, has a precocious digestive system development, supporting the feasibility of early weaning strategies. For these reasons, this study evaluated survival, growth, proximate and fatty acid composition, and gene expression of Mugil cephalus larvae reared under three different weaning protocols. Three co-feeding treatments, two with different Artemia sp. concentrations (A100 and A50, 2 and 1 Artemia sp. mL-1 day-1, respectively) and one with only rotifers administered as live feed along the feeding trial (A0), were assessed from 22 to 36 days post-hatching (dph). The A0 treatment performed better in survival (64.79 ± 7.40%) than the A100 protocol (32.46 ± 12.82%). In contrast, the larvae of the A100 treatment presented significantly higher final length (15.51 ± 0.86 mm) than those of the A0 treatment (12.19 ± 1.45 mm) and higher final weight (41.28 ± 1.48 mg) than those of the A50 and A0 treatments (31.23 ± 3.65 mg and 24.03 ± 7.99 mg, respectively). On the other hand, the expression of digestive enzyme- and somatotropic factor-related genes did not show differences between treatments. The present results support the convenience of treatment A0 in maximizing survival, as rotifers should be maintained until 30-32 dph (until a total larval length of at least 10 mm). However, to improve growth and minimize size dispersion, Artemia sp. addition is recommended from day 26 to day 29 post-hatching (total larval length of 8 to 9 mm).
| S-EPMC10215270 | biostudies-literature
Project description:Flathead gray mullet (Mugil cephalus) is a cosmopolitan mugilid species popular in fishery and aquaculture with an economic preference for all-female population. However, it displays neither sexual dimorphisms nor heteromorphic sex chromosomes. We have previously presented a microsatellite-based linkage map for this species locating a single sex determination region (SDR) on linkage group 9 (LG9) with evidence for XX/XY sex determination (SD) mechanism. In this work, we refine the critical SDR on LG9, and propose positional- and functional- candidate genes for SD. To elucidate the genetic mechanism of SD, we assembled and compared male and female genomic sequences of 19 syntenic genes within the putative SDR on mullet's LG9, based on orthology to tilapia's LG8 (tLG8) physical map. A total of 25 sequence-based markers in 12 genes were developed. For all markers, we observed association with sex in at least one of the two analyzed M. cephalus full-sib families, but not in the wild-type population. Recombination events were inferred within families thus setting the SDR boundaries to a region orthologous to ?0.9 Mbp with 27 genes on tLG8. As the sexual phenotype is evident only in adults, larvae were assigned into two putative sex-groups according to their paternal haplotypes, following a model of XY/XX SD-system. A total of 107 sex-biased differentially expressed genes in larvae were observed, of which 51 were mapped to tLG8 (48% enrichment), as compared to 5% in random control. Furthermore, 23 of the 107 genes displayed sex-specific expression; and 22 of these genes were positioned to tLG8, indicating 96% enrichment. Of the 27 SDR genes, BCCIP, DHX32A, DOCK1, and FSHR (GTH-RI) are suggested as positional and functional gene candidates for SD.
| S-EPMC7472742 | biostudies-literature
Project description:With the expansion and diversification of global aquaculture, efforts continue to develop new bio-technologies for assisted reproduction in species that present reproductive dysfunctions. Flathead grey mullet (Mugil cephalus) males held in intensive conditions in the Mediterranean region do not produce fluent milt and most females are arrested at previtellogenesis. The weekly injections of recombinant follicle stimulating hormone (rFsh) and luteinizing hormone (rLh) induced and completed vitellogenesis in treated females (n = 21), and treated males produced fluent sperm (n = 9). The application of a priming dose of 30 µg kg-1 rLh and resolving dose of 40 mg kg-1 Progesterone, or priming and resolving doses of 30 µg kg-1 rLh, resulted in the induction of maturation, ovulation, and spontaneous spawns with a spawning success of the 85% (8 of 9 females) and 100% (n = 6), respectively. The eggs collected had 63 ± 21% fertilization with embryo development and 58 ± 23% hatching. In comparison, control individuals did not show advances in gonadal development and did not produce fluent sperm. The present results confirm the possibility of controlling oogenesis from previtellogenesis to the completion of maturation and fertilised tank spawning using exclusively rFsh and rLh in a teleost species.
| S-EPMC9023507 | biostudies-literature
Project description:BackgroundThe study of speciation in the marine realm is challenging because of the apparent absence of physical barriers to dispersal, which are one of the main drivers of genetic diversity. Although phylogeographic studies using mitochondrial DNA (mtDNA) information often reveal significant genetic heterogeneity within marine species, the evolutionary significance of such diversity is difficult to interpret with these markers. In the northwestern (NW) Pacific, several studies have emphasised the potential importance of sea-level regression during the most recent glaciations as a driver of genetic diversity in marine species. These studies have failed, however, to determine whether the period of isolation was long enough for divergence to attain speciation. Among these marine species, the cosmopolitan estuarine-dependent fish Mugil cephalus represents an interesting case study. Several divergent allopatric mtDNA lineages have been described in this species worldwide, and three occur in sympatry in the NW Pacific.ResultsTen nuclear microsatellites were surveyed to estimate the level of genetic isolation of these lineages and determine the role of sea-level fluctuation in the evolution of NW Pacific M. cephalus. Three cryptic species of M. cephalus were identified within this region (NWP1, 2 and 3) using an assignment test on the microsatellite data. Each species corresponds with one of the three mtDNA lineages in the COI phylogenetic tree. NWP3 is the most divergent species, with a distribution range that suggests tropical affinities, while NWP1, with a northward distribution from Taiwan to Russia, is a temperate species. NWP2 is distributed along the warm Kuroshio Current. The divergence of NWP1 from NWP2 dates back to the Pleistocene epoch and probably corresponds to the separation of the Japan and China Seas when sea levels dropped. Despite their subsequent range expansion since this period of glaciation, no gene flow was observed among these three lineages, indicating that speciation has been achieved.ConclusionsThis study successfully identified three cryptic species in M. cephalus inhabiting the NW Pacific, using a combination of microsatellites and mitochondrial genetic markers. The current genetic architecture of the M. cephalus species complex in the NW Pacific is the result of a complex interaction of contemporary processes and historical events. Sea level and temperature fluctuations during Plio-Pleistocene epochs probably played a major role in creating the marine species diversity of the NW Pacific that is found today.
| S-EPMC3079632 | biostudies-literature
Project description:Various master key regulators (MKRs) that control a binary switch of sex determination (SD) have been found in fish; these provide an excellent model for the study of vertebrate genetic SD. The SD region in flathead grey mullet has been previously mapped to a 1 Mbp region harboring 27 genes, of which one is follicle-stimulating hormone receptor (fshr). Although this gene is involved in gonad differentiation and function, it has not been considered as an MKR of SD. We systematically investigated polymorphism in mullet fshr using DNA shotgun sequences, and compared them between males and females. Capable of encoding nonconservative amino acid substitutions, c.1732G>A and c.1759T>G exhibited association with sex on a population level (N = 83; P ≤ 6.7 × 10-19). Hence, 1732 A and 1759 G represent a male-specific haplotype of the gene, designated as "fshry." Additional flanking SNPs showed a weaker degree of association with sex, delimiting the SD critical region to 143 nucleotides on exon 14. Lack of homozygotes for fshry, and the resulting divergence from Hardy-Weinberg equilibrium (N = 170; P ≤ 3.9 × 10-5), were compatible with a male heterogametic model (XY/XX). Capable of replacing a phenylalanine with valine, c.1759T>G alters a conserved position across the sixth transmembrane domain of vertebrate FSHRs. Amino acid substitutions in this position in vertebrates are frequently associated with constant receptor activation and consequently with FSH/FSHR signaling alteration; thus, indicating a potential role of fshr as an MKR of SD.
| S-EPMC8022982 | biostudies-literature
Project description:Red sea bream iridovirus (RSIV) causes significant economic losses in the aquaculture industry. We analyzed the pathogenicity of RSIV in flathead grey mullets (Mugil cephalus), the correlation of histopathological lesions, and interspecies horizontal transmission, through immersion infection and cohabitation challenges. Flathead grey mullets, which were challenged by immersion infection, exhibited mortality at 14 and 24 days after RSIV exposure. Viral shedding in seawater peaked 2-3 days before or after the observed mortality. Specific lesions of RSIV were observed in the spleen and kidney, and the correlation between histopathological grade and viral load was the highest in the spleen. In a cohabitation challenge, flathead grey mullets were the donors, and healthy rock bream, red sea bream, and flathead grey mullets were the recipients. Viral shedding in seawater was the highest in flathead grey mullet and rock bream at 25 °C, with 106.0 RSIV copies L/g at 14 dpi. No mortality was observed in any group challenged at 15 °C, and no RSIV was detected in seawater after 30 dpi. The virus shed from RSIV-infected flathead grey mullets caused horizontal transmission through seawater. These findings suggest that rapid decision-making is warranted when managing disease in fish farms.
| S-EPMC10135084 | biostudies-literature
Project description:The black sea urchin (Arbacia lixula) is a keystone species inhabiting the coastal shallow waters of the Mediterranean Sea, which is a key driver of littoral communities' structure. Here, we present the first genome assembly and annotation of this species, standing as the first Arbacioida genome, including both nuclear and mitochondrial genomes. To obtain a chromosome-level assembly, we used a combination of PacBio high fidelity (HiFi) reads and chromatin capture reads (Omni-C). In addition, we generated a high-quality nuclear annotation of both coding and non-coding genes, by using published RNA-Seq data from several individuals of A. lixula and gene models from closely related species. The nuclear genome assembly has a total span of 607.91 Mb, being consistent with its experimentally estimated genome size. The assembly contains 22 chromosome-scale scaffolds (96.52% of the total length), which coincides with its known karyotype. A total of 72,767 transcripts were predicted from the nuclear genome, 24,171 coding, and 48,596 non-coding that included lncRNA, snoRNA, and tRNAs. The circularized mitochondrial genome had 15,740 bp comprising 13 protein-coding genes, 2 rRNA, and 22 tRNA. This reference genome will enhance ongoing A. lixula studies and benefit the wider sea urchin scientific community.
| S-EPMC11310861 | biostudies-literature
Project description:This study investigated wild caught striped mullet (Mugil cephalus) at Merritt Island National Wildlife Refuge (MINWR) for levels of 15 perfluoroalkyl acids (PFAA) in tandem with individual fecundity measurements (Oocyte sub-stage 2 late, n=42) and oocyte reproductive stages (Stages 1-5, n=128). PFAA measurements were quantified in striped mullet liver (n=128), muscle (n=49), and gonad (n=10). No significant negative impacts of liver PFAA burden on wild-caught, mullet fecundity endpoints were observed in this study; however, changes in PFAA were observed in the liver as mullet progressed through different sub-stages of oocyte development. Of the PFAA with significant changes by sub-stage of oocyte development, the carboxylic acids (perfluorooctanoic acid, perfluorononanoic acid, and perfluorotridecanoic acid) increased in the liver with increasing sub-stage while the sulfonic acid and its precursor (perfluorooctanesulfonic acid (PFOS) and perfluorooctanesulfonamide, respectively) decreased in the liver with increasing sub-stage of oocyte development. This is a unique find and suggests PFAA change location of compartmentalization as mullet progress towards spawning. Investigations also revealed higher than expected median muscle and gonad levels of PFOS in striped mullet collected at MINWR (9.01ng/g and 80.2ng/g, respectively).
| S-EPMC7707152 | biostudies-literature
Project description:Lactococcus garvieae is an important pathogen of fish, associated with high rates of mortality and infection recurrence in summer or stressful conditions. Chronic infection and disease recurrence have also been reported to be associated with biofilms. However, the impact of biofilm and planktonic bacterial infection on fish immune responses remains unclear. In this study, de novo sequencing was used to compare differences of the spleen transcriptome in planktonic- and biofilm-infected mullets. Among the 181,024 unigenes obtained, 3,392 unigenes were associated with immune response genes. Comparative analysis of the gene expression between infection with the L. garvieae planktonic type and biofilm type identified a total of 3,120 and 3,489 differentially expressed genes in response to planktonic and biofilm infection, respectively, of which 1,366 and 1,458 genes were upregulated, and 1,754 and 1,458 genes were downregulated, respectively. Gene ontology enrichment analysis of immune genes identified genes involved in the complement system, toll-like receptor signaling, and antigen processing, which were further verified by qPCR. Additionally, genes encoding TLR2, IL-1β, TNF-α, C7, and MHC class II peptides were downregulated in response to biofilm infection. Importantly, the results show that biofilm infection induces a different immune pathway response compared with planktonic bacterial infection and, furthermore, illustrates that the prevention of biofilm formation may be a necessary and new strategy for controlling bacterial infection in aquaculture.
| S-EPMC9168659 | biostudies-literature