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Genome Analysis of Lagocephalus sceleratus: Unraveling the Genomic Landscape of a Successful Invader.

ABSTRACT: The Tetraodontidae family encompasses several species which attract scientific interest in terms of their ecology and evolution. The silver-cheeked toadfish (Lagocephalus sceleratus) is a well-known "invasive sprinter" that has invaded and spread, in less than a decade, throughout the Eastern and part of the Western Mediterranean Sea from the Red Sea through the Suez Canal. In this study, we built and analysed the first near-chromosome level genome assembly of L. sceleratus and explored its evolutionary landscape. Through a phylogenomic analysis, we positioned L. sceleratus closer to T. nigroviridis, compared to other members of the family, while gene family evolution analysis revealed that genes associated with the immune response have experienced rapid expansion, providing a genetic basis for studying how L. sceleratus is able to achieve highly successful colonisation. Moreover, we found that voltage-gated sodium channel (NaV 1.4) mutations previously connected to tetrodotoxin resistance in other pufferfishes are not found in L. sceleratus, highlighting the complex evolution of this trait. The high-quality genome assembly built here is expected to set the ground for future studies on the species biology.

SUBMITTER: Danis T

PROVIDER: S-EPMC8692874 | biostudies-literature |

REPOSITORIES: biostudies-literature

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Genome analysis of Lagocephalus sceleratus: unraveling the genomic aspects of a successful invader

Project description:Genome analysis of Lagocephalus sceleratus: unraveling the genomic aspects of a successful invader

| PRJEB46605 | ENA

The complete mitochondrial genome of Lagocephalus sceleratus (Tetraodontiformes; Tetraodontidae) and phylogenetic studies of Tetraodontidae.

Project description:The complete mitochondrial genome sequence of Lagocephalus sceleratus was determined. The complete mitochondrial genome was 16,444 bp in length and contained 13 protein-coding genes, 22 transfer RNA genes, two ribosomal RNA genes, and two non-coding region (the control region and the origin of light strand replication). The overall base composition was A 27.59%, C 31.43%, G 17.12%, T 23.85%. All protein-coding genes started with an ATG initiation codon, except COI used GTG. With the exception of ND6 and eight tRNA genes, all other genes were encoded on the heavy strand. Additionally, the phylogenetic relationship of 37 Tetraodontidae species based on the complete genome was analyzed, and the result showed that L. sceleratus was clustered with other Lagocephalus species. These results would be useful for the investigation of phylogenetic relationship, taxonomic classification and phylogeography of the Tetraodontidae.

| S-EPMC7800810 | biostudies-literature

Monthly Variation of Tetrodotoxin Levels in Pufferfish (Lagocephalus sceleratus) Caught from Antalya Bay, Mediterranean Sea.

Project description:The silver-cheeked toadfish (Lagocephalus sceleratus), an invasive alien pufferfish species that has rapidly settled throughout the Mediterranean region, poses significant threats not only to native marine species and fisheries but also to public health due to the tetrodotoxin (TTX) they harbor. In this study, TTX concentrations in L. sceleratus from Antalya Bay in the Northeastern Mediterranean Sea were investigated using Q-TOF-LC-MS on a monthly basis over a one-year period. Pufferfish were caught by angling from May 2018 to April 2019. The TTX levels in three different tissues (gonads, liver, and muscle) of 110 pufferfish in total were determined in both male and female individuals caught for 11 months. The highest TTX mean levels generally occurred in the gonads and the lowest in the muscle samples. As regards the maximum TTX contents, the highest concentrations determined were 68.2, 34.2, and 7.8 µg/g in the gonad, liver, and muscle tissues, respectively. The highest levels were generally observed in late autumn to winter (especially in November and December) in all tissues from both genders. Female individuals were generally found to be more toxic than male individuals. The TTX levels found confirm that the consumption of L. sceleratus from Antalya Bay remains dangerous throughout the year, and thus L. sceleratus constantly constitutes an important risk source for public health.

| S-EPMC10608123 | biostudies-literature

Keeping Lagocephalus sceleratus off the Table: Sources of Variation in the Quantity of TTX, TTX Analogues, and Risk of Tetrodotoxication.

Project description:The invasion of the tetrodotoxin (TTX)-bearing silver-cheeked toadfish and potential poisoning due to its consumption (tetrodotoxication) threatens public safety in the Mediterranean Sea. In this study, TTX and TTX analogues of Lagocephalus sceleratus (Gmelin, 1789) were measured using liquid chromatography tandem mass spectrometry (LC-MS/MS) in fish collected off the island of Crete (Southern Mediterranean). We tested the synergistic effect of a suite of factors potentially affecting toxins' levels and tetrodotoxication risk using general and generalized linear models, respectively. The type of tissue, geographic origin (Cretan Sea, Libyan Sea), sex, and fish maturity stage were significant predictors of toxin concentrations. Mean TTX was higher in gonads and lower in muscles, higher in the Libyan Sea and in female fish, and lower in juvenile (virgin) fish. The concentration of TTX was also significantly and positively correlated with the concentration of several TTX analogues (4-epiTTX, 4,9-anhydroTTX, 11-deoxyTTX, 5,11/6,11-dideoxyTTX, 5,6,11-trideoxyTTX, 11-norTTX-6-ol). The analysis showed that fish originating from the Libyan Sea had significantly higher probability to cause tetrodotoxication in case of consumption. The variability explained by the models developed in this study was relatively low, indicating that toxin levels are hard to predict and the consumption of L. sceleratus should therefore be avoided.

| S-EPMC8706384 | biostudies-literature

The complete mitochondrial genome of oceanic puffer (Lagocephalus lagocephalus) from South China Sea.

Project description:Lagocephalus lagocephalus is one of genus Lagocephalus and widely distributed in tropical and temperate oceans. In this study, we described the complete mitochondrial genome of L. lagocephalus. The genome is 166,443 bp in length, encoding the standard set of 13 protein-coding genes (PCGs), 22 transfer RNA genes, 2 ribosomal RNA genes, and a non-coding D-loop, with circular organization. The overall base composition of the whole mitochondrial genome was A (27.95%), T (25.07%), G (16.14%), and C (30.83%) with an AT bias of 53.03%. The longest PCG of these species was ND5, whereas the shortest ATP8.

| S-EPMC7707739 | biostudies-literature

Unraveling the genomic underpinnings of unbalanced MYC break-apart FISH results using whole genome sequencing analysis.

Project description: Not available

| S-EPMC10730864 | biostudies-literature

Concentrations of Tetrodotoxin (TTX) and Its Analogue 4,9-Anhydro TTX in Different Tissues of the Silver-Cheeked Pufferfish (Lagocephalus sceleratus, Gmelin, 1789) Caught in the South-Eastern Mediterranean Sea, Lebanon.

Project description:Pufferfishes are among the best-known marine organisms that accumulate marine biotoxins such as Tetrodotoxin (TTX). In the Mediterranean Sea, the silver-cheeked toadfish Lagocephalus sceleratus is the most reported TTX-bearer, causing many fatal and non-fatal cases. In Lebanon, no previous studies have measured TTX levels although the possibility of TTX-poisoning is high since L. sceleratus is caught in different sizes and can be mistaken with other small fishes. Hence, this study reports TTX and its analogue 4,9-anhydro TTX in L. sceleratus collected from Lebanese waters in the Eastern Mediterranean Sea. The results show that TTX concentrations in fish tissues varied between 0.10 and 252.97 µg/g, while those of 4,9-anhydro TTX oscillated between 0.01 and 43.01 µg/g. Internal organs of L. sceleratus were the most toxic parts of its body, with the highest TTX levels found in gonads (mainly ovaries) and liver, followed by the muscles and skin with concentrations always exceeding the safety level. Toxicity fluctuations of L. sceleratus, its expansion, ecological and economic effects were also elucidated. Based on the present findings, it has been confirmed that L. sceleratus constitutes a health, ecological and economic risks, and therefore its trade in seafood markets should be banned to avoid any potential intoxication.

| S-EPMC8877804 | biostudies-literature

Genome-wide analysis of DNA methylation in Hirschsprung enteric precursor cells: unraveling the epigenetic landscape of enteric nervous system development.

Project description:BackgroundHirschsprung disease (HSCR, OMIM 142623) is a rare congenital disorder that results from a failure to fully colonize the gut by enteric precursor cells (EPCs) derived from the neural crest. Such incomplete gut colonization is due to alterations in EPCs proliferation, survival, migration and/or differentiation during enteric nervous system (ENS) development. This complex process is regulated by a network of signaling pathways that is orchestrated by genetic and epigenetic factors, and therefore alterations at these levels can lead to the onset of neurocristopathies such as HSCR. The goal of this study is to broaden our knowledge of the role of epigenetic mechanisms in the disease context, specifically in DNA methylation. Therefore, with this aim, a Whole-Genome Bisulfite Sequencing assay has been performed using EPCs from HSCR patients and human controls.ResultsThis is the first study to present a whole genome DNA methylation profile in HSCR and reveal a decrease of global DNA methylation in CpG context in HSCR patients compared with controls, which correlates with a greater hypomethylation of the differentially methylated regions (DMRs) identified. These results agree with the de novo Methyltransferase 3b downregulation in EPCs from HSCR patients compared to controls, and with the decrease in the global DNA methylation level previously described by our group. Through the comparative analysis of DMRs between HSCR patients and controls, a set of new genes has been identified as potential susceptibility genes for HSCR at an epigenetic level. Moreover, previous differentially methylated genes related to HSCR have been found, which validates our approach.ConclusionsThis study highlights the relevance of an adequate methylation pattern for a proper ENS development. This is a research area that provides a novel approach to deepen our understanding of the etiopathogenesis of HSCR.

| S-EPMC7942176 | biostudies-literature

An inferior competitor is a successful invader due to its stress tolerance and productivity.

Project description:The invasion of ecosystems by non-native species is recognized as one of the most significant global challenges, particularly in semiarid regions where native biodiversity is already under stress from drought and land degradation. The implicit assumption is that invaders are strong competitors, but a greenhouse pairwise experiment conducted to examine intraspecific and interspecific competition effects of Opuntia ficus-indica, a widespread invader in semiarid ecosystems, with two species native to the highlands of Eritrea, Ricinus communis and Solanum marginatum, revealed that O. ficus-indica is a weak competitor. The unique ability of O. ficus-indica's fallen cladodes to undergo vegetative growth becomes a fundamental trait contributing to its spread. This growth strategy allows O. ficus-indica to outgrow native species and establish a significant presence. In direct interaction, the competition in aboveground productivity measured by the logarithmic response ratio for O. ficus-indica was 3.4-fold and 5.9-fold higher than for R. communis and S. marginatum, respectively. Belowground, the native R. communis was facilitated (- 1.00 ± 0.69) by O. ficus-indica which itself suffered from high competition. This pattern became even more evident under water shortage, where aboveground competition for S. marginatum decreased 5.7-fold, and for O. ficus-indica, it increased 1.4-fold. Despite being a poor competitor, O. ficus-indica outperformed R. communis and S. marginatum in both aboveground (4.3 and 3.8 times more) and belowground (27 and 2.8 times more) biomass production, respectively. The findings of this study challenge the common interpretation that invasive species are strong competitors and highlight the importance of considering other factors, such as productivity and tolerance limits when assessing the potential impacts of invasive species on semiarid ecosystems.

| S-EPMC10673848 | biostudies-literature

Old world versus new world: life-history alterations in a successful invader introduced across Europe.

Project description:We examined differences in pumpkinseed (Lepomis gibbosus) life-history traits between native North American and introduced European populations, and tested three life-history predictions related to the effect of temperature, growth, waterbody size, and the presence/absence of predators on native and non-native populations. Pumpkinseed populations exhibit more 'opportunistic' traits (earlier maturity, smaller size at maturity, and higher reproductive allocation) in their introduced European range than those in their native range. Predictions of life-history traits were improved when indicators of juvenile growth rate (mean length at age 2), waterbody size (surface area), and thermal regime (air temperature degree-days above 10 °C) were incorporated into models along with continental location, but European pumpkinseed populations exhibit more opportunistic life-history traits than North American populations even when these factors are accounted for. Native pumpkinseed in waterbodies containing piscivores mature later and at a larger size, and have lower gonadosomatic indices than those in waterbodies lacking piscivores, whereas there is no significant difference in the same three life-history traits between European waterbodies containing or lacking piscivores. Because congeneric competitors of the pumpkinseed are absent from Europe, the apparent absence of a predator life-history effect there could also be due to the absence of the major sunfish competitors. In either case, the evolution and maintenance of more opportunistic traits in European pumpkinseed can likely be attributed to enemy release, and this may explain the successful establishment and spread of pumpkinseed in many parts of Europe.

| S-EPMC3897869 | biostudies-literature

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