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

2021 ◽  
Vol 12 ◽  
Author(s):  
Theodoros Danis ◽  
Vasileios Papadogiannis ◽  
Alexandros Tsakogiannis ◽  
Jon B. Kristoffersen ◽  
Daniel Golani ◽  
...  
Keyword(s):  
Genome Assembly ◽  
Western Mediterranean ◽  
Gene Family Evolution ◽  
Rapid Expansion ◽  
Phylogenomic Analysis ◽  
Western Mediterranean Sea ◽  
Evolution Analysis ◽  
Genomic Landscape ◽  
Lagocephalus Sceleratus ◽  
Successful Invader

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.

scholarly journals Building a high-quality reference genome assembly for the the eastern Mediterranean Sea invasive sprinter Lagocephalus sceleratus (Tetraodontiformes, Tetraodontidae)

2020 ◽  
Author(s):  
Theodoros Danis ◽  
Alexandros Tsakogiannis ◽  
Jon B. Kristoffersen ◽  
Daniel Golani ◽  
Dimitris Tsaparis ◽  
...  
Keyword(s):  
Mediterranean Sea ◽  
Genome Assembly ◽  
Eastern Mediterranean ◽  
Western Mediterranean ◽  
High Quality ◽  
Total Size ◽  
Western Mediterranean Sea ◽  
Invasive Biology ◽  
The Family ◽  
Lagocephalus Sceleratus

ABSTRACTThe Tetraodontidae family encompasses several species which attract scientific interest in terms of their ecology and evolution. However, the genomic resources and especially reference assemblies are sparse for the members of the family. In this study, we focus on the silver-cheeked toadfish (Lagocephalus sceleratus) a well-known ‘invasive sprinter’ that has invaded and spread throughout the Eastern and part of the Western Mediterranean Sea from the Red Sea through the Suez Canal within a decade. We sequenced the genome of L. sceleratus using a single MinION flow cell for the main assembly, and Illumina reads for polishing the assembly. The resulted assembly consisted of 241 contigs (N50 = 11,3 Mb) with a total size of 360 Mb and yielded 98% BUSCO completeness. The high-quality genome assembly built here is expected to set the ground for future studies on this focal species’ invasive biology.

scholarly journals Lagocephalus sceleratus (Gmelin, 1789) expands through the African coasts towards the Western Mediterranean Sea: A call for awareness

2014 ◽  
Vol 5 (4) ◽  
pp. 357-362 ◽  
Author(s):  
Jamila Ben Souissi ◽  
Mouna Rifi ◽  
Raouia Ghanem ◽  
Lotfi Ghozzi ◽  
Wassim Boughedir ◽  
...  
Keyword(s):  
Mediterranean Sea ◽  
Western Mediterranean ◽  
Western Mediterranean Sea ◽  
Lagocephalus Sceleratus

Abundance of Pelagia noctiluca early life stages in the western Mediterranean Sea scales with surface chlorophyll

2020 ◽  
Author(s):  
D Ottmann ◽  
D Álvarez-Berastegui ◽  
L Prieto ◽  
R Balbín ◽  
F Alemany ◽  
...  
Keyword(s):  
Mediterranean Sea ◽  
Early Life ◽  
Western Mediterranean ◽  
Life Stages ◽  
Early Life Stages ◽  
Western Mediterranean Sea ◽  
Pelagia Noctiluca

scholarly journals Phylogenomic analysis of Clostridioides difficile ribotype 106 strains reveals novel genetic islands and emergent phenotypes

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Bryan Angelo P. Roxas ◽  
Jennifer Lising Roxas ◽  
Rachel Claus-Walker ◽  
Anusha Harishankar ◽  
Asad Mansoor ◽  
...  
Keyword(s):  
Biofilm Formation ◽  
Diarrheal Disease ◽  
The United States ◽  
Genomic Islands ◽  
Rapid Expansion ◽  
Phylogenomic Analysis ◽  
Community Settings ◽  
Hamster Model ◽  
Clostridioides Difficile ◽  
Healthcare Associated

AbstractClostridioides difficile infection (CDI) is a major healthcare-associated diarrheal disease. Consistent with trends across the United States, C. difficile RT106 was the second-most prevalent molecular type in our surveillance in Arizona from 2015 to 2018. A representative RT106 strain displayed robust virulence and 100% lethality in the hamster model of acute CDI. We identified a unique 46 KB genomic island (GI1) in all RT106 strains sequenced to date, including those in public databases. GI1 was not found in its entirety in any other C. difficile clade, or indeed, in any other microbial genome; however, smaller segments were detected in Enterococcus faecium strains. Molecular clock analyses suggested that GI1 was horizontally acquired and sequentially assembled over time. GI1 encodes homologs of VanZ and a SrtB-anchored collagen-binding adhesin, and correspondingly, all tested RT106 strains had increased teicoplanin resistance, and a majority displayed collagen-dependent biofilm formation. Two additional genomic islands (GI2 and GI3) were also present in a subset of RT106 strains. All three islands are predicted to encode mobile genetic elements as well as virulence factors. Emergent phenotypes associated with these genetic islands may have contributed to the relatively rapid expansion of RT106 in US healthcare and community settings.

scholarly journals Tracking the global reduction of marine traffic during the COVID-19 pandemic

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
David March ◽  
Kristian Metcalfe ◽  
Joaquin Tintoré ◽  
Brendan J. Godley
Keyword(s):  
Large Scale ◽  
Human Mobility ◽  
Western Mediterranean ◽  
Western Mediterranean Sea ◽  
Marine Traffic ◽  
Human Movements ◽  
Exclusive Economic Zones ◽  
Global Impacts ◽  
Economic Zones

AbstractThe COVID-19 pandemic has resulted in unparalleled global impacts on human mobility. In the ocean, ship-based activities are thought to have been impacted due to severe restrictions on human movements and changes in consumption. Here, we quantify and map global change in marine traffic during the first half of 2020. There were decreases in 70.2% of Exclusive Economic Zones but changes varied spatially and temporally in alignment with confinement measures. Global declines peaked in April, with a reduction in traffic occupancy of 1.4% and decreases found across 54.8% of the sampling units. Passenger vessels presented more marked and longer lasting decreases. A regional assessment in the Western Mediterranean Sea gave further insights regarding the pace of recovery and long-term changes. Our approach provides guidance for large-scale monitoring of the progress and potential effects of COVID-19 on vessel traffic that may subsequently influence the blue economy and ocean health.

scholarly journals Parasites of the head of Scomber colias (Osteichthyes: Scombridae) from the western Mediterranean Sea

2014 ◽  
Vol 59 (1) ◽  
Author(s):  
Salvatore Mele ◽  
Maria Pennino ◽  
Maria Piras ◽  
José Bellido ◽  
Giovanni Garippa ◽  
...  
Keyword(s):  
Mediterranean Sea ◽  
Eastern Mediterranean ◽  
Western Mediterranean ◽  
Parasite Fauna ◽  
Point Of View ◽  
Published Data ◽  
Multivariate Techniques ◽  
Western Mediterranean Sea ◽  
Scomber Colias ◽  
Non Parametric

AbstractThe metazoan parasite assemblage of the head of 30 specimens of the Atlantic chub mackerel (Scomber colias) from the western Mediterranean Sea was analysed. Eight species of parasites were found, four mazocraeid monogeneans: Grubea cochlear (prevalence = 10%), Kuhnia scombercolias (59%), K. scombri (52%), Pseudokuhnia minor (86%); three didymozoid trematodes: Nematobothrium cf. faciale (21%), N. filiforme (41%), N. scombri (7%); and one laerneopodid copepod: Clavelissa scombri (7%). Results were compared with previously published data from 14 localities of the eastern Mediterranean Sea and the Atlantic Ocean, using non-parametric univariate and multivariate analyses, and the whole parasite fauna of S. colias was compared with that of the congeners (S. australasicus, S. japonicus and S. scombrus). Parasites showed to reflect the biogeographical and phylogenetic history of host. From a methodological point of view, the use of both non-parametric univariate and multivariate techniques proved to be effective tools to detect dissimilarities between parasite assemblages.

An algorithmic model for invasive species: Application to Caulerpa taxifolia (Vahl) C. Agardh development in the North-Western Mediterranean Sea

1998 ◽  
Vol 109 (3) ◽  
pp. 251-266 ◽  
Author(s):  
David Hill ◽  
Patrick Coquillard ◽  
Jean de Vaugelas ◽  
Alexandre Meinesz
Keyword(s):  
Invasive Species ◽  
Mediterranean Sea ◽  
Western Mediterranean ◽  
Caulerpa Taxifolia ◽  
The North ◽  
Western Mediterranean Sea ◽  
Algorithmic Model ◽  
North Western

scholarly journals Amynthas corticis genome reveals molecular mechanisms behind global distribution

2021 ◽  
Vol 4 (1) ◽  
Author(s):  
Xing Wang ◽  
Yi Zhang ◽  
Yufeng Zhang ◽  
Mingming Kang ◽  
Yuanbo Li ◽  
...  
Keyword(s):  
Genome Assembly ◽  
Molecular Mechanisms ◽  
Gene Families ◽  
The Body ◽  
Gene Family Evolution ◽  
Complex Environments ◽  
Protein Coding ◽  
Itraq Analysis ◽  
Rdna Sequencing ◽  
Long Read

AbstractEarthworms (Annelida: Crassiclitellata) are widely distributed around the world due to their ancient origination as well as adaptation and invasion after introduction into new habitats over the past few centuries. Herein, we report a 1.2 Gb complete genome assembly of the earthworm Amynthas corticis based on a strategy combining third-generation long-read sequencing and Hi-C mapping. A total of 29,256 protein-coding genes are annotated in this genome. Analysis of resequencing data indicates that this earthworm is a triploid species. Furthermore, gene family evolution analysis shows that comprehensive expansion of gene families in the Amynthas corticis genome has produced more defensive functions compared with other species in Annelida. Quantitative proteomic iTRAQ analysis shows that expression of 147 proteins changed in the body of Amynthas corticis and 16 S rDNA sequencing shows that abundance of 28 microorganisms changed in the gut of Amynthas corticis when the earthworm was incubated with pathogenic Escherichia coli O157:H7. Our genome assembly provides abundant and valuable resources for the earthworm research community, serving as a first step toward uncovering the mysteries of this species, and may provide molecular level indicators of its powerful defensive functions, adaptation to complex environments and invasion ability.

scholarly journals Dynamical Downscaling of ERA5 Data on the North-Western Mediterranean Sea: From Atmosphere to High-Resolution Coastal Wave Climate

2021 ◽  
Vol 9 (2) ◽  
pp. 208
Author(s):  
Valentina Vannucchi ◽  
Stefano Taddei ◽  
Valerio Capecchi ◽  
Michele Bendoni ◽  
Carlo Brandini
Keyword(s):  
Mediterranean Sea ◽  
Wind Wave ◽  
Dynamical Downscaling ◽  
Wave Climate ◽  
Western Mediterranean ◽  
Limited Area ◽  
Computational Domain ◽  
Wave Hindcast ◽  
The North ◽  
Western Mediterranean Sea

A 29-year wind/wave hindcast is produced over the Mediterranean Sea for the period 1990–2018. The dataset is obtained by downscaling the ERA5 global atmospheric reanalyses, which provide the initial and boundary conditions for a numerical chain based on limited-area weather and wave models: the BOLAM, MOLOCH and WaveWatch III (WW3) models. In the WW3 computational domain, an unstructured mesh is used. The variable resolutions reach up to 500 m along the coasts of the Ligurian and Tyrrhenian seas (Italy), the main objects of the study. The wind/wave hindcast is validated using observations from coastal weather stations and buoys. The wind validation provides velocity correlations between 0.45 and 0.76, while significant wave height correlations are much higher—between 0.89 and 0.96. The results are also compared to the original low-resolution ERA5 dataset, based on assimilated models. The comparison shows that the downscaling improves the hindcast reliability, particularly in the coastal regions, and especially with regard to wind and wave directions.

Sign in / Sign up

Export Citation Format

Share Document