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.

Chromosome genome assembly for the meagre, Argyrosomus regius, reveals species adaptations and sciaenid sex-related locus evolution

“…A total of 3, 003, 301 reads were generated with a quality score above 7, with an N50 of 30,600, totalling 37,962,807,176 bp and 99.94% passed quality control ( Supplementary Table S1 ). For Illumina sequencing, 2-day old frozen blood was used, following the same extraction protocol described above, similar to Danis et al (2021) . Extracted DNA was fragmented via sonication, followed by PCR free library preparation with the Kapa Hyper Prep DNA kit and paired end (150 bp) sequencing on an Illumina Hiseq4000 platform (Norwegian Sequencing Center, NSC).…”

SnakeCube: containerized and automated pipeline for de novo genome assembly in HPC environments

“…SnakeCube was first evaluated by reproducing the initial non-automated L. sceleratus analysis [ 3 ] used as the basis for the establishment of the pipeline. The produced output was generated as expected and SnakeCube scored similarly to the original work (Table 1 ).…”

“…We present SnakeCube, a de novo genome assembly pipeline which can operate with both long MinION and short Illumina reads. The workflow is based on our previous work on Lagocephalus sceleratus genome [ 3 ]. Furthermore, it is benchmarked and optimized using two additional publicly available datasets on distantly related organisms, with different genome sizes and raw data amounts, to monitor the response of the software.…”

The Dynamics of Maximum Lengths for the Invasive Silver-Cheeked Toadfish (Lagocephalus sceleratus) in the Eastern Mediterranean Sea

“…The genome of L. sceleratus has a higher percentage of repeated content of transposable elements (16.5%) than other pufferfish species [39]. A high percentage rate of transposable elements in various species has been shown to correlate to rapid adaptations to new environments, suggesting they may aid with invasiveness [40]; • Tolerance to a wide range of temperatures, which is suggested by the fact that, despite being native to the warmer Indo-West Pacific region [22], L. sceleratus has been found in the Black Sea, which experiences near freezing temperatures during winter [12].…”