Phylogenomics investigation of sparids (Teleostei: Spariformes) using high-quality proteomes highlights the importance of taxon sampling

Natsidis, Paschalis; Tsakogiannis, Alexandros; Pavlidis, Pavlos; Tsigenopoulos, Costas S.; Manousaki, Tereza

doi:10.1038/s42003-019-0654-5

Cited by 10 publications

(9 citation statements)

References 80 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Moreover, the Tetraodontidae group was recovered confidently as monophyletic in accordance with Yamanoue et al (2011) . Our results suggest that Tetraodontiformes are the closest group to Sparidae and corroborates the results of Natsidis et al (2019) and of others ( Kawahara et al, 2008 ; Meynard et al, 2012 ), based both on six mitochondrial and two nuclear genes.…”

Section: Discussionsupporting

confidence: 91%

“…To identify paralogous and orthologous genes, we compared 30 whole-genome protein-coding gene sets from teleost fish ( Supplementary Table S3 ) (27 species from our previous dataset of Natsidis et al (2019) in addition with two extra Tetraodontidae species i.e., Takifugu bimaculatus. T. flavidus , and L. sceleratus ) with Orthofinder v2.3.12 ( Emms and Kelly, 2015 ) using default parameters.…”

Section: Methodsmentioning

confidence: 99%

See 1 more Smart Citation

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

et al. 2021

Self Cite

View full text Add to dashboard Cite

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.

show abstract

Section: Discussionsupporting

confidence: 91%

Section: Methodsmentioning

confidence: 99%

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

et al. 2021

Self Cite

View full text Add to dashboard Cite

show abstract

“…In the context of this study, an automated containerized pipeline allowing high-quality genome assemblies from Oxford Nanopore and Illumina data was developed ( SnakeCube [ 54 ]). The availability of standardized pipelines offers great perspective for in-depth studies of numerous marine species of interest in aquaculture and conservation biology, including rigorous phylogenomic analyses to position each species in the tree of life (e.g., Natsidis et al [ 55 ]).…”

Section: Scientific Impact Storiesmentioning

confidence: 99%

0s and 1s in marine molecular research: a regional HPC perspective

et al. 2021

Self Cite

View full text Add to dashboard Cite

High-performance computing (HPC) systems have become indispensable for modern marine research, providing support to an increasing number and diversity of users. Pairing with the impetus offered by high-throughput methods to key areas such as non-model organism studies, their operation continuously evolves to meet the corresponding computational challenges. Here, we present a Tier 2 (regional) HPC facility, operating for over a decade at the Institute of Marine Biology, Biotechnology, and Aquaculture of the Hellenic Centre for Marine Research in Greece. Strategic choices made in design and upgrades aimed to strike a balance between depth (the need for a few high-memory nodes) and breadth (a number of slimmer nodes), as dictated by the idiosyncrasy of the supported research. Qualitative computational requirement analysis of the latter revealed the diversity of marine fields, methods, and approaches adopted to translate data into knowledge. In addition, hardware and software architectures, usage statistics, policy, and user management aspects of the facility are presented. Drawing upon the last decade’s experience from the different levels of operation of the Institute of Marine Biology, Biotechnology, and Aquaculture HPC facility, a number of lessons are presented; these have contributed to the facility’s future directions in light of emerging distribution technologies (e.g., containers) and Research Infrastructure evolution. In combination with detailed knowledge of the facility usage and its upcoming upgrade, future collaborations in marine research and beyond are envisioned.

show abstract

“…To identify if candidate loci are enriched for certain genomic regions (i.e., genic, intergenic, exonic, intronic), we conducted BLAST searches with the 34 bp sequences of all loci against the genome of Sparus aurata Linnaeus, 1758. We selected S. aurata since it is the phylogenetically closest available reference genome to D. puntazzo , as reported in a previous study on the Sparidae family 55 . To do so, we performed local Nucleotide BLAST searches (Blast v2.10.1) against the S. aurata genome downloaded from NCBI (GCA_900880675.1), using an E-value cut-off of 10 –4 .…”

Section: Methodsmentioning

confidence: 99%

Genomic basis for early-life mortality in sharpsnout seabream

Torrado

Pegueroles

Raventós

et al. 2022

Sci Rep

View full text Add to dashboard Cite

Mortality at early life stages of fishes is common in nature and can be shaped by stochastic and selective processes. Selective mortality has rarely been assessed in natural conditions but can now be studied by combining genomic data with information on different life stages that realates to fitness. Here we investigate selective mortality between settlers and six-month survivors of the sharpsnout seabream by genotype-phenotype/environmental association studies in three localities along a geographic gradient. We gathered information on 105 individuals at 85,031 SNPs, obtained from individual based 2b-RAD libraries, as well as 9 phenotypic and environmental variables derived from individual otolith readings. We found common signals across localities for potential selection, such as lower survival rates for individuals hatching earlier, growing faster and experiencing higher temperatures during their planktonic phase. We identified 122 loci with parallel significant association to phenotypic and environmental variables. Importantly, one of these loci mapped to the exonic region of the il20rb, a gene involved in immune response, in the phylogenetically closest reference genome, showing parallel frequency changes in non-synonymous mutations in the three studied populations. Further temporal assessments are needed to understand how polymorphisms that are key to selective mortality are maintained.

show abstract

Phylogenomics investigation of sparids (Teleostei: Spariformes) using high-quality proteomes highlights the importance of taxon sampling

Cited by 10 publications

References 80 publications

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

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

0s and 1s in marine molecular research: a regional HPC perspective

Genomic basis for early-life mortality in sharpsnout seabream

Contact Info

Product

Resources

About