4.8 Article

Genomic, functional and structural analyses elucidate evolutionary innovation within the sea anemone 8 toxin family

Related references

Note: Only part of the references are listed.
Article Food Science & Technology

Acontia, a Specialised Defensive Structure, Has Low Venom Complexity in Calliactis polypus

Hayden L. Smith et al.

Summary: The venom delivery system of Phylum Cnidaria is unique, consisting of individual organelles known as nematocysts. Acontia, found in a limited number of sea anemone species, are packed with large nematocysts used for defense. This study identified the venom profile of acontia in Calliactis polypus, revealing limited toxin diversity and a novel toxin with two ShK-like domains. This research provides a foundation for further investigating the function of acontial toxins in sea anemones.

TOXINS (2023)

Article Biochemistry & Molecular Biology

Venoms for all occasions: The functional toxin profiles of different anatomical regions in sea anemones are related to their ecological function

Lauren M. Ashwood et al.

Summary: This study explored the relationship between toxin expression patterns and ecological roles of different anatomical structures in a specific species of sea anemone. The findings revealed that the venom profiles of different anatomical regions vary according to their ecological functions, and there is a direct correlation between the functional similarity of regions and the similarity of their associated toxin expression profiles.

MOLECULAR ECOLOGY (2022)

Article Oceanography

The genome of a new anemone species (Actiniaria: Hormathiidae) provides insights into deep-sea adaptation

Chenguang Feng et al.

Summary: The high-quality genome assembly of a new deep-sea anemone species living at a depth of 3230 m in the Xisha Trough revealed molecular signatures of adaptation to the deep-sea environment. The genomic analyses showed rapid evolution of genes and amino acid substitutions to cope with high hydrostatic pressure or low temperature, while demographic events of the deep-sea anemone coincided with post-Pliocene climate transformations, suggesting the impact of global climate changes on deep-sea creatures.

DEEP-SEA RESEARCH PART I-OCEANOGRAPHIC RESEARCH PAPERS (2021)

Article Evolutionary Biology

Phylogenomics, Origin, and Diversification of Anthozoans (Phylum Cnidaria)

Catherine S. McFadden et al.

Summary: Anthozoan cnidarians, such as corals and sea anemones, are crucial foundation species capable of building massive reef complexes supporting entire ecosystems. With a time-calibrated phylogeny for 234 species constructed from ultraconserved elements and exon loci, evolutionary origins of major Anthozoa clades and salient morphological features have been explored. Notable findings include the monophyly of Hexacorallia and Octocorallia, divergence dating placing Anthozoa in the Cryogenian to Tonian periods, and the evolution of colonial growth forms and photosymbiont associations in the Ediacaran and Cambrian periods respectively.

SYSTEMATIC BIOLOGY (2021)

Article Biochemistry & Molecular Biology

Pfam: The protein families database in 2021

Jaina Mistry et al.

Summary: The Pfam database has recently added a large number of protein families and domains, made revisions for COVID-19 research, and introduced Pfam-B as a supplement. These updates and improvements can help researchers classify protein sequences more effectively and conduct related studies.

NUCLEIC ACIDS RESEARCH (2021)

Article Biochemistry & Molecular Biology

IQ-TREE 2: New Models and Efficient Methods for Phylogenetic Inference in the Genomic Era

Bui Quang Minh et al.

MOLECULAR BIOLOGY AND EVOLUTION (2020)

Article Multidisciplinary Sciences

The origin and diversification of a novel protein family in venomous snakes

Matt W. Giorgianni et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2020)

Review Pharmacology & Pharmacy

The voltage-gated potassium channel KV1.3 as a therapeutic target for venom-derived peptides

Gabor Tajti et al.

BIOCHEMICAL PHARMACOLOGY (2020)

Article Multidisciplinary Sciences

Toxin-like neuropeptides in the sea anemone Nematostella unravel recruitment from the nervous system to venom

Maria Y. Sachkova et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2020)

Article Biochemistry & Molecular Biology

Evolution of cnidarian trans-defensins: Sequence, structure and exploration of chemical space

Michela L. Mitchell et al.

PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS (2019)

Article Biochemistry & Molecular Biology

The Birth and Death of Toxins with Distinct Functions: A Case Study in the Sea Anemone Nematostella

Maria Y. Sachkova et al.

MOLECULAR BIOLOGY AND EVOLUTION (2019)

Review Chemistry, Medicinal

Sea Anemone Toxins: A Structural Overview

Bruno Madio et al.

MARINE DRUGS (2019)

Article Pharmacology & Pharmacy

Mapping the chemical and sequence space of the ShKT superfamily

Thomas Shafee et al.

TOXICON (2019)

Article Ecology

The draft genome of Actinia tenebrosa reveals insights into toxin evolution

Joachim M. Surm et al.

ECOLOGY AND EVOLUTION (2019)

Review Biochemistry & Molecular Biology

New Structures and Gating of Voltage-Dependent Potassium (Kv) Channels and Their Relatives: A Multi-Domain and Dynamic Question

Francisco Barros et al.

INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES (2019)

Article Biochemistry & Molecular Biology

The PRIDE database and related tools and resources in 2019: improving support for quantification data

Yasset Perez-Riverol et al.

NUCLEIC ACIDS RESEARCH (2019)

Article Biotechnology & Applied Microbiology

OrthoFinder: phylogenetic orthology inference for comparative genomics

David M. Emms et al.

GENOME BIOLOGY (2019)

Article Biochemical Research Methods

Minimap2: pairwise alignment for nucleotide sequences

Heng Li

BIOINFORMATICS (2018)

Article Evolutionary Biology

Evidence for a Large Expansion and Subfunctionalization of Globin Genes in Sea Anemones

Hayden L. Smith et al.

GENOME BIOLOGY AND EVOLUTION (2018)

Review Food Science & Technology

Sea Anemones: Quiet Achievers in the Field of Peptide Toxins

Peter J. Prentis et al.

TOXINS (2018)

Article Biochemistry & Molecular Biology

PHAB toxins: a unique family of predatory sea anemone toxins evolving via intra-gene concerted evolution defines a new peptide fold

Bruno Madio et al.

CELLULAR AND MOLECULAR LIFE SCIENCES (2018)

Article Biochemical Research Methods

Purge Haplotigs: allelic contig reassignment for third-gen diploid genome assemblies

Michael J. Roach et al.

BMC BIOINFORMATICS (2018)

Article Biochemistry & Molecular Biology

Identification, chemical synthesis, structure, and function of a new KV1 channel blocking peptide from Oulactis sp.

Punnepalli Sunanda et al.

PEPTIDE SCIENCE (2018)

Article Biochemistry & Molecular Biology

UniProt: the universal protein knowledgebase

Alex Bateman et al.

NUCLEIC ACIDS RESEARCH (2017)

Article Biotechnology & Applied Microbiology

Accurate assembly of transcripts through phase-preserving graph decomposition

Mingfu Shao et al.

NATURE BIOTECHNOLOGY (2017)

Letter Biotechnology & Applied Microbiology

MMseqs2 enables sensitive protein sequence searching for the analysis of massive data sets

Martin Steinegger et al.

NATURE BIOTECHNOLOGY (2017)

Article Biochemistry & Molecular Biology

Cryo-EM Structure of the Open Human Ether-a-go-go-Related K+ Channel hERG

Weiwei Wang et al.

Article Biochemical Research Methods

BRAKER1: Unsupervised RNA-Seq-Based Genome Annotation with GeneMark-ET and AUGUSTUS

Katharina J. Hoff et al.

BIOINFORMATICS (2016)

Article Biotechnology & Applied Microbiology

Insights into the innate immunome of actiniarians using a comparative genomic approach

Chloe A. van der Burg et al.

BMC GENOMICS (2016)

Article Biochemistry & Molecular Biology

The Deep Origin and Recent Loss of Venom Toxin Genes in Rattlesnakes

Noah L. Dowell et al.

CURRENT BIOLOGY (2016)

Article Evolutionary Biology

Tissue-Specific Venom Composition and Differential Gene Expression in Sea Anemones

Jason Macrander et al.

GENOME BIOLOGY AND EVOLUTION (2016)

Article Multidisciplinary Sciences

detectMITE: A novel approach to detect miniature inverted repeat transposable elements in genomes

Congting Ye et al.

SCIENTIFIC REPORTS (2016)

Article Biochemical Research Methods

BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs

Felipe A. Simao et al.

BIOINFORMATICS (2015)

Article Biotechnology & Applied Microbiology

Combined de novo and genome guided assembly and annotation of the Pinus patula juvenile shoot transcriptome

Erik A. Visser et al.

BMC GENOMICS (2015)

Article Chemistry, Medicinal

Development of Highly Selective Kv1.3-Blocking Peptides Based on the Sea Anemone Peptide ShK

Michael W. Pennington et al.

MARINE DRUGS (2015)

Article Multidisciplinary Sciences

The genome of Aiptasia, a sea anemone model for coral symbiosis

Sebastian Baumgarten et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2015)

Article Biochemical Research Methods

UniRef clusters: a comprehensive and scalable alternative for improving sequence similarity searches

Baris E. Suzek et al.

BIOINFORMATICS (2015)

Article Biochemistry & Molecular Biology

The Dynamically Evolving Nematocyst Content of an Anthozoan, a Scyphozoan, and a Hydrozoan

Tamar Rachamim et al.

MOLECULAR BIOLOGY AND EVOLUTION (2015)

Article Biochemistry & Molecular Biology

CDD: NCBI's conserved domain database

Aron Marchler-Bauer et al.

NUCLEIC ACIDS RESEARCH (2015)

Article Biochemical Research Methods

SOAPdenovo-Trans: de novo transcriptome assembly with short RNA-Seq reads

Yinlong Xie et al.

BIOINFORMATICS (2014)

Article Biochemical Research Methods

Trimmomatic: a flexible trimmer for Illumina sequence data

Anthony M. Bolger et al.

BIOINFORMATICS (2014)

Article Evolutionary Biology

Restriction and Recruitment-Gene Duplication and the Origin and Evolution of Snake Venom Toxins

Adam D. Hargreaves et al.

GENOME BIOLOGY AND EVOLUTION (2014)

Article Biochemistry & Molecular Biology

Pfam: the protein families database

Robert D. Finn et al.

NUCLEIC ACIDS RESEARCH (2014)

Article Biochemistry & Molecular Biology

A novel sea anemone peptide that inhibits acid-sensing ion channels

Armando Alexei Rodriguez et al.

PEPTIDES (2014)

Article Genetics & Heredity

On the optimal trimming of high-throughput mRNA sequence data

Matthew D. MacManes

FRONTIERS IN GENETICS (2014)

Article Biochemistry & Molecular Biology

MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

Kazutaka Katoh et al.

MOLECULAR BIOLOGY AND EVOLUTION (2013)

Article Biochemical Research Methods

Oases: robust de novo RNA-seq assembly across the dynamic range of expression levels

Marcel H. Schulz et al.

BIOINFORMATICS (2012)

Article Biochemical Research Methods

CD-HIT: accelerated for clustering the next-generation sequencing data

Limin Fu et al.

BIOINFORMATICS (2012)

Review Genetics & Heredity

Venom evolution through gene duplications

Emily S. W. Wong et al.

Review Chemistry, Medicinal

Sea Anemone (Cnidaria, Anthozoa, Actiniaria) Toxins: An Overview

Barbara Frazao et al.

MARINE DRUGS (2012)

Article Pharmacology & Pharmacy

Development of a rational nomenclature for naming peptide and protein toxins from sea anemones

Joacir Stolarz Oliveira et al.

TOXICON (2012)

Article Biotechnology & Applied Microbiology

The mining of toxin-like polypeptides from EST database by single residue distribution analysis

Sergey Kozlov et al.

BMC GENOMICS (2011)

Article Biochemistry & Molecular Biology

Domain Loss Facilitates Accelerated Evolution and Neofunctionalization of Duplicate Snake Venom Metalloproteinase Toxin Genes

Nicholas R. Casewell et al.

MOLECULAR BIOLOGY AND EVOLUTION (2011)

Review Biochemical Research Methods

Computational methods for transcriptome annotation and quantification using RNA-seq

Manuel Garber et al.

NATURE METHODS (2011)

Article Biochemical Research Methods

Accelerated Profile HMM Searches

Sean R. Eddy

PLOS COMPUTATIONAL BIOLOGY (2011)

Article Biochemical Research Methods

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

Mark D. Robinson et al.

BIOINFORMATICS (2010)

Article Multidisciplinary Sciences

The dynamic genome of Hydra

Jarrod A. Chapman et al.

NATURE (2010)

Article Biochemistry & Molecular Biology

MITE-Hunter: a program for discovering miniature inverted-repeat transposable elements from genomic sequences

Yujun Han et al.

NUCLEIC ACIDS RESEARCH (2010)

Article Biochemical Research Methods

The Sequence Alignment/Map format and SAMtools

Heng Li et al.

BIOINFORMATICS (2009)

Article Pharmacology & Pharmacy

Engineering a Stable and Selective Peptide Blocker of the Kv1.3 Channel in T Lymphocytes

M. W. Pennington et al.

MOLECULAR PHARMACOLOGY (2009)

Article Biochemical Research Methods

WGCNA: an R package for weighted correlation network analysis

Peter Langfelder et al.

BMC BIOINFORMATICS (2008)

Article Biochemical Research Methods

LTRharvest, an efficient and flexible software for de novo detection of LTR retrotransposons

David Ellinghaus et al.

BMC BIOINFORMATICS (2008)

Article Biochemistry & Molecular Biology

Defensins and the convergent evolution of platypus and reptile venom genes

Camilla M. Whittington et al.

GENOME RESEARCH (2008)

Article Biochemistry & Molecular Biology

Velvet: Algorithms for de novo short read assembly using de Bruijn graphs

Daniel R. Zerbino et al.

GENOME RESEARCH (2008)

Article Biochemistry & Molecular Biology

Concerted evolution of sea anemone neurotoxin genes is revealed through analysis of the Nematostella vectensis genome

Yehu Moran et al.

MOLECULAR BIOLOGY AND EVOLUTION (2008)

Article Biochemistry & Molecular Biology

An improved general amino acid replacement matrix

Si Quang Le et al.

MOLECULAR BIOLOGY AND EVOLUTION (2008)

Article Multidisciplinary Sciences

Sea anemone genome reveals ancestral eumetazoan gene repertoire and genomic organization

Nicholas H. Putnam et al.

SCIENCE (2007)

Article Biochemistry & Molecular Biology

LTR_FINDER: an efficient tool for the prediction of full-length LTR retrotransposons

Zhao Xu et al.

NUCLEIC ACIDS RESEARCH (2007)

Article Biochemistry & Molecular Biology

Repositioning-dependent fate of duplicate genes

SN Rodin et al.

DNA AND CELL BIOLOGY (2005)

Article Biochemical Research Methods

GMAP: a genomic mapping and alignment program for mRNA and EST sequences

TD Wu et al.

BIOINFORMATICS (2005)

Article Pharmacology & Pharmacy

Stichodactyla helianthus peptide, a pharmacological tool for studying Kv3.2 channels

LZ Yan et al.

MOLECULAR PHARMACOLOGY (2005)

Article Biochemistry & Molecular Biology

AUGUSTUS: a web server for gene finding in eukaryotes

M Stanke et al.

NUCLEIC ACIDS RESEARCH (2004)

Article Biochemistry & Molecular Biology

Improving the Arabidopsis genome annotation using maximal transcript alignment assemblies

BJ Haas et al.

NUCLEIC ACIDS RESEARCH (2003)

Article Pharmacology & Pharmacy

Molecular moulds with multiple missions: Functional sites in three-finger toxins

RM Kini

CLINICAL AND EXPERIMENTAL PHARMACOLOGY AND PHYSIOLOGY (2002)

Article Multidisciplinary Sciences

The evolutionary fate and consequences of duplicate genes

M Lynch et al.

SCIENCE (2000)