4.8 Article

The compact genome of the sponge Oopsacas minuta (Hexactinellida) is lacking key metazoan core genes

Related references

Note: Only part of the references are listed.
Article Chemistry, Multidisciplinary

Arrested in Glass: Actin within Sophisticated Architectures of Biosilica in Sponges

Hermann Ehrlich et al.

Summary: Actin is an ancient intracellular protein that plays a crucial role in cell functions and also affects biosilica deposition in metazoans.

ADVANCED SCIENCE (2022)

Article Biochemistry & Molecular Biology

Human Follicular Mites: Ectoparasites Becoming Symbionts

Gilbert Smith et al.

Summary: We propose that Demodex folliculorum represents a transitional stage from a host-injuring obligate parasite to an obligate symbiont. Genome sequencing revealed extensive genome reduction and a decrease in the number of cells in the mite. This is the first evolutionary step in adopting a reductive, parasitic, or endosymbiotic lifestyle in an arthropod species.

MOLECULAR BIOLOGY AND EVOLUTION (2022)

Article Biochemistry & Molecular Biology

Massive Loss of Transcription Factors Promotes the Initial Diversification of Placental Mammals

Xin-Wei Zhao et al.

Summary: The study found that there was a peak of TF loss in placental mammals around 100 million years ago and after the massive extinction of dinosaurs, which led to a deceleration in the molecular evolutionary rates of their target genes.

INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES (2022)

Article Microbiology

Genomic Insights Into the Lifestyles of Thaumarchaeota Inside Sponges

Markus Haber et al.

Summary: Sponges are ancient metazoans with diverse microbial symbionts, including Thaumarchaeota. Analysis of 11 Thaumarchaeota sponge symbiont genomes revealed adaptations for life inside sponge hosts, such as enriched transposases and toxin-antitoxin systems. Unique features like exopolyphosphatases and specific interactions with host sponges suggest a highly specific relationship between Thaumarchaeota and their sponge hosts.

FRONTIERS IN MICROBIOLOGY (2021)

Article Multidisciplinary Sciences

Evidence for sponges as sister to all other animals from partitioned phylogenomics with mixture models and recoding

Anthony K. Redmond et al.

Summary: This study demonstrates significant progress in partitioned phylogenomic analysis by using site-heterogeneous models and amino acid recoding to alleviate branching artefacts caused by systematic errors. The reanalysis of key datasets shows that partitioned phylogenomics does not support comb jellies as sister to other animals. Branching artefacts can confound the reconstruction of deep evolutionary relationships.

NATURE COMMUNICATIONS (2021)

Article Biochemistry & Molecular Biology

OMA orthology in 2021: website overhaul, conserved isoforms, ancestral gene order and more

Adrian M. Altenhoff et al.

Summary: OMA is a resource that elucidates evolutionary relationships among 2326 genes, providing functions such as pairwise and groupwise orthologs and functional annotations. The updated OMA database has been reorganized into gene-, group-, and genome-centric pages, with new features and improvements added.

NUCLEIC ACIDS RESEARCH (2021)

Review Developmental Biology

The significance of sponges for comparative studies of developmental evolution

Jeffrey Colgren et al.

WILEY INTERDISCIPLINARY REVIEWS-DEVELOPMENTAL BIOLOGY (2020)

Article Multidisciplinary Sciences

A cnidarian parasite of salmon (Myxozoa: Henneguya) lacks a mitochondrial genome

Dayana Yahalomi et al.

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

Article Genetics & Heredity

A Screen for Gene Paralogies Delineating Evolutionary Branching Order of Early Metazoa

Albert Erives et al.

G3-GENES GENOMES GENETICS (2020)

Article Biochemistry & Molecular Biology

Evolution of centriole assembly

Catarina Nabais et al.

CURRENT BIOLOGY (2020)

Article Multidisciplinary Sciences

Tracing animal genomic evolution with the chromosomal-level assembly of the freshwater sponge Ephydatia muelleri

Nathan J. Kenny et al.

NATURE COMMUNICATIONS (2020)

Article Biochemical Research Methods

Scaling read aligners to hundreds of threads on general-purpose processors

Ben Langmead et al.

BIOINFORMATICS (2019)

Article Microbiology

Integrated mobile genetic elements in Thaumarchaeota

Mart Krupovic et al.

ENVIRONMENTAL MICROBIOLOGY (2019)

Review Cell Biology

Biology of multiciliated cells

Camille Boutin et al.

CURRENT OPINION IN GENETICS & DEVELOPMENT (2019)

Article Zoology

Sponge Behavior and the Chemical Basis of Responses: A Post-Genomic View

Sally P. Leys et al.

INTEGRATIVE AND COMPARATIVE BIOLOGY (2019)

Article Ecology

Convergent evolution of a vertebrate-like methylome in a marine sponge

Alex de Mendoza et al.

NATURE ECOLOGY & EVOLUTION (2019)

Article Evolutionary Biology

Diverse cell junctions with unique molecular composition in tissues of a sponge (Porifera)

Jennyfer M. Mitchell et al.

EVODEVO (2019)

Article Biotechnology & Applied Microbiology

Molecular evolution and expression of opsin genes in Hydra vulgaris

Aide Macias-Munoz et al.

BMC GENOMICS (2019)

Article Evolutionary Biology

Wnt signaling and polarity in freshwater sponges

Pamela J. Windsor Reid et al.

BMC EVOLUTIONARY BIOLOGY (2018)

Article Evolutionary Biology

Tracing the evolution of the heterotrimeric G protein a subunit in Metazoa

A. D. Lokits et al.

BMC EVOLUTIONARY BIOLOGY (2018)

Article Biotechnology & Applied Microbiology

New genomic data and analyses challenge the traditional vision of animal epithelium evolution

Hassiba Belahbib et al.

BMC GENOMICS (2018)

Article Microbiology

Reef invertebrate viromics: diversity, host specificity and functional capacity

Patrick W. Laffy et al.

ENVIRONMENTAL MICROBIOLOGY (2018)

Article Biochemistry & Molecular Biology

Analysis of a vinculin homolog in a sponge (phylum Porifera) reveals that vertebrate-like cell adhesions emerged early in animal evolution

Phillip W. Miller et al.

JOURNAL OF BIOLOGICAL CHEMISTRY (2018)

Article Virology

Insights into Circovirus Host Range from the Genomic Fossil Record

Tristan P. W. Dennis et al.

JOURNAL OF VIROLOGY (2018)

Article Multidisciplinary Sciences

Reconstruction of the ancestral metazoan genome reveals an increase in genomic novelty

Jordi Paps et al.

NATURE COMMUNICATIONS (2018)

Article Biochemistry & Molecular Biology

FZD(5) is a G alpha(q)-coupled receptor that exhibits the functional hallmarks of prototypical GPCRs

Shane C. Wright et al.

SCIENCE SIGNALING (2018)

Article Multidisciplinary Sciences

Morphological characterization of virus-like particles in coral reef sponges

Cecilia Pascelli et al.

PEERJ (2018)

Review Biology

Phylogenetic evidence for the modular evolution of metazoan signalling pathways

Leslie S. Babonis et al.

PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES (2017)

Article Biochemistry & Molecular Biology

Canu: scalable and accurate long-read assembly via adaptive k-mer weighting and repeat separation

Sergey Koren et al.

GENOME RESEARCH (2017)

Review Biochemistry & Molecular Biology

The nature and biology of basement membranes

Ambra Pozzi et al.

MATRIX BIOLOGY (2017)

Article Cell Biology

Single and collective cell migration: the mechanics of adhesions

Chiara De Pascalis et al.

MOLECULAR BIOLOGY OF THE CELL (2017)

Article Ecology

Ctenophore relationships and their placement as the sister group to all other animals

Nathan V. Whelan et al.

NATURE ECOLOGY & EVOLUTION (2017)

Article Multidisciplinary Sciences

Dating early animal evolution using phylogenomic data

Martin Dohrmann et al.

SCIENTIFIC REPORTS (2017)

Article Multidisciplinary Sciences

Animal multicellularity and polarity without Wnt signaling

Quentin Schenkelaars et al.

SCIENTIFIC REPORTS (2017)

Article Biochemistry & Molecular Biology

Improved Modeling of Compositional Heterogeneity Supports Sponges as Sister to All Other Animals

Roberto Feuda et al.

CURRENT BIOLOGY (2017)

Review Cell Biology

Breaking down barriers: the evolution of cell invasion

Taylor N. Medwig et al.

CURRENT OPINION IN GENETICS & DEVELOPMENT (2017)

Review Developmental Biology

Think like a sponge: The genetic signal of sensory cells in sponges

Jasmine L. Mah et al.

DEVELOPMENTAL BIOLOGY (2017)

Review Cell Biology

The Origin of Animal Multicellularity and Cell Differentiation

Thibaut Brunet et al.

DEVELOPMENTAL CELL (2017)

Article Biochemistry & Molecular Biology

A Large and Consistent Phylogenomic Dataset Supports Sponges as the Sister Group to All Other Animals

Paul Simion et al.

CURRENT BIOLOGY (2017)

Review Biochemistry & Molecular Biology

Homeodomain proteins: an update

Thomas R. Buerglin et al.

CHROMOSOMA (2016)

Review Biochemistry & Molecular Biology

The PLK4-STIL-SAS-6 module at the core of centriole duplication

Christian Arquint et al.

BIOCHEMICAL SOCIETY TRANSACTIONS (2016)

Article Evolutionary Biology

Retracing the path of planar cell polarity

Quentin Schenkelaars et al.

BMC EVOLUTIONARY BIOLOGY (2016)

Article Marine & Freshwater Biology

Three-dimensional fate mapping of larval tissues through metamorphosis in the glass sponge Oopsacas minuta

Sally P. Leys et al.

INVERTEBRATE BIOLOGY (2016)

Article Biochemistry & Molecular Biology

The Evolution of Silicon Transport in Eukaryotes

Alan O. Marron et al.

MOLECULAR BIOLOGY AND EVOLUTION (2016)

Article Multidisciplinary Sciences

Ecogenomics and potential biogeochemical impacts of globally abundant ocean viruses

Simon Roux et al.

NATURE (2016)

Article Biochemistry & Molecular Biology

tRNAscan-SE On-line: integrating search and context for analysis of transfer RNA genes

Todd M. Lowe et al.

NUCLEIC ACIDS RESEARCH (2016)

Article Multidisciplinary Sciences

Proteomics and comparative genomics of Nitrososphaera viennensis reveal the core genome and adaptations of archaeal ammonia oxidizers

Melina Kerou et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2016)

Article Multidisciplinary Sciences

Diversity, structure and convergent evolution of the global sponge microbiome

Torsten Thomas et al.

NATURE COMMUNICATIONS (2016)

Article Evolutionary Biology

Conservation and divergence of bHLH genes in the calcisponge Sycon ciliatum

Sofia A. V. Fortunato et al.

EVODEVO (2016)

Article Biochemical Research Methods

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

Felipe A. Simao et al.

BIOINFORMATICS (2015)

Article Cell Biology

The evolution of animal genomes

Casey W. Dunn et al.

CURRENT OPINION IN GENETICS & DEVELOPMENT (2015)

Article Evolutionary Biology

Insights into Frizzled evolution and new perspectives

Quentin Schenkelaars et al.

EVOLUTION & DEVELOPMENT (2015)

Article Biochemistry & Molecular Biology

CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes

Donovan H. Parks et al.

GENOME RESEARCH (2015)

Review Biology

Elements of a 'nervous system' in sponges

Sally P. Leys

JOURNAL OF EXPERIMENTAL BIOLOGY (2015)

Article Biochemistry & Molecular Biology

A Proposal for the Evolution of Cathepsin and Silicatein in Sponges

Ana Riesgo et al.

JOURNAL OF MOLECULAR EVOLUTION (2015)

Article Multidisciplinary Sciences

Glassin, a histidine-rich protein from the siliceous skeletal system of the marine sponge Euplectella, directs silica polycondensation

Katsuhiko Shimizu et al.

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

Article Multidisciplinary Sciences

Genomic and proteomic characterization of Candidatus Nitrosopelagicus brevis: An ammonia-oxidizing archaeon from the open ocean

Alyson E. Santoro et al.

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

Article Multidisciplinary Sciences

Genomic insights into the evolutionary origin of Myxozoa within Cnidaria

E. Sally Chang et al.

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

Review Ecology

The hidden biology of sponges and ctenophores

Casey W. Dunn et al.

TRENDS IN ECOLOGY & EVOLUTION (2015)

Review Cell Biology

Molecular architecture and function of the hemidesmosome

Gernot Walko et al.

CELL AND TISSUE RESEARCH (2015)

Article Biochemistry & Molecular Biology

Structural Molecular Components of Septate Junctions in Cnidarians Point to the Origin of Epithelial Junctions in Eukaryotes

Philippe Ganot et al.

MOLECULAR BIOLOGY AND EVOLUTION (2015)

Review Plant Sciences

THE EVOLUTIONARY-DEVELOPMENTAL ORIGINS OF MULTICELLULARITY

Karl J. Niklas

AMERICAN JOURNAL OF BOTANY (2014)

Article Microbiology

Nitrososphaera viennensis gen. nov., sp nov., an aerobic and mesophilic, ammonia-oxidizing archaeon from soil and a member of the archaeal phylum Thaumarchaeota

Michaela Stieglmeier et al.

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY (2014)

Article Ecology

Potential role of viruses in white plague coral disease

Nitzan Soffer et al.

ISME JOURNAL (2014)

Article Biochemistry & Molecular Biology

The Analysis of Eight Transcriptomes from All Poriferan Classes Reveals Surprising Genetic Complexity in Sponges

Ana Riesgo et al.

MOLECULAR BIOLOGY AND EVOLUTION (2014)

Article Multidisciplinary Sciences

Calcisponges have a ParaHox gene and dynamic expression of dispersed NK homeobox genes

Sofia A. V. Fortunato et al.

NATURE (2014)

Article Multidisciplinary Sciences

Comparison of Deep-Water Viromes from the Atlantic Ocean and the Mediterranean Sea

Christian Winter et al.

PLOS ONE (2014)

Article Multidisciplinary Sciences

Innexin gap junctions in nerve cells coordinate spontaneous contractile behavior in Hydra polyps

Yasuharu Takaku et al.

SCIENTIFIC REPORTS (2014)

Article Evolutionary Biology

Evolution of the Pax-Six-Eya-Dach network: the calcisponge case study

Sofia A. V. Fortunato et al.

EVODEVO (2014)

Article Biotechnology & Applied Microbiology

A first exploration of genome size diversity in sponges

Nicholas W. Jeffery et al.

GENOME (2013)

Article Multidisciplinary Sciences

Transcription factor evolution in eukaryotes and the assembly of the regulatory toolkit in multicellular lineages

Alex de Mendoza et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2013)

Article Biochemical Research Methods

SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing

Anton Bankevich et al.

JOURNAL OF COMPUTATIONAL BIOLOGY (2012)

Article Biology

Blue-light-receptive cryptochrome is expressed in a sponge eye lacking neurons and opsin

Ajna S. Rivera et al.

JOURNAL OF EXPERIMENTAL BIOLOGY (2012)

Article Evolutionary Biology

Epithelia, an Evolutionary Novelty of Metazoans

Sally P. Leys et al.

JOURNAL OF EXPERIMENTAL ZOOLOGY PART B-MOLECULAR AND DEVELOPMENTAL EVOLUTION (2012)

Article Biochemistry & Molecular Biology

Origin and Evolution of Laminin Gene Family Diversity

Bryony Fahey et al.

MOLECULAR BIOLOGY AND EVOLUTION (2012)

Review Biochemistry & Molecular Biology

Assessing calcareous sponges and their associated bacteria for the discovery of new bioactive natural products

Melanie Roue et al.

NATURAL PRODUCT REPORTS (2012)

Article Multidisciplinary Sciences

Origin of metazoan cadherin diversity and the antiquity of the classical cadherin/β-catenin complex

Scott Anthony Nichols et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2012)

Article Multidisciplinary Sciences

Centrosome Loss in the Evolution of Planarians

Juliette Azimzadeh et al.

SCIENCE (2012)

Article Biotechnology & Applied Microbiology

Occurrence of a Silicatein Gene in Glass Sponges (Hexactinellida: Porifera)

Galina N. Veremeichik et al.

MARINE BIOTECHNOLOGY (2011)

Article Biochemistry & Molecular Biology

CDD: a Conserved Domain Database for the functional annotation of proteins

Aron Marchler-Bauer et al.

NUCLEIC ACIDS RESEARCH (2011)

Article Biochemical Research Methods

Accelerated Profile HMM Searches

Sean R. Eddy

PLOS COMPUTATIONAL BIOLOGY (2011)

Article Evolutionary Biology

Origin of animal epithelia: insights from the sponge genome

Bryony Fahey et al.

EVOLUTION & DEVELOPMENT (2010)

Article Multidisciplinary Sciences

The Amphimedon queenslandica genome and the evolution of animal complexity

Mansi Srivastava et al.

NATURE (2010)

Article Biochemistry & Molecular Biology

Ab initio gene identification in metagenomic sequences

Wenhan Zhu et al.

NUCLEIC ACIDS RESEARCH (2010)

Article Multidisciplinary Sciences

Competing Activities of Heterotrimeric G Proteins in Drosophila Wing Maturation

Natalya Katanayeva et al.

PLOS ONE (2010)

Article Multidisciplinary Sciences

Nitrosopumilus maritimus genome reveals unique mechanisms for nitrification and autotrophy in globally distributed marine crenarchaea

C. B. Walker et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2010)

Review Cell Biology

Diverse evolutionary paths to cell adhesion

Monika Abedin et al.

TRENDS IN CELL BIOLOGY (2010)

Review Evolutionary Biology

Origin and evolution of the Notch signalling pathway: an overview from eukaryotic genomes

Eve Gazave et al.

BMC EVOLUTIONARY BIOLOGY (2009)

Article Zoology

Epithelia and integration in sponges

Sally P. Leys et al.

INTEGRATIVE AND COMPARATIVE BIOLOGY (2009)

Review Zoology

Origin of the neuro-sensory system: new and expected insights from sponges

Emmanuelle Renard et al.

INTEGRATIVE ZOOLOGY (2009)

Article Biochemistry & Molecular Biology

Bio-sintering processes in hexactinellid sponges: Fusion of bio-silica in giant basal spicules from Monorhaphis chuni

Werner E. G. Mueller et al.

JOURNAL OF STRUCTURAL BIOLOGY (2009)

Article Multidisciplinary Sciences

The fifth class of Gα proteins

Yuichiro Oka et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2009)

Article Biochemistry & Molecular Biology

Sponge genes provide new insight into the evolutionary origin of the neurogenic circuit

Gemma S. Richards et al.

CURRENT BIOLOGY (2008)

Article Zoology

Sponge cytogenetics - Mitotic chromosomes of ten species of freshwater sponge

Junko Ishijima et al.

ZOOLOGICAL SCIENCE (2008)

Article Biology

Coordinated contractions effectively expel water from the aquiferous system of a freshwater sponge

Glen R. D. Elliott et al.

JOURNAL OF EXPERIMENTAL BIOLOGY (2007)

Article Biochemistry & Molecular Biology

The NK homeobox gene cluster predates the origin of Hox genes

Claire Larroux et al.

CURRENT BIOLOGY (2007)

Article Developmental Biology

The echinoderm adhesome

Charles A. Whittaker et al.

DEVELOPMENTAL BIOLOGY (2006)

Article Multidisciplinary Sciences

Genomic analysis of the uncultivated marine crenarchaeote Cenarchaeum symbiosum

Steven J. Hallam et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2006)

Article Multidisciplinary Sciences

Early evolution of animal cell signaling and adhesion genes

Scott A. Nichols et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2006)

Review Zoology

The ecology of the sponge larva

M Maldonado

CANADIAN JOURNAL OF ZOOLOGY (2006)

Review Zoology

Physiology of coordination in sponges

SP Leys et al.

CANADIAN JOURNAL OF ZOOLOGY-REVUE CANADIENNE DE ZOOLOGIE (2006)

Review Genetics & Heredity

The genesis and evolution of homeobox gene clusters

J Garcia-Fernàndez

NATURE REVIEWS GENETICS (2005)

Article Biochemistry & Molecular Biology

InterProScan: protein domains identifier

E Quevillon et al.

NUCLEIC ACIDS RESEARCH (2005)

Letter Biochemistry & Molecular Biology

Evolution of gap junctions:: The missing link?

H Alexopoulos et al.

CURRENT BIOLOGY (2004)

Article Biochemistry & Molecular Biology

A combined transmembrane topology and signal peptide prediction method

L Käll et al.

JOURNAL OF MOLECULAR BIOLOGY (2004)

Review Biotechnology & Applied Microbiology

An overview of the basic helix-loop-helix proteins

S Jones

GENOME BIOLOGY (2004)

Article Biochemistry & Molecular Biology

Molecular and functional analysis of the (6-4) photolyase from the hexactinellid Aphrocallistes vastus

HC Schröder et al.

BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS (2003)

Article Zoology

Epithelium - The primary building block for metazoan complexity

S Tyler

INTEGRATIVE AND COMPARATIVE BIOLOGY (2003)

Article Anatomy & Morphology

Comparative study of spiculogenesis in demosponge and hexactinellid larvae

SP Leys

MICROSCOPY RESEARCH AND TECHNIQUE (2003)

Review Biotechnology & Applied Microbiology

Microbial production of vitamin B-12

JH Martens et al.

APPLIED MICROBIOLOGY AND BIOTECHNOLOGY (2002)

Article Biology

Cytological basis of photoresponsive behavior in a sponge larva

SP Leys et al.

BIOLOGICAL BULLETIN (2001)