• Join EchinoClub Monthly Forums

     

    The Wessel lab will lead off on Friday March 26, 2021 at 7am PST, 10am EST and 4pm CET.

    Hope you can join us, connection details will be available before the event.

    Read More...

  • FAQs - General

    Trying to find information?

    Check the FAQs!

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  • DBSUMI meeting postponed until 2022

     

    The DBSUMI meeting has been rescheduled for April 13-17, 2022 due to the COVID-19 pandemic. 

    This international conference has occurred every 18 months since 1981.

    Check back for updates about the 26th meeting of echinoderm scientists.

    Read More...

  • Data Exploration

    Echinobase has data available for download through the FTP site.

    Links to other echinoderm datasets are collected.

    Tutorial video here.

    Read More...

  • FAQs - Gene Names and IDs

    Discovery of new genes, or analysis of current genes sometimes leads to gene nomenclature questions.

    Genome-wide studies involving transcripts and proteins require related IDs.

    Here we have listed a few of the more common questions.

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  • CRISPR/Cas Resources

    Echinobase curators have collected the gRNA sequences that have been used to date.

    Read More...

  • Echinobase Identifiers

     

    Echinobase identifiers have been updated.

    Suggestions for finding your gene of interest and using the new identifiers are available in this

    video tutorial.

     

     

    Read More...

  • The Echinoderm Anatomical Ontology (ECAO)

     

    An ontology has been developed for echinoderms using standardized terms to describe anatomical cell types and structures and developmental stages.

     

    These spatiotemporal terms will be used by curators to link to gene expression data.

     

     

    Read More...

  • New crinoid genome

    Echinobase is providing partial support for the newly released feather star, Anneissia japonica, genome.

    The genome can be viewed in JBrowse and BLAST is supported.

    Read More...

  • Resources, Community, Literature and Genomics

    Echinobase has resources and community support content in addition to collected and curated literature and extensive genomic content.
    A short tutorial video.

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  • Echinoderms are Deuterostomes

     

    The superphylum

    Deuterostomia includes

    Chordata, 

    Echinodermata and

    Hemichordata phyla.

    Echinodermata includes

    marine only species,

    7,000 extant and

    13,000 extinct. 

    . 

    Read More...

  • Join EchinoClub Monthly Forums

     

    The Wessel lab will lead off on Friday March 26, 2021 at 7am PST, 10am EST and 4pm CET.

    Hope you can join us, connection details will be available before the event.

    Read More...
The New Echinobase
Latest Echinobase Content
Visit the previous echinobase.org
Announcements

Wessel lab 10am EST March 26, 2021.

Virtual EchinoClub until then.

Check here for answers to questions and how-to notes.

Gene nomenclature and related ID questions.

The wiki page has gRNA sequences that have been used in Echinoderms.

A brief overview of Echinobase content and a video.

Echinobase has data available for download through the FTP site with a tutorial video.

Finding your gene and using new identifiers, a brief video tutorial.

Anneissia japonica (feather star)

Archived Announcements

Tutorial Videos

Echinobase Data Statistics

Free-Usage Images

Genes & Expressions
Genome Browsers

Browse the past and present versions of genomes and community contributed datasets. If you find a dataset missing or have a new dataset to contribute for one of our supported genomes please contact us!

[+] S. purpuratus v.5.0

  S. purpuratus v.4.2

  S. purpuratus v.3.1

A. planci v.1.0

A. japonica v.1.0

EchinoBLAST

BLAST Echinoderm nucleotide and protein databases.

Strongylocentrotus purpuratus

Genome, RNA, Proteins, CDS

Acanthaster planci

Genome, RNA, Proteins, CDS

Anneissia japonica

Genome

Deuterostomia (superphylum) includes Chordata, Echinodermata and Hemichordata phylum, Echinodermata emerged in the Lower Cambrian (> 540 million years ago, MYA) and split from Chordata 400-500 MYA, Echinodermata includes 7,000 extant and 13,000 extinct, marine only species. Echinodermata has 5 Classes: the basal branching Crinoidea (crinoids), and the 4 motile Eleutherozoa Classes including Asterozoa, the Ophiuroidea (brittle stars) and Asteroidea (starfish) and the Echinozoa, the Echinoidea (sea urchins and sand dollars) and Holotheroidea (sea cucumber).

Echinoderms are model organisms for studying embryo development and regeneration due to many unique features including:
  • the ability to synchronize fertilization of millions of eggs
  • transparent embryos and larvae
  • varied development within and between a genus
Echinobase exists to support the international research community with a centralized, comprehensive, integrated and easy to use web based resource that provides access to the diverse and rich genomic, expression and functional data available for Echinoderm research.

Echinobase is organized around the genepage which collects and displays information about genes, orthology, and links to research papers and gene models of echinoderm species are associated with the genome sequence using JBrowse. Temporal developmental gene expression data will be displayed when available, and spatial cell type information will be associated using the Echinoderm Anatomical Ontology (ECAO).

Echinobase provides a critical data sharing infrastructure for other NIH-funded projects, and is a focal point for the echinoderm community. In addition to our primary goal of supporting echinoderm researchers, Echinobase enhances the availability and visibility of Echinoderm data to the broader biomedical research community.
S. purpuratus
The purple sea urchin, Strongylocentrotus purpuratus, lives in lower intertidal and nearshore subtidal communities along the eastern edge of the Pacific Ocean extending from Ensenada, Mexico to British Columbia, Canada. Morphological development of S. purpuratus from embryo to adult has been studied for over 100 years and recent decades have added genetic and genomic data to our knowledge of this model organism.

The substantially improved current release of the purple sea urchin genome assembly (Spur5.0) is sixth in the series.

Learn more about the genomics of the purple sea urchin.

A. planci
The crown-of-thorns seastar (COTS), Acanthaster planci, is is named for the spines that cover the top of its large body and multiple arms. A. planci lives in Indo-Pacific waters and preys upon corals. Outbreaks where large numbers of COTS aggregate can decimate coral reefs. Due to their destructive nature the genome was sequenced in the search for biocontrol strategies. The current version of the A. planci genome, v1.0, is available on Echinobase.

Learn more about the genomics of the crown-of-thorns seastar.

The development of echinoderm embryos and larvae has been studied for over 100 years. Echinoderm eggs are fertilized externally and embryos and larvae are transparent, enabling detailed descriptions of the structure and timing of the development of multiple species. The variation in developmental patterns is used to improve understanding of these vital processes in echinoderms and deuterostomes.

Skeletogenesis in echinoderms is diverse and well documented and an area of active research.

Regeneration capability makes echinoderms ideal organisms for the study of these processes at the anatomical and genetic levels.

Echinoderms are marine organisms harvested from the wild, live in aquariums, fertilize and reproduce externally.

Animal suppliers and protocols

Protocols and reagents for studying gene expression:

qPCR and immunofluorescence

Microinjection, morpholinos and BACs

Genomics methods:

RNA-seq and scRNA-seq

ChIP-seq and ATAC-seq

For studies of regulatory sequences BAC Libraries are available. Refer to the BAC Table for those that can been identified using BAC-ENDs and the genome browser or screen the BAC library for your gene of interest. An in-frame fusion of a reporter gene can be engineered into the locus of interest by recombineering to assess gene expression and putative regulatory sequences.

Echinobase has engines that automatically search the scientific literature and collect articles related to Echinoderms allowing users to come to a site to access all currently available information regarding in one centralized location. Papers are manually curated to link genomic information to protocols and reagents for studies of development and evolution.

Search for papers

Search for books

The Echinoderm Community is able to submit new genomes for partial support when assembly and annotation are publicly available through Genbank. The assemblies, annotations, and functional data tracks (GFF files) will be available on JBrowse and can be searched via BLAST.

The Echinobase PIs and SAB members will decide the new species for full support and integration into the database as gene pages with complete functionality, including gene names and symbols, synonyms, literature, orthology, and developmental gene expression display. This process will only be possible when the genome has been fully processed by the NCBI annotation pipeline. Suggestions for priority species are always welcome.

Useful links: