Echinobase - a resource for studies of evolution and development
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Echinobase

Echinobase - a resource for studies of evolution and development

Echinoderms are an exclusively marine phylum of Deuterostomes which emerged in the lower Cambrian (>540 MYA) and split from Chordata 400-500 MYA. Echinodermata includes 7,000 extant and 13,000 extinct species.

The echinoderms are split into five classes: the basal branch Crinoidea (feather lilies), Ophiuroidea (brittle stars), Asteroridea (star fish), Echinoidea (sea urchins and sand dollars), and Holotheroidea (sea cucumber). The Ophiuroids and Asteroids form the superclass Asterozoa, the Echinoids and Holotheroids from the superclass Echinozoa, and these two superclasses form the subphyla Eleutherozoa which contains all four motile classes of Echinodermata.

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 providing abundant material for developmental research
  • transparent embryos and larvae have enabled detailed descriptions of anatomical structures and developmental stages
  • there is variation in development within and between a genus providing insights from evolutionary "experiments"

The Echinoderm Anatomical Ontology (ECAO), a structured ontology of anatomical structures is in development for Echinobase so that molecular data can be mapped to developmental cell types and stages of echinoderms.

 
 

Last Updated: 2020-04-30
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Finding your gene and using new identifiers, a brief video tutorial.

Anneissia japonica (feather star)


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Echinobase Data Statistics

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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: