Latest News

  • June 16, 2017 | A new Patiria miniata genome assembly is posted
      We sought to improve the Patiria miniata genome assembly with additional PacBio sequences. We generated a new PacBio read dataset at the Duke University Sequencing Center using our reference individual DNA. The read dataset contains 2 million reads and 15.8 billion bp. The read N50 is 10.4 Kb. We used PBJelly2 to combine the PacBio reads with the previously assembled contigs. The results were an improvement in contig size and number with only a small reduction in the number of scaffolds (Table). The P. miniata Gene v2.0 set was generated using MAKER2 pipeline from v2.0 genome assembly.
    Pm v1.0 Pm v2.0
    Scaffold number 60,183 57,698
    Scaffold N50 52,6141 76,341
    Contig number 179,756 131,779
    Contig N50 9,466 18,676

      Since the reagents and references were manually curated using V1.0 gene models and will not change, we transferred this information directly to the new version. The genome browser displays the new version but the BLAST and Download pages have assemblies, gene models, database dumps and gff3 for the current and previous assemblies.

  • May 03, 2017 | Attention: Take the Echinobase website survey please!


    Dear EchinoBase Users:

    We would greatly appreciate your input on the following survey:

    https://www.surveymonkey.com/r/MPMK576

    We will use this information to prioritize upcoming work on the database as well as justify requests for funding for this resource. Only the first two questions are required, and will take just a couple minutes, but we hope you can add more information through the comments.

    Please also encourage all members of your group to respond.

    Best Wishes
    Veronica, Andy Cameron and Chuck Ettensohn.

  • February 09, 2017 | Ovary Transcriptome back by popular demand
    1. Ovary Transcriptome can be accessed here
    2. Blast database can be accessed here
    3. Transcriptome Search can be accessed here
  • February 06, 2017 | Link-out to Echinoderm Transcriptome @SRA and @GEO
  • February 06, 2017 | Ovary Transcriptome retired
    We have retired the BLAST and transcriptome search pages for ovary transcriptome. The raw reads and assembled transcriptomes in this collection have been deposited in the GenBank database (NCBI BioProject no. PRJNA236087). Assembly statistics and agalma resource reports can be found at: https://bitbucket.org/AdrianReich/phylogenetic-analysis-of-echinoderms.
  • January 03, 2017 | Final Gene Regulatory Network White Paper posted
  • December 01, 2016 | SAVE THE DATE! The Developmental Biology of the Sea Urchin XXIV Meeting will be held from April 5-9, 2017 at the Marine Biological Laboratory, Woods Hole, MA. A broad and inclusive program that will include research done on other marine invertebrates is planned. A meeting web site is coming soon.
  • 7 November 2016 | Manual annotation: Reagent and literature updates for S.purpuratus, P.miniata and L.variegatus posted
      Reagent and literature updated for S.purpuratus,P.miniata and L.variegatus which can be accessed at Gene Search Page
  • 1 November 2016 | Gene Regulatory Network White Paper posted
  • 15 June 2016 | Manual annotation: Reagent and literature updates for S.purpuratus and L.variegatus posted
      Reagent and literature updated for S.purpuratus and L.variegatus which can be accessed at Gene Search Page
  • 30 March 2016 | Assembly statistic plot added to species pages
      The assembly plot is a representation of genome assembly quality which condenses a number of key metrics into a single scale independent visualization.Typically a large red segment (longest scaffold represents a significant proportion of the assembly) and small central pink/purple area (small number of contigs) are features of a good assembly. These graphs were generated using assembly statistics code from github.com/rjchallis/assembly_stats. More information on how to interpret these graphs can be found here
      Strongylocentrotus purpuratus
      Patiria miniata
      Lytechinus variegatus
      Parastichopus parvimensis
  • 27 January 2016 | Sea Urchin Genome Resource white paper posted
  • 21 January 2016 | Reagent and literature updates for S.purpuratus, L.variegatus and P.miniata posted
      Reagent and literature updated for S.purpuratus, L.variegatus and P.miniata which can be accessed at Gene Search Page
  • 1 November 2015|Gene predictions for Lytechinus variegatus 2.2 posted
      The latest version of the Lv genome (v2.2) is an upgrade of version 0.4 using PacBio reads with an N50 length of 2.9kb which produced an improved assembly with a contig N50 of 9.7 kb and a scaffold N50 of 46Kb. MAKER2 pipeline is used for gene predictions.
      Gene Search and electronic annotation for Lytechinus variegatus 2.2 assembly
      Genome Browser for Lytechinus variegatus 2.2 assembly
      Download Lytechinus variegatus 2.2 assembly
  • 1 October 2015|Gene predictions for Parastichopus parvimensis 1.0 posted
      Parastichopus parvimensis 1.0 genome assembly used Illumina sequencing technology with contig N50 9.5kb and scaffold N50 of 89kb. MAKER2 pipeline is used for gene predictions.
      Gene Search and electronic annotation for Parastichopus parvimensis 1.0 assembly
      Genome Browser for Parastichopus parvimensis 1.0 assembly
      Download Parastichopus parvimensis 1.0 assembly
  • 1 September 2015 | Reannotation of GLEAN prediction models
      A subset of the original GLEAN prediction models generated against the Spur0.5 assembly has been structurally reannotated on the Spur3.1 assembly using the WebApollo genomic annotation editor. Genes encoding transcription factors and developmental signaling molecules were given priority in these reannotation efforts. The resulting modifications are now available for viewing on Echinobase as a track on the Jbrowse genome browser.
  • 18 August 2015 | ATAC-seq Genome Browser for S.purpuratus posted
    1. This is to let you know that a new resource is now available on JBrowse in Echinobase. This is a developmental series of ATACseq measurements for S. purpuratus embryos. In our experience and that of others focused on encoded genomic regulatory sequences, ATACseq data provide a vastly superior indication of the genomic location of putative cis-regulatory elements of all forms (see Buenrostro et al., Nature Methods 10, 1213–1218, 2013). The direct link is here.

      A comparative repeat on a second timed batch of embryos will soon be posted, as will a similar set of observations on L. variegatus. The data included in this resource were created in our laboratory by Erika Vielmas, and were computationally reduced by Parul Kudtarkar at Echinobase, although of course the whole Echinobase team contributed essentially.

      We shall presently submit for publication an analysis of various aspects of these data, including validation in respect to some known genes. We wanted this to be available for your use as soon as possible, however.

      Eric Davidson

  • 4 August 2015 | 85 S.purpuratus genes manually re-annotated
    1. 85 Strongylocentrotus purpuratus genes have been re-annotated. You can access the list of re-annotated genes here
  • 29 April 2015 | Echinobase literature and reagent list has been updated with 125 new reagent and 17 references
    1. Strongylocentrotus purpuratus: 13 new references, 79 new reagents
    2. Lytechinus variegatus: 3 new references
    3. Patiria miniata: 2 new references, 46 new reagents
  • 30 June 2015 | 3146 Strongylocentrotus
    purpuratus genes re-annotated,64 new gene added
    1. 3146 Strongylocentrotus purpuratus genes have been re-annotated. You can access the list of re-annotated genes here
    2. 64 new genes have been added with SPU ids SPU_031052-SPU_031115
  • 26 June 2015 | SpBase has been retired
    1. Please check Echinobase. If you have doubts regarding data or tool usage refer to our user guide or write to us. SpBase web code can be downloaded here
  • 15 May 2015 | BAC Table: Updated list of BAC clones has been posted
    1. You can access BAC table table here
    2. We have also posted a BAC library guide here
  • 14 May 2015 | Parastichopus parvimensis 1.0 genome assembly posted
    1. Parastichopus parvimensis 1.0 genome assembly can be accessed here
    2. Blast database can be accessed here

    Global statistics

    Total sequence length 873,088,235
    Total assembly gap length 112,433,614
    Gaps between scaffolds 0
    Number of scaffolds 21,559
    Scaffold N50 89,133
    Scaffold L50 2,945
    Number of contigs 150,862
    Contig N50 9,587
    Contig L50 22,963


  • 14 May 2015 | Lytechinus variegatus 2.2 genome assembly posted
    1. Lytechinus variegatus 2.2 genome assembly can be accessed here
    2. Blast database can be accessed here

    Global statistics

    Total sequence length 1,061,195,396
    Total assembly gap length 57,125,815
    Gaps between scaffolds 0
    Number of scaffolds 322,794
    Scaffold N50 46,348
    Scaffold L50 6,117
    Number of contigs 452,418
    Contig N50 9,657
    Contig L50 26,801


  • 14 May 2015 | Ophiothrix spiculata 1.0 genome assembly posted
    1. Ophiothrix spiculata 1.0 genome assembly can be accessed here
    2. Blast database can be accessed here

    Global statistics

    Total sequence length 2,764,315,159
    Total assembly gap length 554,173,354
    Number of contigs 644,798
    Contig N50 6,474
    Contig L50 97,818


  • 14 May 2015 | Strongylocentrotus purpuratus 4.2 assembly posted
    1. Strongylocentrotus purpuratus 4.2 genome assembly can be accessed here
    2. Blast database can be accessed here

    Global statistics

    Total sequence length 990,915,289
    Total assembly gap length 88,403,955
    Gaps between scaffolds 0
    Number of scaffolds 31,897
    Scaffold N50 419,550
    Number of contigs 146,295
    Contig N50 16,785


  • 29 April 2015 | Echinobase literature and reagent list has been updated with 24 new reagent and 281 references
    1. Strongylocentrotus purpuratus: 172 new references, 10 new reagents
    2. Lytechinus variegatus: 80 new references
    3. Patiria miniata: 29 new references, 14 new reagents
  • 03 April 2015 | Ovary Transcriptome posted
    1. Ovary Transcriptome can be accessed here
    2. Blast database can be accessed here
    3. Transcriptome Search can be accessed here
  • Echinobase goes public
  • SpBase 7 goes public
  • SpBase 6 goes public
  • SpBase 5 goes public