Transcriptomes

Transcriptomes for Strongylocentrotus purpuratus, Lytechinus variegatus, Patiria miniata, Eucidaris tribuloides and Parastichopus parvamensis are posted here.

Ovary transcriptomes from 18 echinoderms with representatives from all 5 groups of echinoderms are posted here.

Strongylocentrotus purpuratus Transcriptome

These RNA-seq data were generated from a comprehensive transcriptome survey of 22 samples, including 10 embryonic stages, 6 feeding larval and metamorphosed juvenile stages, and 6 adult tissues.

In total 784 million 76bp pair-end reads were obtained. The reads were mapped onto the S. purpuratus genome v3.0, and new gene models were constructed. These RNA-seq models are identified with WHL22 prefix. Various information about the analysis is provided on this page.

The analysis was done based on S. purpuratus genome v3.0. The genome v3.0 differs with the current v3.1 in only a few places due to the removal of contaminating microbial sequences. The assembled transcript sequences remain the same, although the coordinates of exons might change.

For more detailed information, please see the Publications

  • Tu Q, Cameron RA, Worley KC, Gibbs RA, Davidson EH. 2012. Gene structure in the sea urchin Strongylocentrotus purpuratus based on transcriptome analysis. Genome Res 22: 2079-2087. doi:10.1101/gr.139170.112
  • Tu Q, Cameron RA, Davidson EH. 2014. Quantitative developmental transcriptomes of the sea urchin Strongylocentrotus purpuratus. Dev Biol 385: 160–167. doi:10.1016/j.ydbio.2013.11.019

    • Lytechinus variegatus

    Two RNA pools, a pre-gastrula developmental stage pool and one of post-gastrular embryonic stages, were sequenced on the 454 platform as part of the original genome project. These were used to assess the completeness of the sequence assembly. To facilitate gene discovery by the community the two pools of reads were separately assembled using Velvet (ref) and the assembled transcripts were mounted at Echinobase as both a blast database and a query database. There is a BLAST database and a query tool reporting matches against the SPU gene models

    Patiria miniata

    Contigs assembled from a series of Patiria miniata transcriptome sequencing runs from 454 XLR sequencing of Patiria miniata single-direction libraries were submitted to the NCBI Nucleotide Sequence Database on August 4, 2010by the Human Genome Sequencing Center, Department, of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA. The accession numbers are HP081117-HP139664. The assembly was made from reads in the Sequence Read Archive: under projects: SRX021529, SRX021530 and SRX021531. From these projects a total of 700 million reads were collected. About 58,000 individual contigs were derived. There is a BLAST database and a query tool reporting matches against the SPU gene models

    Eucidaris tribuloides

    E. tribloides RNA sequence database is assembled from the transcriptome of a sea urchin in the gastrula stage and combined it with the Roche 454 transcriptome assemblies from Baylor HGSC. The transcriptome sequences from Baylor are available at NCBI under BioPoject 62465. There is a BLAST database and a query tool reporting matches against the SPU gene models

    Parastichopus parvimensis

    There is a BLAST database and a query tool reporting matches against the SPU gene models

    Ovary Transcriptomes

    The ovarian transcriptomes that were produced by Adrian Reich and published as Phylogenomic Analyses of Echinodermata Support the Sister Groups of Asterozoa and Echinozoa.
    Adrian Reich Thesis 2014 p. 13
    "We sequenced 23 de novo transcriptomes from all five classes of echinoderms. Using multiple phylogenetic methods at a variety of sampling depths we have constructed a well-supported phylogenetic tree of Echinodermata, including support for the sister groups of Asterozoa (sea stars and brittle stars) and Echinozoa (sea urchins and sea cucumbers). The larger of the two analyzed datasets includes 630,945 amino acid sites across 4,645 peptide sequences and 30 taxa. These results will help inform developmental and evolutionary studies specifically in echinoderms and deuterostomes in general."

    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.

    There is a BLAST database and a query tool reporting matches against the SPU gene models