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This repository has four functions:

  1. Host the script that will generate a semi annotated transcriptome from the submitted transcriptomes to NCBI Transcriptome Shotgun Assembly (TSA)
  2. Host other scripts used in the analysis of the paper
  3. Host the run statistics for the de novo assemblies
  4. Link to the data hosted at external locations (NCBI and Data Dryad Repository)

Publication

Reich A., Dunn C.W., Akasaka K., Wessel, G.M. 2015. Phylogenomic Analyses of Echinodermata support the sister groups of Asterozoa and Echinozoa. PLoS One. 10(3) (Epub ahead of print).

Link to manuscript at NCBI and PLoS One

1. Generate a semi annotated transcriptome

  • Click on link for transcriptome of interest (see Table 1)
  • Download and unzip the fsa_nt.gz file
  • Download and unzip the Master_accs.gz file from this repository
  • Run AnnotateTSAfasta.py script (found here)

2. Scripts used in analyses

3. Agalma resource reports for assemblies

4. Data hosted at external sites

  • NCBI BioProject which includes links to the raw reads in the Short Read Archive
  • Data Dryad Repository which includes the constraint trees and supermatrix alignments in phylip format

Table 1

Species name with link to NCBI TSA Taxonomy ID with link to NCBI Taxonomy Ovary Transcriptome Accession Prefix
Leptasterias sp. 1462732 GAVC
Henricia sp. 1462731 GAVP
Echinaster spinulosus 1451296 GAVE
Apostichopus japonicus 307972 GAVS
Lytechinus variegatus 7654 GAUR
Sphaerechinus granularis 39374 GAVR
Asterias amurensis 7602 GAVJ
Asterina pectinifera 7594 GAVK
Parastichopus californicus 7689 GAVO
Pisaster ochraceus 7612 GAVN
Marthasterias glacialis 7609 GAVI
Luidia clathrata 133437 GAVQ
Echinarachnius parma 869203 GAVF
Asterias rubens 7604 GAUU
Sclerodactyla briareus 7710 GAUT
Asterias forbesi 7603 GAUS
Ophiocoma echinata 331088 GAUQ
Oxycomanthus japonicus 693457 GAZO
Patiria miniata 46514 GAWB
Eucidaris tribuloides 7632 GAZP