Ovary Transcriptomes

The ovarian transcriptomes posted here were produced by Adrian Reich and published as Phylogenomic Analyses of Echinodermata Support the Sister Groups of Asterozoa and Echinozoa. Below are several excerpts from his thesis explaining the data.
Echinoderms (sea urchins, sea stars, brittle stars, sea lilies and sea cucumbers) are a very rich group of organisms, second only in the number of species in Deuterostomia after chordates. Echinoderms serve as excellent model systems for developmental biology due to their diverse developmental mechanisms, tractable laboratory use, and close phylogenetic distance to chordates. In addition, echinoderms are very well represented in the fossil record, including some larval features, making echinoderms a valuable system for studying evolutionary development. However, the phylogenetic relationships within the phylum have been contentious; generating little overlap between molecular, morphological and combined analyses. In order to resolve the controversies, 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. Adrian Reich Thesis 2014 p. 13
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.

Table 1: Assembly and post assembly summary by taxa. Adrian Reich Thesis 2014 p. 32

Species Assembled Transcripts Sample Source SwissProt Transcripts SwissProt N50
Aplysia californica 26,249 RefSeq 18,424 4,099
Branchiostoma floridae 28,575 RefSeq 21,881 2,127
Gallus gallus 36,995 RefSeq 31,868 4,527
Homo sapiens 91,944 RefSeq 77,696 4,208
Nematostella vectensis 24,462 RefSeq 18,261 1,609
Saccoglossus kowalevskii 12,851 RefSeq 10,936 2,294
Strongylocentrotus purpuratus 23,078 RefSeq 19,554 4,363
Ophiocoma wendtii 5,025 454 1,995 771
Ophionotus victoriae 3,210 454 694 1,645
Parastichopus parvimensis 107,585 72bp PE 34,809 3,076
Eucidaris tribuloides 45,385 80bp PE 7,410 1,307
Patiria miniata 76,847 80bp PE 24,679 2,494
Oxycomanthus japonicus 39,225 80bp PE 15,868 2,816
Ophiocoma echinata 111,491 80bp PE 21,485 2,454
Lytechinus variegatus 90,621 80bp PE 25,994 2,914
Asterias forbesi 68,714 80bp PE 22,625 2,784
Sclerodactyla briareus 58,273 80bp PE 19,297 3,154
Asterias rubens 81,470 100bp PE 25,733 2,349
Henricia species 137,160 100bp PE 36,754 2,231
Echinaster spinulosus 119,580 100bp PE 34,231 2,314
Echinarachnius parma 96,977 100bp PE 26,016 2,017
Leptasterias species 108,544 100bp PE 33,803 3,172
Luidia clathrata 84,380 100bp PE 23,407 1,835
Marthasterias glacialis 118,847 100bp PE 28,327 1,928
Pisaster ochraceus 37,111 100bp PE 10,361 1,225
Parastichopus californicus 30,607 100bp PE 10,379 1,132
Sphaerechinus granularis 92,460 100bp PE 24,024 2,008
Apostichopus japonicus 85,061 100bp PE 26,902 1,943
Patiria pectinifera 118,294 100bp PE 33,009 1,746
Asterias amurensis 63,300 100bp PE 19,592 2,088