Transcriptome Analysis of the Scleractinian Coral Stylophora pistillata

Abstract

The principal architects of coral reefs are the scleractinian corals; these species are divided in two major clades referred to as “robust” and “complex” corals. Although the molecular diversity of the “complex” clade has received considerable attention, with several expressed sequence tag (EST) libraries and a complete genome sequence having been constructed, the “robust” corals have received far less attention, despite the fact that robust corals have been prominent focal points for ecological and physiological studies. Filling this gap affords important opportunities to extend these studies and to improve our understanding of the differences between the two major clades. Here, we present an EST library from Stylophora pistillata (Esper 1797) and systematically analyze the assembled transcripts compared to putative homologs from the complete proteomes of six well-characterized metazoans: Nematostella vectensis, Hydra magnipapillata, Caenorhabditis elegans, Drosophila melanogaster, Strongylocentrotus purpuratus, Ciona intestinalis and Homo sapiens. Furthermore, comparative analyses of the Stylophora pistillata ESTs were performed against several Cnidaria from the Scleractinia, Actiniaria and Hydrozoa, as well as against other stony corals separately. Functional characterization of S. pistillata transcripts into KOG/COG categories and further description of Wnt and bone morphogenetic protein (BMP) signaling pathways showed that the assembled EST library provides sufficient data and coverage. These features of this new library suggest considerable opportunities for extending our understanding of the molecular and physiological behavior of “robust” corals.

Insights into Frizzled evolution and new perspectives

“…Transcriptomes were compared to reference genomes ( A. queenslandica for sponges and N. vectensis for C. rubrum ) in order to estimate their relative coverage (Supplemental data S2). For instance, this analysis revealed that the number of orthologous proteins found in our transcriptomes is comparable to those found in previous studies in Cnidarians (e.g., Karako‐Lampert et al ). Moreover, 50% of the total sequence length in the O. lobularis transcriptome (44.8 Mbp) is contained in 26,440 contigs of more than 570 bp; 50% of total sequence length in the O. minuta transcriptome (28.1 Mbp) is contained in 9133 contigs of more than 914 bp; and 50% of total sequence length in the C. rubrum transcriptome (87.3 Mbp) is contained in 10,493 contigs of more than 2470 bp.…”

Gene expression profiles during short‐term heat stress in the red sea coral Stylophora pistillata

“…An Agilent two-color gene expression microarray platform with 8 9 15 K probes per slide was used. Oligonucleotide probes (60-mers) were designed based on the approximately 12 000 genes that are predicted to encode proteins retrieved from a recent de novo assembly of 454sequenced EST libraries of S. pistillata (Karako-Lampert et al, 2014). Labeling and hybridization were conducted using the Agilent Low Input Quick Amp Labeling Kit according to the manufacturer's instructions.…”

Recent advances in genomics and transcriptomics of cnidarians

“…These include transcriptomes of Nematostella at different developmental stages Helm et al, 2013;Fredman et al, 2013), but also of Edwardsiella lineata, a species closely related to Nematostella (Stefanik et al, 2014) and corals (Karako-Lampert et al, 2014;Pooyaei Mehr et al, 2013). These data are publicly available and some of them are stored in a database (Fischer et al, 2014), which will certainly support further research activities in cnidarian development and evolution.…”