Abstract

The amount of genomic sequence information continues to grow at an exponential rate, while the identification and characterization of genes without known homologs remains a major challenge. For non-model organisms with limited resources for manipulative studies, high-throughput transcriptomic data combined with bioinformatics methods provide a powerful approach to obtain initial insights into the function of unknown genes. In this study, we report the identification and characterization of a novel family of putatively secreted, small, cysteine-rich proteins herein named Small Cysteine-Rich Proteins (SCRiPs). Their discovery in expressed sequence tag (EST) libraries from the coral Montastraea faveolata required the performance of an iterative search strategy based on BLAST and Hidden-Markov-Model algorithms. While a discernible homolog could neither be identified in the genome of the sea anemone Nematostella vectensis, nor in a large EST dataset from the symbiotic sea anemone Aiptasia pallida, we identified SCRiP sequences in multiple scleractinian coral species. Therefore, we postulate that this gene family is an example of lineage-specific gene expansion in reef-building corals. Previously published gene expression microarray data suggest that a sub-group of SCRiPs is highly responsive to thermal stress. Furthermore, data from microarray experiments investigating developmental gene expression in the coral Acropora millepora suggest that different SCRiPs may play distinct roles in the development of corals. The function of these proteins remains to be elucidated, but our results from in silico, transcriptomic, and phylogenetic analyses provide initial insights into the evolution of SCRiPs, a novel, taxonomically restricted gene family that may be responsible for a lineage-specific trait in scleractinian corals.

Highlights

  • The genome biology of basal metazoan phyla, such as the Cnidaria, promises to provide great insight into animal evolution

  • We named this protein Small Cysteine-Rich Protein 1 (Mfav-SCRiP1). We subsequently used this novel sequence in a tBLASTn search against the expressed sequence tag (EST) library and discovered three additional sequences: Mfav-SCRiP2, Mfav-SCRiP3a, and Mfav-SCRiP4

  • The resulting maximum likelihood tree supports the grouping of Mfav-SCRiP2 and Mfav-SCRiP5, Mfav-SCRiP4 and Mfav-SCRiP6, and Mcap-SCRiP1 and AmilSCRiP3, while the relationship between the remaining Small Cysteine-Rich Proteins (SCRiPs), i.e. Mfav-SCRiP1, 8 and Amil-SCRiP2 could not be resolved (Figure 2). These results suggest that Mfav-SCRiP2/5 and MfavSCRiP4/6 arose through gene duplication within M. faveolata

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Summary

Introduction

The genome biology of basal metazoan phyla, such as the Cnidaria, promises to provide great insight into animal evolution. In terms of genomic resources, the hexacorallian lineage currently provides the largest dataset among the anthozoan cnidarians [1]. These resources include a draft genome of the sea anemone Nematostella vectensis [2], and expressed sequence tag (EST) datasets from the sea anemone Aiptasia pallida [3] and the reef-building corals Acropora millepora [4], Acropora palmata, and Montastraea faveolata [5]. Hexacorallians include stony corals (order Scleractinia), which commonly maintain a stable symbiosis with unicellular algae in the genus Symbiodinium and have the ability to build complex skeletal structures of calcium carbonate. The discovery of genes that are found in only one or a limited number of taxa is of particular interest, since they may code for proteins responsible for taxon-specific adaptations [8]

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