Abstract
BackgroundContemporary coral reef research has firmly established that a genomic approach is urgently needed to better understand the effects of anthropogenic environmental stress and global climate change on coral holobiont interactions. Here we present KEGG orthology-based annotation of the complete genome sequence of the scleractinian coral Acropora digitifera and provide the first comprehensive view of the genome of a reef-building coral by applying advanced bioinformatics.DescriptionSequences from the KEGG database of protein function were used to construct hidden Markov models. These models were used to search the predicted proteome of A. digitifera to establish complete genomic annotation. The annotated dataset is published in ZoophyteBase, an open access format with different options for searching the data. A particularly useful feature is the ability to use a Google-like search engine that links query words to protein attributes. We present features of the annotation that underpin the molecular structure of key processes of coral physiology that include (1) regulatory proteins of symbiosis, (2) planula and early developmental proteins, (3) neural messengers, receptors and sensory proteins, (4) calcification and Ca2+-signalling proteins, (5) plant-derived proteins, (6) proteins of nitrogen metabolism, (7) DNA repair proteins, (8) stress response proteins, (9) antioxidant and redox-protective proteins, (10) proteins of cellular apoptosis, (11) microbial symbioses and pathogenicity proteins, (12) proteins of viral pathogenicity, (13) toxins and venom, (14) proteins of the chemical defensome and (15) coral epigenetics.ConclusionsWe advocate that providing annotation in an open-access searchable database available to the public domain will give an unprecedented foundation to interrogate the fundamental molecular structure and interactions of coral symbiosis and allow critical questions to be addressed at the genomic level based on combined aspects of evolutionary, developmental, metabolic, and environmental perspectives.
Highlights
Contemporary coral reef research has firmly established that a genomic approach is urgently needed to better understand the effects of anthropogenic environmental stress and global climate change on coral holobiont interactions
Threats to productivity are being imposed by the disruption of coral symbiosis caused in response to increasing thermal stress attributed to global warming [10,11], from an increase in stress-related coral disease [12,13,14], from the discharge of domestic and industrial wastes, pollutants from agricultural development and the transport of sediments in terrestrial runoff [15,16], and potentially from imminent declines in coral calcification owing to rising ocean acidification [17,18,19]
We offer ZoophyteBase as an unprecedented foundation to interrogate the molecular structure of the predicted A. digitifera proteome
Summary
We offer ZoophyteBase as an unprecedented foundation to interrogate the molecular structure of the predicted A. digitifera proteome. Availability and requirements ZoophyteBase was constructed using the Metagenome/ Genome Annotated Sequence Natural Language Search Engine (MEGGASENSE). This is a general system for the annotation of sequence collections and presentation of the results in a database that can be searched using biologically intuitive search terms. In this implementation, the predicted proteome of A. digitifera (genome assembly v1.0 [48]) was used as the source of protein sequences. The predicted proteome sequences of A. digitifera were searched with HMM profiles to link proteins to appropriate KEGG orthologues [50,512].
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