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KEGG orthology-based annotation of the predicted proteome of Acropora digitifera: ZoophyteBase - an open access and searchable database of a coral genome.

Dunlap WC, Starcevic A, Baranasic D, Diminic J, Zucko J, Gacesa R, van Oppen MJ, Hranueli D, Cullum J, Long PF - BMC Genomics (2013)

Bottom Line: 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.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.We 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.

View Article: PubMed Central - HTML - PubMed

Affiliation: Centre for Marine Microbiology and Genetics, Australian Institute of Marine Science, PMB No. 3 Townsville MC, Townsville 4810, Queensland, Australia.

ABSTRACT

Background: 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. 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.

Description: Sequences 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.

Conclusions: We 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.

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Graphical overview of the user-web interface for ZoophyteBase during a typical search. The home page allows several search functions (A). Text queries using an intelligent Google-like search engine is illustrated by using the query “phagocytosis” (B). This finds 42 hits to KEGG orthologue profiles. One of the hits corresponds to amphiphysin with annotation of two protein homologues encoded in the coral genome. On the data page there is a brief description of the function of amphiphysin together with a PUBMED literature reference. The sequences of the predicted coral proteins can be retrieved (C).
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Figure 1: Graphical overview of the user-web interface for ZoophyteBase during a typical search. The home page allows several search functions (A). Text queries using an intelligent Google-like search engine is illustrated by using the query “phagocytosis” (B). This finds 42 hits to KEGG orthologue profiles. One of the hits corresponds to amphiphysin with annotation of two protein homologues encoded in the coral genome. On the data page there is a brief description of the function of amphiphysin together with a PUBMED literature reference. The sequences of the predicted coral proteins can be retrieved (C).

Mentions: The MEGGASENSE system was used to generate a web interface for ZoophyteBase. The home page (Figure 1A) allows the use of several functions. A text version of the entire annotation can be downloaded for manual inspection. There is a proteome overview that gives statistics about the database and a breakdown of the annotated functions into different categories of genes. A particularly useful feature of ZoophyteBase is the ability to use text queries employing a search engine that provides a relevant inquiry in the absence of an exact match between key words of a search and those described for a functional protein. The search engine uses text from the KEGG-database, PubMed and other sources to establish links between query words to access protein data using an intelligent Google-like search engine implemented by the search platform Lucene/Solr [52]. This helps to overcome the common problem that different terminology is used by different groups of researchers. The use of this search function is illustrated by using the query “phagocytosis” (Figure 1B). This inquiry finds 42 hits to KEGG orthologue profiles. One of the hits corresponds to amphiphysin (a synaptic vesicle protein) with annotation of two protein homologues encoded in the coral genome. On the data page there is a brief description of the function of amphiphysin together with a PUBMED literature reference. The sequences of the predicted coral proteins (Figure 1C) can be retrieved, and it is also possible to analyse such data with computer aided drug design methods [53] to look for conserved domains. There are also two tools for the user to examine matches to protein sequences. The user can carry out a BLAST search against the coral protein sequence or analyse the predicted sequence against HMM profiles used to annotate the coral proteome. These tools require only the user to paste their queury into the sequence window.


KEGG orthology-based annotation of the predicted proteome of Acropora digitifera: ZoophyteBase - an open access and searchable database of a coral genome.

Dunlap WC, Starcevic A, Baranasic D, Diminic J, Zucko J, Gacesa R, van Oppen MJ, Hranueli D, Cullum J, Long PF - BMC Genomics (2013)

Graphical overview of the user-web interface for ZoophyteBase during a typical search. The home page allows several search functions (A). Text queries using an intelligent Google-like search engine is illustrated by using the query “phagocytosis” (B). This finds 42 hits to KEGG orthologue profiles. One of the hits corresponds to amphiphysin with annotation of two protein homologues encoded in the coral genome. On the data page there is a brief description of the function of amphiphysin together with a PUBMED literature reference. The sequences of the predicted coral proteins can be retrieved (C).
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3750612&req=5

Figure 1: Graphical overview of the user-web interface for ZoophyteBase during a typical search. The home page allows several search functions (A). Text queries using an intelligent Google-like search engine is illustrated by using the query “phagocytosis” (B). This finds 42 hits to KEGG orthologue profiles. One of the hits corresponds to amphiphysin with annotation of two protein homologues encoded in the coral genome. On the data page there is a brief description of the function of amphiphysin together with a PUBMED literature reference. The sequences of the predicted coral proteins can be retrieved (C).
Mentions: The MEGGASENSE system was used to generate a web interface for ZoophyteBase. The home page (Figure 1A) allows the use of several functions. A text version of the entire annotation can be downloaded for manual inspection. There is a proteome overview that gives statistics about the database and a breakdown of the annotated functions into different categories of genes. A particularly useful feature of ZoophyteBase is the ability to use text queries employing a search engine that provides a relevant inquiry in the absence of an exact match between key words of a search and those described for a functional protein. The search engine uses text from the KEGG-database, PubMed and other sources to establish links between query words to access protein data using an intelligent Google-like search engine implemented by the search platform Lucene/Solr [52]. This helps to overcome the common problem that different terminology is used by different groups of researchers. The use of this search function is illustrated by using the query “phagocytosis” (Figure 1B). This inquiry finds 42 hits to KEGG orthologue profiles. One of the hits corresponds to amphiphysin (a synaptic vesicle protein) with annotation of two protein homologues encoded in the coral genome. On the data page there is a brief description of the function of amphiphysin together with a PUBMED literature reference. The sequences of the predicted coral proteins (Figure 1C) can be retrieved, and it is also possible to analyse such data with computer aided drug design methods [53] to look for conserved domains. There are also two tools for the user to examine matches to protein sequences. The user can carry out a BLAST search against the coral protein sequence or analyse the predicted sequence against HMM profiles used to annotate the coral proteome. These tools require only the user to paste their queury into the sequence window.

Bottom Line: 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.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.We 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.

View Article: PubMed Central - HTML - PubMed

Affiliation: Centre for Marine Microbiology and Genetics, Australian Institute of Marine Science, PMB No. 3 Townsville MC, Townsville 4810, Queensland, Australia.

ABSTRACT

Background: 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. 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.

Description: Sequences 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.

Conclusions: We 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.

Show MeSH
Related in: MedlinePlus