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.
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.
Authors: Tamás Matusek; Alexandre Djiane; Ferenc Jankovics; Damian Brunner; Marek Mlodzik; József Mihály Journal: Development Date: 2006-03 Impact factor: 6.868
Authors: Nedeljka Rosic; Edmund Yew Siang Ling; Chon-Kit Kenneth Chan; Hong Ching Lee; Paulina Kaniewska; David Edwards; Sophie Dove; Ove Hoegh-Guldberg Journal: ISME J Date: 2015-03-17 Impact factor: 10.302
Authors: Ranko Gacesa; Jurica Zucko; Solveig K Petursdottir; Elisabet Eik Gudmundsdottir; Olafur H Fridjonsson; Janko Diminic; Paul F Long; John Cullum; Daslav Hranueli; Gudmundur O Hreggvidsson; Antonio Starcevic Journal: Food Technol Biotechnol Date: 2017-06 Impact factor: 3.918
Authors: Adrian Lutz; Jean-Baptiste Raina; Cherie A Motti; David J Miller; Madeleine J H van Oppen Journal: PLoS One Date: 2015-10-01 Impact factor: 3.240
Authors: Andrew J Weston; Walter C Dunlap; Victor H Beltran; Antonio Starcevic; Daslav Hranueli; Malcolm Ward; Paul F Long Journal: Mol Cell Proteomics Date: 2015-01-05 Impact factor: 5.911