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

BMC Genomics

Database

Madeleine J H van Oppen¹  Walter C Dunlap²  John Cullum³  Paul F Long⁴  Daslav Hranueli⁵  Janko Diminic⁵  Antonio Starcevic⁵  Damir Baranasic⁵  Jurica Zucko⁵  Ranko Gacesa⁵ 

[1] Centre for Marine Microbiology and Genetics, Australian Institute of Marine Science, PMB No. 3 Townsville MC, 4810, Townsville, Queensland, Australia;Centre for Marine Microbiology and Genetics, Australian Institute of Marine Science, PMB No. 3 Townsville MC, 4810, Townsville, Queensland, Australia;Institute of Pharmaceutical Science, King’s College London, Franklin-Wilkins Building, 150 Stamford Street, SE1 9NH, London, United Kingdom;Department of Genetics, University of Kaiserslautern, Postfach 3049, 67653, Kaiserslautern, Germany;Institute of Pharmaceutical Science, King’s College London, Franklin-Wilkins Building, 150 Stamford Street, SE1 9NH, London, United Kingdom;Department of Chemistry King’s College London, Franklin-Wilkins Building, 150 Stamford Street, SE1 9NH, London, United Kingdom;Section for Bioinformatics, Department of Biochemical Engineering, Faculty of Food Technology and Biotechnology, University of Zagreb, Pierottijeva 6, 10000, Zagreb, Croatia;

关键词: Acropora digitifera;    KEGG orthology;    Database;    Annotation;    Proteome;    Genome;    Coral;    Symbiosis;    Cnidaria;   

DOI  :  10.1186/1471-2164-14-509

 received in 2013-03-06, accepted in 2013-07-15,  发布年份 2013

来源: Springer

【 摘 要 】

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.

【 授权许可】

Unknown   
© Dunlap et al.; licensee BioMed Central Ltd. 2013. This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.