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Hindawi Publishing Corporation International Journal of Plant Genomics Volume 2013, Article ID 949564, 3 pages http://dx.doi.org/10.1155/2013/949564 Methodology Report 1 1 1 2 Subhomoi Borkotoky, Vijayakumar Saravanan, Amit Jaiswal, Bipul Das, 3 1 1 Suresh Selvaraj, Ayaluru Murali, andP.T.V.Lakshmi Centre for Bioinformatics, School of Life Science, Pondicherry University, R. V. Nagar, Kalapet, Puducherry 605014, India Parasitology Division, Regional Medical Research Centre (RMRC-ICMR), Dibrugarh 786 001, India Department of Bioinformatics, SRM University, Tamil Nadu 603203, India Correspondence should be addressed to Subhomoi Borkotoky; email@example.com Received 24 October 2012; Revised 12 February 2013; Accepted 18 February 2013 Academic Editor: Jaroslav Dolezel Copyright © 2013 Subhomoi Borkotoky et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Plants in nature may face a wide range of favorable or unfavorable biotic and abiotic factors during their life cycle. Any of these factors may cause stress in plants; therefore, they have to be more adaptable to stressful environments and must acquire greater response to different stresses. The objective of this study is to retrieve and arrange data from the literature in a standardized electronic format for the development of information resources on potential stress responsive genes in Arabidopsis thaliana. This provides a powerful mean for manipulation, comparison, search, and retrieval of records describing the nature of various stress responsive genes in Arabidopsis thaliana. eTh database is based exclusively on published stress tolerance genes associated with plants. 1. Introduction genes. While it contains only 33 genes from Arabidopsis thaliana, our database contains 637 gene entries related to Stress response is the general term for defining the interaction stress response in Arabidopsis thaliana. Another example— between plants and the extreme environmental conditions. STIFDB—Arabidopsis Stress Responsive Transcription Fac- eTh studyofmechanismsofadaptationtostressful and tor Database , is a comprehensive collection of abiotic extreme environments provides the basis for addressing stress responsive genes in Arabidopsis thaliana,withoptions environmental, toxicological, and physiological problems . to identify probable transcription factor binding sites in their Changes in the expression of individual genes and proteins promoters, which is limited to only abiotic stress. Apart from induced by stress have been monitored under different con- these, we have The Arabidopsis Information Resource (TAIR) ditions. As of the year 2000, the sequence of the Arabidopsis [6, 7], genetic and molecular biology data for the model thaliana genome is nearly completed, and soon a catalog of higher plant Arabidopsis thaliana, which is more widespread plant gene expression exceeding a million transcripts will to different aspects apart from the stress response, which be available . Here, we have listed the stress responsive makes it difficult to look for only stress related genes. genes for Arabidopsis thaliana (thale cress), a member of We have listed around 44 types of different stress factors the mustard family, that has become a widely used model related to Arabidopsis thaliana, and the database contains for the study of plant biology because of its small size, short 636 gene entries related to stress response with their related generation time, facile genetics, and ease of transformation information like gene ID, nucleotide and protein sequences, . cross-response, and so forth. eTh database is based exclusively eTh re arefew databasesthathavebeendesignedfor on published stress responsive genes associated with plants. stress responsive genes in plants. Plant Stress Gene Database This database also include BLAST [ 8]searchinterface for  include 259 stress-related genes of 11 species along both nucleotide and proteins. eTh database is freely available with all the available information about the individual and could be accessed via http://srgdb.bicpu.edu.in/. 2 International Journal of Plant Genomics Table 1: Distribution of different stress types in ARGDB. Gene info Gene ID Response type Total genes Gene name Main Salt 139 Chromosome information number Oxidative 132 ASDBID Gene map Stress 75 TAIRID Biotic 10 Stress info Gene Drought 31 Stress tolerance Tolerance/ Osmotic 30 Cross-tolerance response Heat 28 Sequence Sequence info Abiotic 26 Expression Protein Dehydration 19 profile Nucleotide Reference Cadmium 15 Cold 15 Gene expression info Endoplasmic reticulum 13 Genevestigator Light 11 Gene Family Profiler Abscisic acid 11 Aluminium 10 Reference info PUMBED ID Water 8 Chitin 3 Figure 1: Database structure of ASRGDB. Salinity response 2 Freezing 2 Genotoxic 2 2. Materials and Methods Photooxidative 2 Fbox 2 2.1. Data Collection. An extensive literature search has been carried out to identify the potential Arabidopsis thaliana Pathogen 2 genes involved in stress tolerance and stress response. Those Cation 1 literatures that have reported stress tolerance or stress respon- Sugar 1 sive gene have been manually curated to identify the presence Kinase 1 of any cross-response. Genomic and proteomic data for the Phosphate 1 collectedgenehavebeenobtainedfromthe TAIR.Apart UV 1 from these, the database also contains gene expression data Temperature 1 obtained from Genevestigator and ArabidopsisGene Dessication 1 Family Profiler (aGFP) [ 10]. Ethylene 1 Touch 1 2.2. Databse Architecture. The Arabidopsis Stress Responsive Potassium 1 Gene Database (ASRGDB) has been constructed and congfi - DNA damage 1 ured using typical LAMP (Linux, Apache, MySQL, and PHP) Karrikin 1 server. Data was stored as a MySQL table using MySQL 5.5, Cellular 1 andthe MySQLstructure modelfor theASRGDBisshown in Chilling 1 Figure 1. Hydrogen peroxide 1 Reactive oxygen species 1 2.3. Database Access. The database can be queried in a Wound 1 various way, unlike the only browsing option in Plant Stress Gene Database. Various keywords, complete or partial, could Metal 1 be searched against the various el fi ds in the database. For Magnesium 1 easy search, we have included a unique identification number Sodium 1 ASDBID to the database. The searchable efi lds include ASD- Malondialdehyde 1 BID, Response, Cross-response, Gene ID, and Gene name. The results for the search query have been displayed in a user- friendly table view for easy access. A legend is also given in protein and nucleotide sequences can be queried separately. thesearchtab to guidethe usersand to directly access the BLAST 2.2.25+ version is used with BLSOUM62 matrix, Gap particular stress type with a single click. penalties of 11 and extension 1. The window size for the multiple hit is set to 40 (default). eTh BLAST hit result is 2.4. Blast Search. eTh database also has the provision of directly linked to the database, and, hence, the hit record can performing a BLAST search against the ATSRGDB. Both be directly accessed from the BLAST result page. International Journal of Plant Genomics 3 2.5. Database Update. The ATSRGDB also provides interface  K.Shameer,S.Ambika,S.M.Varghese,N.Karaba,M.Udayaku- mar, and R. Sowdhamini, “STIFDB—Arabidopsis stress respon- to update the database. eTh user can add the new data into sive transcription factor dataBase,” International Journal of the database but not allowed to modify or delete the existing Plant Genomics, vol. 2009, Article ID 583429, 8 pages, 2009. data.Thenew entryrequiresthe followingmandatory efi ld  D. Swarbreck, C. Wilks, P. Lamesch et al., “The Arabidopsis TAIRID, Chromosome number, Response, and Reference. All information resource (TAIR): gene structure and function the entries will be subjected to extensive manual validation. annotation,” Nucleic Acids Research,vol.36, no.1,pp. D1009– eTh user hastoregistertomakeanentry into database. D1014, 2008. Database design and interface has been developed using  E.Huala,A.W.Dickerman,M.Garcia-Hernandezetal.,“eTh PHPand MySQL. BLASTsearcheswerecarried outusing Arabidopsis information resource (TAIR): a comprehensive PERL scripts. database and web-based information retrieval, analysis, and visualization system for a model plant,” Nucleic Acids Research, vol. 29,no. 1, pp.102–105,2001. 3. Results and Discussion  S. F. Altschul, T. L. Madden, A. A. Schaff¨er et al., “Gapped The ASRGDB includes a total of 636 records with 44 dif- BLAST and PSI-BLAST: a new generation of protein database ferent types of stress responses. eTh distribution of different search programs,” Nucleic Acids Research,vol.25, no.17, pp. 3389–3402, 1997. response types in the database is tabulated in Table 1.Salt  P. Zimmermann, M. Hirsch-Hoffmann, L. Hennig, and W. response and oxidative responsive genes were found to be Gruissem, “GENEVESTIGATOR. Arabidopsis microarray abundant (139 and 132, resp.), when compared to the other database and analysis toolbox,” Plant Physiology,vol.136,no. 1, stress types in the database. Out of 636 stress responsive pp. 2621–2632, 2004. genes, 238 were found to have cross-response with other  N. Dupl’ak ´ ova, ´ D. Renˇa´k,P.Hovanec,B.Honysova, ´ D. Twell, stress types. Among all, only 9 genes were known not to have and D. Honys, “Arabidopsis gene family profiler (aGFP)— coding proteins. eTh database provides search facility in vfi e user-oriented transcriptomic database with easy-to-use graphic different fileds of the database. eTh database also provides the interface,” BMC Plant Biology,vol.7,article 39,2007. user to perform a BLAST search against the sequences in the database (both protein and nucleotide). With this different facility, the Arabidopsis stress respon- sive gene database stands as a centralized source of informa- tion for scientific investigators who are interested in plant stress physiology, mainly Arabidopsis thaliana.This database provides a powerful mean for manipulation, comparison, search, and retrieval of records describing the nature of stress responsive genes in Arabidopsis thaliana.Thedatabasewillbe updatedand curatedevery sixmonthsincluding individual submissions made by the user. As of future, the addition of more stress-related genes with related information and regular updates with the improvements of several sequencing and analysis techniques will make this database more useful to the research community. Acknowledgments eTh authors thank P. Elavarasan, E. Malanco, and S. Manikan- dan of Centre for Bioinformatics, Pondicherry University, for theirtechnical supportinhosting of thedatabaseontothe web server. References  D. Kultz, “Molecular and evolutionary basis of the cellular stress response,” Annual Review of Physiology,vol.67, pp.225–257,  H. J. Bohnert, P. Ayoubi, C. Borchert et al., “A genomics approach towards salt stress tolerance,” Plant Physiology and Biochemistry,vol.39, no.3-4,pp. 295–311, 2001.  X.Lin, S. Kaul,S.Rounsleyetal.,“Sequence andanalysisof chromosome 2 of the plant Arabidopsis thaliana,” Nature,vol. 402, no. 6763, pp. 761–768, 1999.  R. Prabha, I. Ghosh, and D. P. Singh, “Plant stress gene database,” ARPN Journal of Science and Technology,vol.1,pp. 28–31, 2011. 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International Journal of Plant Genomics – Hindawi Publishing Corporation
Published: Mar 17, 2013
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