Skip to main content

Bioinformatics Resources for the Stress Biology of Plants

  • Chapter
  • First Online:
Biotic and Abiotic Stress Tolerance in Plants

Abstract

Bioinformatics play an invaluable role in many areas of biological research including stress biology. In the present global scenario, almost every organism faces stress as a response to stressors (biotic or abiotic). Any stress has serious impact on the overall growth and development of organisms. Moreover, productivity of plants is also affected by stress. Due to these reasons, stress biology has been the focus of research for many scientists, and the massive data generated by them require appropriate management and analysis tools. The availability of bioinformatics tools including software, databases, and web resources has brought a major change in the stress-related research. These resources help in the analysis and better interpretation of the data generated through experiments. This chapter deals with various general and specialized bioinformatics resources useful for the stress biology community working on plants.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 149.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 199.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 199.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

References

  • Alter S, Bader KC, Spannagl M, Wang Y, Bauer E, Schön CC, Mayer KF (2015) DroughtDB: an expert-curated compilation of plant drought stress genes and their homologs in nine species. Database 2015:bav046

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Altman RB (2004) Building successful biological databases. Brief Bioinform 5:4–5

    Article  PubMed  Google Scholar 

  • Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ (1990) Basic local alignment search tool. J Mol Biol 215:403–410

    Article  CAS  PubMed  Google Scholar 

  • Amid C, Birney E, Bower L, Cerdeño-Tárraga A, Cheng Y, Cleland I, Faruque N, Gibson R, Goodgame N, Hunter C, Jang M (2011) Major submissions tool developments at the European nucleotide archive. Nucleic Acids Res 40:D43–D47

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Atkinson NJ, Urwin PE (2012) The interaction of plant biotic and abiotic stresses: from genes to the field. J Exp Bot 63:3523–3543

    Article  CAS  PubMed  Google Scholar 

  • Attwood TK, Gisel A, Eriksson NE, Bongcam-Rudloff E (2011) Concepts, historical milestones and the central place of bioinformatics in modern biology: a European perspective. In Bioinfo Tren Meth InTech

    Google Scholar 

  • Balaji J, Crouch JH, Petite PV, Hoisington DA (2006) A database of annotated tentative orthologs from crop abiotic stress transcripts. Bioinformation 1:225–227

    PubMed  PubMed Central  Google Scholar 

  • Barker WC, Garavelli JS, Haft DH, Hunt LT, Marzec CR, Orcutt BC, Srinivasarao GY, Yeh LS, Ledley RS, Mewes HW, Pfeiffer F (1998) The PIR-international protein sequence database. Nucleic Acids Res 26:27–32

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Benson DA, Karsch-Mizrachi I, Lipman DJ, Ostell J, Rapp BA, Wheeler DL (2000) GenBank. Nucleic Acids Res 28:15–18

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Berardini TZ, Reiser L, Li D, Mezheritsky Y, Muller R, Strait E, Huala E (2015) The Arabidopsis information resource: making and mining the “gold standard” annotated reference plant genome. Genesis 53:474–485

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Berman HM, Battistuz T, Bhat TN, Bluhm WF, Bourne PE, Burkhardt K, Feng Z, Gilliland GL, Iype L, Jain S, Fagan P (2002) The protein data bank. Acta Crystallogr D Biol Crystallogr 58:899–907

    Article  CAS  PubMed  Google Scholar 

  • Blaszczyk M, Jamroz M, Kmiecik S, Kolinski A (2013) CABS-fold: server for the de novo and consensus-based prediction of protein structure. Nucleic Acids Res 41:W406–W411

    Article  PubMed  PubMed Central  Google Scholar 

  • Bolser D, Staines DM, Pritchard E, Kersey P (2016) Ensembl plants: integrating tools for visualizing, mining, and analyzing plant genomics data. Plant Bioinfo: Meth Proto 1374:115–40

    Google Scholar 

  • Boutet E, Lieberherr D, Tognolli M, Schneider M, Bairoch A (2007) UniProtKB/Swiss-Prot: the manually annotated section of the UniProt Knowledge Base. Plant Bioinfo: Meth Proto 406:89–112

    Google Scholar 

  • Brooks BR, Bruccoleri RE, Olafson BD, States DJ, Swaminathan SA, Karplus M (1983) CHARMM: a program for macromolecular energy, minimization, and dynamics calculations. J Comput Chem 4:187–217

    Article  CAS  Google Scholar 

  • Calzadilla PI, Maiale SJ, Ruiz OA, Escaray FJ (2016) Transcriptome response mediated by cold stress in Lotus japonicus. Front Plant Sci 7:374

    Article  PubMed  PubMed Central  Google Scholar 

  • Chen J, Anderson JB, DeWeese-Scott C, Fedorova ND, Geer LY, He S, Hurwitz DI, Jackson JD, Jacobs AR, Lanczycki CJ, Liebert CA (2003) MMDB: Entrez’s 3D-structure database. Nucleic Acids Res 31:474–477

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Choudhury FK, Rivero RM, Eduardo B, Mittler R (2017) Reactive oxygen species, abiotic stress and stress combination. Plant J 90:856–867

    Article  CAS  PubMed  Google Scholar 

  • Cochrane G, Karsch-Mizrachi I, Takagi T, Sequence Database Collaboration IN (2015) The international nucleotide sequence database collaboration. Nucleic Acids Res 44:D48–D50

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Edgar RC (2004) MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 32:1792–1797

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Friesner RA, Banks JL, Murphy RB, Halgren TA, Klicic JJ, Mainz DT, Repasky MP, Knoll EH, Shelley M, Perry JK, Shaw DE (2004) Glide: a new approach for rapid, accurate docking and scoring. 1. Method and assessment of docking accuracy. J Med Chem 47:1739–1749

    Article  CAS  PubMed  Google Scholar 

  • Guex N, Peitsch MC (1997) SWISS-MODEL and the Swiss-Pdb viewer: an environment for comparative protein modeling. Electrophoresis 18:2714–2723

    Article  CAS  PubMed  Google Scholar 

  • Hess B, Kutzner C, Van Der Spoel D, Lindahl E (2008) GROMACS 4: algorithms for highly efficient, load-balanced, and scalable molecular simulation. J Chem Theory Comput 4:435–447

    Article  CAS  PubMed  Google Scholar 

  • Hirayama T, Shinozaki K (2010) Research on plant abiotic stress responses in the post-genome era: past, present and future. Plant J 61:1041–1052

    Article  CAS  PubMed  Google Scholar 

  • Jayaram B, Singh T, Mukherjee G, Mathur A, Shekhar S, Shekhar V (2012) Sanjeevini: a freely accessible web-server for target directed lead molecule discovery. BMC Bioinforma 13:S7

    Article  Google Scholar 

  • Jayaram B, Dhingra P, Mishra A, Kaushik R, Mukherjee G, Singh A, Shekhar S (2014) Bhageerath-H: a homology/ab initio hybrid server for predicting tertiary structures of monomeric soluble proteins. BMC Bioinforma 15:S7

    Article  Google Scholar 

  • Källberg M, Margaryan G, Wang S, Ma J, Xu J (2014) RaptorX server: a resource for template-based protein structure modeling. Prot Str Prediction 1137:17–27

    Article  CAS  Google Scholar 

  • Kaminuma E, Kosuge T, Kodama Y, Aono H, Mashima J, Gojobori T, Sugawara H, Ogasawara O, Takagi T, Okubo K, Nakamura Y (2010) DDBJ progress report. Nucleic Acids Res 39:D22–D27

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Kanehisa M, Goto S (2000) KEGG: kyoto encyclopedia of genes and genomes. Nucleic Acids Res 28:27–30

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Katoh K, Kuma KI, Toh H, Miyata T (2005) MAFFT version 5: improvement in accuracy of multiple sequence alignment. Nucleic Acids Res 33:511–518

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Kim DE, Chivian D, Baker D (2004) Protein structure prediction and analysis using the Robetta server. Nucleic Acids Res 32:W526–W531

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Kumar SA, Kumari PH, Sundararajan VS, Suravajhala P, Kanagasabai R, Kishor PK (2014) PSPDB: plant stress protein database. Plant Mol Biol Report 32:940–942

    Article  CAS  Google Scholar 

  • Lambert C, Leonard N, De Bolle X, Depiereux E (2002) ESyPred3D: prediction of proteins 3D structures. Bioinformatics 18:1250–1256

    Article  CAS  PubMed  Google Scholar 

  • Leonberger K, Jackson K, Smith R, Ward Gauthier N (2016) Plant diseases [2016]. Agric Nat Res Pub. 182

    Google Scholar 

  • Mochida K, Shinozaki K (2010) Genomics and bioinformatics resources for crop improvement. Plant Cell Physiol 51:497–523

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Moraes Filho RM, Menezes AF, Martins LS (2017) In silico modeling and characterization of phytoparasitic nematodes translationally-controlled tumor proteins. Genet Mol Res:16

    Google Scholar 

  • Morgenstern B (1999) DIALIGN 2: improvement of the segment-to-segment approach to multiple sequence alignment. Bioinformatics (Oxford, England) 15:211–218

    Article  CAS  Google Scholar 

  • Morris GM, Huey R, Lindstrom W, Sanner MF, Belew RK, Goodsell DS, Olson AJ (2009) AutoDock4 and AutoDockTools4: automated docking with selective receptor flexibility. J Comput Chem 30:2785–2791

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Mount DM (2004/2003) Bioinformatics: sequence and genome analysis (2). CSHL Press, New York: 1–8

    Google Scholar 

  • Mousavi SA, Pouya FM, Ghaffari MR, Mirzaei M, Ghaffari A, Alikhani M, Ghareyazie M, Komatsu S, Haynes PA, Salekdeh GH (2016) PlantPReS: a database for plant proteome response to stress. J Proteome 143:69–72

    Article  CAS  Google Scholar 

  • Naika M, Shameer K, Mathew OK, Gowda R, Sowdhamini R (2013) STIFDB2: an updated version of plant stress-responsive transcription factor database with additional stress signals, stress-responsive transcription factor binding sites and stress-responsive genes in Arabidopsis and rice. Plant Cell Physiol 54:e8

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Nawaz M, Iqbal N, Idrees S, Ullah I (2014) DREB1A from Oryza sativa var. IR6: homology modelling and molecular docking. Turk J Bot 38:1095–1102

    Article  CAS  Google Scholar 

  • Needleman SB, Wunsch CD (1970) A general method applicable to the search for similarities in the amino acid sequence of two proteins. J Mol Biol 48:443–453

    Article  CAS  PubMed  Google Scholar 

  • Nielsen M, Lundegaard C, Lund O, Petersen TN (2010) CPHmodels-3.0-remote homology modeling using structure-guided sequence profiles. Nucleic Acids Res 38:W576–W581

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Notredame C, Higgins DG, Heringa J (2000) T-coffee: a novel method for fast and accurate multiple sequence alignment. J Mol Biol 302:205–217

    Article  CAS  PubMed  Google Scholar 

  • Pearlman DA, Case DA, Caldwell JW, Ross WS, Cheatham TE, DeBolt S, Ferguson D, Seibel G, Kollman P (1995) AMBER, a package of computer programs for applying molecular mechanics, normal mode analysis, molecular dynamics and free energy calculations to simulate the structural and energetic properties of molecules. Comput Phys Commun 91:1–41

    Article  CAS  Google Scholar 

  • Pearson WR (1990) Rapid and sensitive sequence comparison with FASTP and FASTA. Methods Enzymol 183:63–98

    Google Scholar 

  • Prabha R, Ghosh I, Singh DP (2011) Plant stress gene database: a collection of plant genes responding to stress condition. ARPN J Sci Techno 1:28–31

    Google Scholar 

  • Priya P, Jain M (2013) RiceSRTFDB: a database of rice transcription factors containing comprehensive expression, cis-regulatory element and mutant information to facilitate gene function analysis. Database 2013:bat027

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Purty RS, Sachar M, Chatterjee S (2017) Structural and expression analysis of salinity stress responsive phosphoserine phosphatase from Brassica juncea (L.) J Proteomics Bioinform 10:119–127

    Article  Google Scholar 

  • Rice P, Longden I, Bleasby A (2000) EMBOSS: the European molecular biology open software suite. Trends Genet 16:276–277

    Article  CAS  PubMed  Google Scholar 

  • Rodziewicz P, Swarcewicz B, Chmielewska K, Wojakowska A, Stobiecki M (2014) Influence of abiotic stresses on plant proteome and metabolome changes. Acta Physiol Plant 36:1–9

    Article  CAS  Google Scholar 

  • Schwede T, Kopp J, Guex N, Peitsch MC (2003) SWISS-MODEL: an automated protein homology-modeling server. Nucleic Acids Res 31:3381–3385

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Sham A, Aly MA (2012) Bioinformatics based comparative analysis of omega-3 fatty acids in desert plants and their role in stress resistance and tolerance. Int J Plant Sci 2:80–89

    Google Scholar 

  • Shameer K, Ambika S, Varghese SM, Karaba N, Udayakumar M, Sowdhamini R (2009) STIFDB- Arabidopsis stress responsive transcription factor dataBase. Int J Plant Genomics 2009:583429

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Sharma V, Munjal A, Shanker A (2016) A text book of bioinformatics, 2nd edn. Rastogi Publications, Meerut, p 350

    Google Scholar 

  • Shen Y, Maupetit J, Derreumaux P, Tufféry P (2014) Improved PEP-FOLD approach for peptide and miniprotein structure prediction. J Chem Theory Comput 10:4745–4758

    Article  CAS  PubMed  Google Scholar 

  • Smita S, Lenka SK, Katiyar A, Jaiswal P, Preece J, Bansal KC (2011) QlicRice: a web interface for abiotic stress responsive QTL and loci interaction channels in rice. Database 2011:bar037

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Smith K (2013) A brief history of NCBI’s formation and growth. The NCBI Handbook

    Google Scholar 

  • Smith TF, Waterman MS (1981) Identification of common molecular subsequences. J Mol Biol 147:195–197

    Article  CAS  PubMed  Google Scholar 

  • Tatusova T, Smith-White B, Ostell J (2007) A collection of plant-specific genomic data and resources at NCBI. Plant Bioinfo: Meth Proto 406:61–87

    Article  CAS  Google Scholar 

  • Thompson JD, Higgins DG, Gibson TJ (1994) CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 22:4673–4680

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Trott O, Olson AJ (2010) AutoDock Vina: improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading. J Comput Chem 31:455–461

    PubMed  PubMed Central  CAS  Google Scholar 

  • Wang L, Guo Z, Zhang Y, Wang Y, Yang G, Yang L, Wang R, Xie Z (2017) Characterization of LhSorP5CS, a gene catalyzing proline synthesis in Oriental hybrid lily Sorbonne: molecular modelling and expression analysis. Bot Stud 58:10

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Webb B, Sali A (2014) Protein structure modeling with MODELLER. Protein Struct Prediction 2014:1–15

    Google Scholar 

  • Wei Z, Zeng X, Qin C, Wang Y, Bai L, Xu Q, Yuan H, Tang Y, Nyima T (2016) Comparative transcriptome analysis revealed genes commonly responsive to varied nitrate stress in leaves of Tibetan hulless barley. Front Plant Sci 7:1067

    PubMed  PubMed Central  Google Scholar 

  • Wheeler DL, Barrett T, Benson DA, Bryant SH, Canese K, Chetvernin V, Church DM, DiCuccio M, Edgar R, Federhen S, Feolo M (2007) Database resources of the national center for biotechnology information. Nucleic Acids Res 36:D13–D21

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Wu S, Zhang Y (2007) LOMETS: a local meta-threading-server for protein structure prediction. Nucleic Acids Res 35:3375–3382

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Xiong H, Guo H, Xie Y, Zhao L, Gu J, Zhao S, Li J, Liu L (2017) RNAseq analysis reveals pathways and candidate genes associated with salinity tolerance in a spaceflight-induced wheat mutant. Sci Rep 7:2731

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Yang JM, Chen CC (2004) GEMDOCK: a generic evolutionary method for molecular docking. Proteins: Struct Funct Bioinfo 55:288–304

    Article  CAS  Google Scholar 

  • Yang J, Yan R, Roy A, Xu D, Poisson J, Zhang Y (2015) The I-TASSER suite: protein structure and function prediction. Nat Methods 12:7–8

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Zhang S, Yue Y, Sheng L, Wu Y, Fan G, Li A, Hu X, ShangGuan M, Wei C (2013) PASmiR: a literature curated database for miRNA molecular regulation in plant response to abiotic stress. BMC Plant Biol 13:33

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Zhu JK (2016) Abiotic stress signaling and responses in plants. Cell 167:313–324

    Article  CAS  PubMed  PubMed Central  Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

© 2018 Springer Nature Singapore Pte Ltd.

About this chapter

Check for updates. Verify currency and authenticity via CrossMark

Cite this chapter

Kumar, S., Shanker, A. (2018). Bioinformatics Resources for the Stress Biology of Plants. In: Vats, S. (eds) Biotic and Abiotic Stress Tolerance in Plants. Springer, Singapore. https://doi.org/10.1007/978-981-10-9029-5_14

Download citation

Publish with us

Policies and ethics