EXPLORING PLANT RESEARCH WITH THE HELP OF VITAL BIOINFORMATICS DATABASES AND ONLINE RESOURCES

Main Article Content

Noreen Fatima
Haris Abdul Rehman
, Mah Noor Hassan
Iqra Naeem
Babur Ali Akbar
Muhammad Nabeel Aslam
Zanib Fatima
Aqsa Qurban
Muhammad Umar
Tayyaba Arif

Keywords

Databases, Genomics, Bioinformatics, Plant, Crop, Web Servers

Abstract

Bioinformatics plays a role, in the field of plant science today. With an increase in data volume, there is a growing demand for tools and methods for managing, visualizing, implementing, evaluating, modeling, and predicting this data. However many biology researchers may lack familiarity with the bioinformatics resources, which can lead to missed opportunities and misinterpretation of the data. In this review article, we highlighted the web resources that offer analysis capabilities for plant research data including genomics, transcriptomics, comparative genomics, bio-ontologies, sequence and structural comparisons plant disease related databases well as proteomics databases. Additionally we provide insights into integrated modules found within these resources that are specifically tailored for analyzing plant associated data. Overall this review aims to assist plant researchers in accessing bioinformatics resources for their data analysis needs while promoting the use of bioinformatics tools to effectively address experimental challenges, within the field of plant sciences.

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References

1. Millstone, E. and T. Lang, The atlas of food: who eats what, where, and why. 2008: University of California Press.
2. Mann, J., Natural products in cancer chemotherapy: past, present and future. Nature Reviews Cancer, 2002. 2(2): p. 143-148.
3. Lippman, Z., et al., Role of transposable elements in heterochromatin and epigenetic control. Nature, 2004. 430(6998): p. 471-476.
4. Schuster, S.C., Next-generation sequencing transforms today's biology. Nature methods, 2008. 5(1): p. 16-18.
5. Govindaraj, M., M. Vetriventhan, and M. Srinivasan, Importance of genetic diversity assessment in crop plants and its recent advances: an overview of its analytical perspectives. Genetics research international, 2015. 2015.
6. Rigden, D.J., X.M. Fernández-Suárez, and M.Y. Galperin, The 2016 database issue of Nucleic Acids Research and an updated molecular biology database collection. Nucleic acids research, 2016. 44(D1): p. D1-D6.
7. Kind, T., M. Scholz, and O. Fiehn, How large is the metabolome? A critical analysis of data exchange practices in chemistry. PloS one, 2009. 4(5): p. e5440.
8. Edwards, D. and J. Batley, Plant bioinformatics: from genome to phenome. Trends in biotechnology, 2004. 22(5): p. 232-237.
9. Benson, D.A., et al., GenBank. Nucleic acids research, 2012. 41(D1): p. D36-D42.
10. Coordinators, N.R., Database resources of the national center for biotechnology information. Nucleic acids research, 2017. 45(Database issue): p. D12.
11. Cochrane, G., et al., The international nucleotide sequence database collaboration. Nucleic acids research, 2016. 44(D1): p. D48-D50.
12. Kanz, C., et al., The EMBL nucleotide sequence database. Nucleic acids research, 2005. 33(suppl_1): p. D29-D33.
13. Tateno, Y., et al., DNA Data Bank of Japan (DDBJ) for genome scale research in life science. Nucleic acids research, 2002. 30(1): p. 27-30.
14. Rose, P.W., et al., The RCSB protein data bank: integrative view of protein, gene and 3D structural information. Nucleic acids research, 2016: p. gkw1000.
15. UniProt: the universal protein knowledgebase. Nucleic acids research, 2017. 45(D1): p. D158-D169.
16. Garg, P. and P. Jaiswal, Databases and bioinformatics tools for rice research. Current Plant Biology, 2016. 7: p. 39-52.
17. Bolser, D., et al., Ensembl plants: integrating tools for visualizing, mining, and analyzing plant genomics data, in Plant bioinformatics. 2016, Springer. p. 115-140.
18. Youens-Clark, K., et al., Gramene database in 2010: updates and extensions. Nucleic acids research, 2010. 39(suppl_1): p. D1085-D1094.
19. Dash, S., et al., PLEXdb: gene expression resources for plants and plant pathogens. Nucleic acids research, 2012. 40(D1): p. D1194-D1201.
20. Ong, Q., et al., Bioinformatics Approach in Plant Genomic Research. Current genomics, 2016. 17(4): p. 368-378.
21. Myers, E.W., Toward simplifying and accurately formulating fragment assembly. Journal of Computational Biology, 1995. 2(2): p. 275-290.
22. Patil, N., et al., Blocks of limited haplotype diversity revealed by high-resolution scanning of human chromosome 21. Science, 2001. 294(5547): p. 1719-1723.
23. Hinds, D.A., et al., Whole-genome patterns of common DNA variation in three human populations. Science, 2005. 307(5712): p. 1072-1079.
24. Frazer, K.A., et al., Genomic DNA insertions and deletions occur frequently between humans and nonhuman primates. Genome research, 2003. 13(3): p. 341-346.
25. Bruskiewich, R., et al., Generation Challenge Programme (GCP): standards for crop data. Omics: a journal of integrative biology, 2006. 10(2): p. 215-219.
26. van Berloo, R., GGT 2.0: versatile software for visualization and analysis of genetic data. Journal of Heredity, 2008. 99(2): p. 232-236.
27. Riaño-Pachón, D.M., et al., GabiPD: the GABI primary database—a plant integrative ‘omics’ database. Nucleic acids research, 2009. 37(suppl_1): p. D954-D959.
28. Carollo, V., et al., GrainGenes 2.0. An improved resource for the small-grains community. Plant physiology, 2005. 139(2): p. 643-651.
29. Jung, S., et al., GDR (Genome Database for Rosaceae): integrated web-database for Rosaceae genomics and genetics data. Nucleic acids research, 2007. 36(suppl_1): p. D1034-D1040.
30. Lawrence, C.J., et al., MaizeGDB, the community database for maize genetics and genomics. Nucleic acids research, 2004. 32(suppl_1): p. D393-D397.
31. Mower, J.P., The PREP suite: predictive RNA editors for plant mitochondrial genes, chloroplast genes and user-defined alignments. Nucleic acids research, 2009. 37(suppl_2): p. W253-W259.
32. Zhang, Z., et al., PMRD: plant microRNA database. Nucleic acids research, 2010. 38(suppl_1): p. D806-D813.
33. Nakano, M., et al., Plant MPSS databases: signature-based transcriptional resources for analyses of mRNA and small RNA. Nucleic acids research, 2006. 34(suppl_1): p. D731-D735.
34. Brown, J.W., et al., Plant snoRNA database. Nucleic acids research, 2003. 31(1): p. 432-435.
35. Lescot, M., et al., PlantCARE, a database of plant cis-acting regulatory elements and a portal to tools for in silico analysis of promoter sequences. Nucleic acids research, 2002. 30(1): p. 325-327.
36. Shahmuradov, I.A., et al., PlantProm: a database of plant promoter sequences. Nucleic acids research, 2003. 31(1): p. 114-117.
37. Meng, Y., et al., PmiRKB: a plant microRNA knowledge base. Nucleic acids research, 2010. 39(suppl_1): p. D181-D187.
38. Canaran, P., et al., Panzea: an update on new content and features. Nucleic acids research, 2007. 36(suppl_1): p. D1041-D1043.
39. Bai, Y., et al., PlncRNADB: A Repository of Plant lncRNAs and lncRNA-RBP Protein Interactions. Current Bioinformatics, 2019. 14(7): p. 621-627.
40. Zonneveld, B., I. Leitch, and M. Bennett, First nuclear DNA amounts in more than 300 angiosperms. Annals of botany, 2005. 96(2): p. 229-244.
41. Dicks, J., et al., UK CropNet: a collection of databases and bioinformatics resources for crop plant genomics. Nucleic acids research, 2000. 28(1): p. 104-107.
42. Dai, X. and P.X. Zhao, pssRNAMiner: a plant short small RNA regulatory cascade analysis server. Nucleic acids research, 2008. 36(suppl_2): p. W114-W118.
43. Dai, X., Z. Zhuang, and P.X. Zhao, psRNATarget: a plant small RNA target analysis server (2017 release). Nucleic acids research, 2018. 46(W1): p. W49-W54.
44. Xia, E.H., et al., Tea Plant Information Archive: a comprehensive genomics and bioinformatics platform for tea plant. Plant biotechnology journal, 2019. 17(10): p. 1938-1953.
45. Ye, J., et al., AtCircDB: a tissue-specific database for Arabidopsis circular RNAs. Briefings in bioinformatics, 2019. 20(1): p. 58-65.
46. Gupta, N., et al., PVsiRNAdb: a database for plant exclusive virus-derived small interfering RNAs. Database, 2018. 2018.
47. Chen, D., et al., PlantNATsDB: a comprehensive database of plant natural antisense transcripts. Nucleic acids research, 2012. 40(D1): p. D1187-D1193.
48. Lamesch, P., et al., The Arabidopsis Information Resource (TAIR): improved gene annotation and new tools. Nucleic acids research, 2012. 40(D1): p. D1202-D1210.
49. Bedell, J.A., et al., Sorghum genome sequencing by methylation filtration. PLoS Biol, 2005. 3(1): p. e13.
50. Coughlan, S.J., V. Agrawal, and B. Meyers, A comparison of global gene expression measurement technologies in Arabidopsis thaliana. Comparative and Functional Genomics, 2004. 5(3): p. 245-252.
51. Buck, M.J. and J.D. Lieb, ChIP-chip: considerations for the design, analysis, and application of genome-wide chromatin immunoprecipitation experiments. Genomics, 2004. 83(3): p. 349-360.
52. Liu, X., et al., DIP-chip: rapid and accurate determination of DNA-binding specificity. Genome research, 2005. 15(3): p. 421-427.
53. Drăghici, S., Data analysis tools for DNA microarrays. 2019: CRC Press.
54. Eilbeck, K., et al., The Sequence Ontology: a tool for the unification of genome annotations. Genome biology, 2005. 6(5): p. R44.
55. Shen, L., et al., BarleyBase—an expression profiling database for plant genomics. Nucleic Acids Research, 2005. 33(suppl_1): p. D614-D618.
56. Samson, F., et al., FLAGdb++: a database for the functional analysis of the Arabidopsis genome. Nucleic acids research, 2004. 32(suppl_1): p. D347-D350.
57. Courcelle, E., et al., Narcisse: a mirror view of conserved syntenies. Nucleic acids research, 2008. 36(suppl_1): p. D485-D490.
58. Ogata, Y., et al., CoP: a database for characterizing co-expressed gene modules with biological information in plants. Bioinformatics, 2010. 26(9): p. 1267-1268.
59. Roth, C., et al., The Adaptive Evolution Database (TAED): a phylogeny based tool for comparative genomics. Nucleic acids research, 2005. 33(suppl_1): p. D495-D497.
60. Hartmann, S., et al., Phytome: a platform for plant comparative genomics. Nucleic Acids Research, 2006. 34(suppl_1): p. D724-D730.
61. Vandepoele, K., A guide to the PLAZA 3.0 plant comparative genomic database, in Plant Genomics Databases. 2017, Springer. p. 183-200.
62. Zheng, H.-Q., et al., EXPath tool—a system for comprehensively analyzing regulatory pathways and coexpression networks from high-throughput transcriptome data. DNA Research, 2017. 24(4): p. 371-375.
63. Botstein, D., et al., Construction of a genetic linkage map in man using restriction fragment length polymorphisms. American journal of human genetics, 1980. 32(3): p. 314.
64. Phillips, R.L. and I.K. Vasil, DNA-based markers in plants. Vol. 6. 2013: Springer Science & Business Media.
65. Takeya, M., et al., NIASGBdb: NIAS Genebank databases for genetic resources and plant disease information. Nucleic acids research, 2010. 39(suppl_1): p. D1108-D1113.
66. Button, D.K., et al., DRASTIC—INSIGHTS: querying information in a plant gene expression database. Nucleic acids research, 2006. 34(suppl_1): p. D712-D716.
67. Sanseverino, W., et al., PRGdb 2.0: towards a community-based database model for the analysis of R-genes in plants. Nucleic acids research, 2012. 41(D1): p. D1167-D1171.
68. Naika, M., et al., 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 and Cell Physiology, 2013. 54(2): p. e8-e8.
69. Sandhu, M., et al., RiceMetaSys for salt and drought stress responsive genes in rice: a web interface for crop improvement. BMC bioinformatics, 2017. 18(1): p. 432.
70. Priya, P. and M. Jain, RiceSRTFDB: a database of rice transcription factors containing comprehensive expression, cis-regulatory element and mutant information to facilitate gene function analysis. Database, 2013. 2013.
71. Alter, S., et al., DroughtDB: an expert-curated compilation of plant drought stress genes and their homologs in nine species. Database, 2015. 2015.
72. Zhang, D., et al., CSTDB: A Crop Stress-tolerance Gene and Protein Database Integrated by Convolutional Neural Networks. bioRxiv, 2018: p. 456343.
73. Berz, J., et al., HEATSTER: a database and web server for identification and classification of heat stress transcription factors in plants. Bioinformatics and biology insights, 2019. 13: p. 1177932218821365.
74. Kumar, S.A., et al., PSPDB: plant stress protein database. Plant molecular biology reporter, 2014. 32(4): p. 940-942.
75. Mansueto, L., et al., SNP-Seek II: A resource for allele mining and analysis of big genomic data in Oryza sativa. Current Plant Biology, 2016. 7-8: p. 16-25.
76. Rafalski, J.A., Novel genetic mapping tools in plants: SNPs and LD-based approaches. Plant Science, 2002. 162(3): p. 329-333.
77. Wilkinson, P.A., et al., CerealsDB 2.0: an integrated resource for plant breeders and scientists. BMC bioinformatics, 2012. 13(1): p. 219.
78. Rudd, S., H. Schoof, and K. Mayer, PlantMarkers—a database of predicted molecular markers from plants. Nucleic Acids Research, 2005. 33(suppl_1): p. D628-D632.
79. Gonzalez-Ibeas, D., et al., MELOGEN: an EST database for melon functional genomics. BMC Genomics, 2007. 8(1): p. 306.
80. Jorrín, J.V., A.M. Maldonado, and M.A. Castillejo, Plant proteome analysis: a 2006 update. Proteomics, 2007. 7(16): p. 2947-2962.
81. Amme, S., et al., Proteome analysis of cold stress response in Arabidopsis thaliana using DIGE-technology. Journal of experimental botany, 2006. 57(7): p. 1537-1546.
82. Leo, F.D., et al., PLANT-PIs: a database for plant protease inhibitors and their genes. Nucleic acids research, 2002. 30(1): p. 347-348.
83. Walker, N.S., N. Stiffler, and A. Barkan, POGs/PlantRBP: a resource for comparative genomics in plants. Nucleic acids research, 2007. 35(suppl_1): p. D852-D856.
84. Gendler, K., T. Paulsen, and C. Napoli, ChromDB: the chromatin database. Nucleic acids research, 2008. 36(suppl_1): p. D298-D302.
85. Mewes, H.-W., et al., MIPS: a database for genomes and protein sequences. Nucleic acids research, 2002. 30(1): p. 31-34.
86. Yao, Q., et al., P3DB 3.0: from plant phosphorylation sites to protein networks. Nucleic acids research, 2014. 42(D1): p. D1206-D1213.
87. Mohseni‐Zadeh, S., et al., PHYTOPROT: a database of clusters of plant proteins. Nucleic acids research, 2004. 32(suppl_1): p. D351-D353.
88. Mihara, M., T. Itoh, and T. Izawa, SALAD database: a motif-based database of protein annotations for plant comparative genomics. Nucleic acids research, 2010. 38(suppl_1): p. D835-D842.
89. Kushwaha, S.K., et al., NBSPred: a support vector machine-based high-throughput pipeline for plant resistance protein NBSLRR prediction. Bioinformatics, 2016. 32(8): p. 1223-1225.
90. Chandra, N.R., et al., Lectindb: a plant lectin database. Glycobiology, 2006. 16(10): p. 938-946.
91. Gribskov, M., et al., PlantsP: a functional genomics database for plant phosphorylation. Nucleic acids research, 2001. 29(1): p. 111-113.
92. Tchieu, J.H., et al., The PlantsP and PlantsT functional genomics databases. Nucleic acids research, 2003. 31(1): p. 342-344.
93. Su, B., et al., PlantMP: a database for moonlighting plant proteins. Database, 2019. 2019.
94. Mani, M., et al., MoonProt: a database for proteins that are known to moonlight. Nucleic acids research, 2015. 43(D1): p. D277-D282.
95. Franco-Serrano, L., et al., MultitaskProtDB-II: an update of a database of multitasking/moonlighting proteins. Nucleic acids research, 2018. 46(D1): p. D645-D648.
96. Jin, J., et al., PlantTFDB 4.0: toward a central hub for transcription factors and regulatory interactions in plants. Nucleic acids research, 2016: p. gkw982.
97. Szcześniak, M.W., et al., ERISdb: a database of plant splice sites and splicing signals. Plant and Cell Physiology, 2013. 54(2): p. e10-e10.
98. Mathelier, A., et al., JASPAR 2016: a major expansion and update of the open-access database of transcription factor binding profiles. Nucleic acids research, 2016. 44(D1): p. D110-D115.
99. Bard, J.B. and S.Y. Rhee, Ontologies in biology: design, applications and future challenges. Nature Reviews Genetics, 2004. 5(3): p. 213-222.
100. Ashburner, M., et al., Gene ontology: tool for the unification of biology. Nature genetics, 2000. 25(1): p. 25-29.
101. Mao, X., et al., Automated genome annotation and pathway identification using the KEGG Orthology (KO) as a controlled vocabulary. Bioinformatics, 2005. 21(19): p. 3787-3793.
102. Consortium, G.O., The Gene Ontology (GO) database and informatics resource. Nucleic acids research, 2004. 32(suppl_1): p. D258-D261.
103. Künne, C., et al., CR-EST: a resource for crop ESTs. Nucleic acids research, 2005. 33(suppl_1): p. D619-D621.
104. Johnson, C., et al., CSRDB: a small RNA integrated database and browser resource for cereals. Nucleic Acids Res, 2007. 35(Database issue): p. D829-33.
105. Schlueter, S.D., Q. Dong, and V. Brendel, GeneSeqer@ PlantGDB: gene structure prediction in plant genomes. Nucleic acids research, 2003. 31(13): p. 3597-3600.
106. Schreiber, F., et al., MetaCrop 2.0: managing and exploring information about crop plant metabolism. Nucleic acids research, 2012. 40(D1): p. D1173-D1177.
107. Higo, K., et al., PLACE: a database of plant cis-acting regulatory DNA elements. Nucleic acids research, 1998. 26(1): p. 358-359.
108. Childs, K.L., et al., The TIGR plant transcript assemblies database. Nucleic Acids Research, 2007. 35(suppl_1): p. D846-D851.
109. Cooper, L., et al., The Planteome database: an integrated resource for reference ontologies, plant genomics and phenomics. Nucleic acids research, 2018. 46(D1): p. D1168-D1180.
110. Ge, S.X., D. Jung, and R. Yao, ShinyGO: a graphical gene-set enrichment tool for animals and plants. Bioinformatics, 2020. 36(8): p. 2628-2629.
111. Zeng, X., et al., CMAUP: a database of collective molecular activities of useful plants. Nucleic acids research, 2019. 47(D1): p. D1118-D1127.
112. Kriventseva, E.V., et al., OrthoDB v10: sampling the diversity of animal, plant, fungal, protist, bacterial and viral genomes for evolutionary and functional annotations of orthologs. Nucleic acids research, 2019. 47(D1): p. D807-D811.
113. Rayson, S., et al., A role for nonsense-mediated mRNA decay in plants: pathogen responses are induced in Arabidopsis thaliana NMD mutants. PloS one, 2012. 7(2): p. e31917.
114. Urban, M., et al., PHI-base: a new interface and further additions for the multi-species pathogen–host interactions database. Nucleic acids research, 2017. 45(D1): p. D604-D610.
115. Bülow, L., M. Schindler, and R. Hehl, PathoPlant®: a platform for microarray expression data to analyze co-regulated genes involved in plant defense responses. Nucleic acids research, 2007. 35(suppl_1): p. D841-D845.
116. Mano, S., et al., The Plant Organelles Database 2 (PODB2): an updated resource containing movie data of plant organelle dynamics. Plant and cell physiology, 2011. 52(2): p. 244-253.
117. Fernandez-Pozo, N., et al., The Sol Genomics Network (SGN)—from genotype to phenotype to breeding. Nucleic acids research, 2015. 43(D1): p. D1036-D1041.
118. Ruiz, M., et al., TropGENE‐DB, a multi‐tropical crop information system. Nucleic acids research, 2004. 32(suppl_1): p. D364-D367.
119. Miettinen, K., et al., The TriForC database: a comprehensive up-to-date resource of plant triterpene biosynthesis. Nucleic acids research, 2018. 46(D1): p. D586-D594.

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