Integrative Approaches to Abiotic Stress Management in Crops: Combining Bioinformatics Educational Tools and Artificial Intelligence Applications
Abstract
:1. Introduction
2. Computational Biological Tools and Databases for Crop Improvement Research
2.1. Genomics
2.2. Transcriptomics
2.3. Proteomics
2.4. Metabolomics
3. Integrated Omics and Its Role in Addressing Crop Abiotic Stress
4. AI-Assisted Techniques for Abiotic Stress Management and Applications of AI in Crop Stress Biology
5. Major Deep Learning Architectures
6. Validation of ML Predictions in Crop Genomics
7. Why Is Machine Learning Preferred for Analyzing Plant-Omics Data over Traditional Methods?
8. AI Applications in Plant and Crop Omics for Combating Abiotic Stress
9. Challenges in Bioinformatics Education and AI for Crop Improvement under Abiotic Stress
10. Conclusions
Author Contributions
Funding
Conflicts of Interest
References
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Databases | Features/Description/Function | Website Links |
---|---|---|
AtMAD | Provides omics data of Arabidopsis thaliana | http://www.megabionet.org/atmad (accessed on 28 Feburary 2024) |
GoMapMan | Functional annotation of plant-related genes | http://www.gomapman.org/ (accessed on 4 March 2024) |
PGDBj | Database for DNA markers and their linkage | http://pgdbj.jp/en/index (accessed on 1 March 2024) |
Phytozome | A comparative genomics database for plants | https://phytozome-next.jgi.doe.gov/ (accessed on 3 March 2024) |
PlantGDB | A genomics database that provides annotated transcript assemblies for >100 plant (Viridiplantae) species | http://www.plantgdb.org/ (accessed on 22 Feburary 2024) |
PMRD | Plant miRNA database | http://bioinformatics.cau.edu.cn/PMRD/ (accessed on 5 March 2024) |
SALAD | Compares proteomic data across different species | https://salad.dna.affrc.go.jp/salad/en/ (accessed on 8 March 2024) |
FastQC | Quality checks on raw sequence data coming from high-throughput sequencing pipelines | https://www.bioinformatics.babraham.ac.uk/projects/fastqc/ (accessed on 28 Feburary 2024) |
Bowtie2 | Aligns sequencing reads in an ultrafast and memory-efficient manner | http://bowtie-bio.sourceforge.net/bowtie2/index.shtml (accessed on 28 Feburary 2024) |
kngMap | Aligns long reads to a reference sequence | https://github.com/zhang134/kngMap (accessed on 2 March 2024) |
MOSAIK | Maps 2nd- and 3rd-generation sequencing reads | https://github.com/wanpinglee/MOSAIK (accessed on 1 March 2024) |
Novoalign | Maps short reads onto a reference genome from different NGS platforms | http://www.novocraft.com/products/novoalign/ (accessed on 29 Feburary 2024) |
SOAP3-dp | First short-read alignment tool that leverages the multiprocessors in a graphic processing unit (GPU) to achieve a drastic improvement in speed. | http://soap.genomics.org.cn/ (accessed on 3 March 2024) |
Minimap2 | Accurate and efficient for long, noisy RNA and genomic sequences | https://github.com/lh3/minimap2 (accessed on 26 March 2024) |
GATK | Bioinformatics tool set for analyzing high-throughput sequencing and variant call format data | https://software.broadinstitute.org/gatk/ (accessed on 26 Feburary 2024) |
Freebayes | Excels at calling haplotype-based variants from a population | https://github.com/ekg/freebayes (accessed on 2 March 2024) |
Platypus | A haplotype-based variant caller | https://www.rdm.ox.ac.uk/research/lunter-group/lunter-group/platypus-a-haplotype-based-variant-caller-for-next-generation-sequence-data (accessed on 6 March 2024) |
IGV | A tool for high-performance interactive exploration of large, integrated genomic datasets | https://igv.org/ (accessed on 26 Feburary 2024) |
VISTA | Utilizes global alignment strategies and a curve-based visualization technique and is also used for comparative analysis | https://genome.lbl.gov/vista/index.shtml (accessed on 2 March 2024) |
R software | Gosling: A grammar for scalable and interactive visualization of genomic data | http://gosling-lang.org/ (accessed on 4 March 2024) |
GET_HOMOLOGUES-EST | A highly customized and automated pipeline specifically designed for individuals with a non-bioinformatics background | https://github.com/eead-csic-compbio/get_homologues/releases (accessed on 4 March 2024) |
PAN2HGENE | Computational tool that allows identification of gene products missing from the original genome sequence | https://sourceforge.net/projects/pan2hgene-software/ (accessed on 28 Feburary 2024) |
Pantools | A versatile tool for mapping metagenomic and genomic reads in both prokaryotes and eukaryotes | https://git.wur.nl/bioinformatics/pantools (accessed on 2 March 2024) |
PanViz | An interactive visualization tool for comparing individual genomes to the pangenome | https://github.com/thomasp85/PanViz/blob/master/package.json (accessed on 26 Feburary 2024) |
ppsPCP | Detects presence-absence variations and assembles a comprehensive pangenome | http://cbi.hzau.edu.cn/ppsPCP/ (accessed on 1 March 2024) |
RPAN | A rich source for rice genomic research and breeding | https://cgm.sjtu.edu.cn/3kricedb/ (accessed on 1 March 2024) |
Hap10 | A novel algorithm for haplotype assembly of polyploid genomes using linked reads | https://sourceforge.net/projects/sdhap/ (accessed on 8 March 2024) |
HapCut2 | Provides robust and accurate haplotype assembly for various sequencing technologies | https://github.com/vibansal/HapCUT2 (accessed on 23 Feburary 2024) |
HaploConduct | A package designed for the reconstruction of individual haplotypes | https://github.com/HaploConduct/HaploConduct (accessed on 8 March 2024) |
HAPLOVIEW | Analysis and visualization of linkage disequilibrium (LD) and haplotype maps | https://www.broadinstitute.org/haploview/haploview (accessed on 6 March 2024) |
HapTree | Provides a polyploid haplotype assembly tool based on a statistical framework | http://cb.csail.mit.edu/cb/haptree/ (accessed on 27 Feburary 2024) |
BFCounter | A program for counting k-mers in DNA sequence data | http://pritch.bsd.uchicago.edu/bfcounter.html (accessed on 2 March 2024) |
iMOKA | Utilizes a fast and accurate feature reduction step | https://github.com/RitchieLabIGH/iMOKA (accessed on 3 March 2024) |
KAT | A multi-purpose software toolkit for reference-free quality control (QC) of whole-genome sequencing (WGS) reads and de novo genome assemblies | https://github.com/TGAC/KAT (accessed on 28 Feburary 2024) |
KITSUNE | Identifies the optimal k-mer length for alignment-free phylogenomic analysis | https://github.com/natapol/kitsune (accessed on 5 March 2024) |
KmerGO | Identifies group-specific sequences using k-mers | https://github.com/ChnMasterOG/KmerGO (accessed on 3 March 2024) |
CHOPCHOP | A web-based tool for selecting target sites for CRISPR/Cas9- or TALEN-directed mutagenesis (generating primers and displaying the chromosomal site) | https://chopchop.cbu.uib.no/ (accessed on 26 Feburary 2024) |
CLD | Suitable for designing libraries using modified CRISPR enzymes and targeting non-coding regions | https://github.com/boutroslab/cld (accessed on 3 March 2024) |
CRISPETa | Designs optimal pairs of sgRNAs for the deletion of desired genomic regions | http://crispeta.crg.eu/ (accessed on 3 March 2024) |
CROPSR | Highly effective and efficient for designing gRNA in crops | https://github.com/H2muller/CROPSR (accessed on 2 March 2024) |
BioNIX | Integrates the output of several programs, including BLAST, FEX, FGENE, GRAIL, GENEFINDER, HEXON, MZEF, POLYAH, REPEATMASKER, and TRNASCAN | https://en.wikipedia.org/wiki/List_of_gene_prediction_software#cite_note-37 (accessed on 27 Feburary 2024) |
IntFOLD | A unified interface used for tertiary structure prediction/3D modeling, 3D model quality assessment, intrinsic disorder prediction, domain prediction, and prediction of protein–ligand binding residues | http://www.reading.ac.uk/bioinf/IntFOLD/ (accessed on 9 March 2024) |
RaptorX | Performs protein 3D modeling, distant homology discovery, and binding site prediction | http://raptorx.uchicago.edu/ (accessed on 24 Feburary 2024) |
ESyPred3D | Recognizes templates, aligns sequences, and performs 3D modeling | http://www.fundp.ac.be/urbm/bioin (accessed on 4 March 2024) |
FoldX | Designs protein and performs energy calculations | http://foldx.crg.es/ (accessed on 4 March 2024) |
Phyre and Phyre2 | Used for remote template identification, alignment, 3D modeling, multi-template modeling, and ab initio studies | http://www.sbg.bio.ic.ac.uk/~phyre/ (accessed on 3 March 2024) |
HHpred | Assists in template recognition, alignment, and 3D modeling | http://arquivo.pt/wayback/20160514083149/http%3A//toolkit.tuebingen.mpg.de/hhpred (accessed on 3 March 2024) |
MODELLER | Satisfies spatial restraints for protein structure modeling | https://salilab.org/modeller/ (accessed on 7 March 2024) |
CAN FOLD | Satisfies contact and distance constraints for protein folding | https://github.com/multicom-toolbox/CONFOLD (accessed on 28 Feburary 2024) |
MOE (Molecular Operating Environment) | Performs loop modeling, utilizes rotamer libraries for sidechain conformations and MM forcefields, identifies templates, uses multiple templates, and accounts for additional environments (e.g., excluded ligand volumes) | http://www.chemcomp.com/ (accessed on 2 March 2024) |
ROBETTA | Uses Rosetta homology modeling and fragment assembly for Ginzu domain prediction | http://robetta.bakerlab.org/ (accessed on 1 March 2024) |
BHAGEERATH-H | Predicts protein tertiary structure by combining methods of ab initio folding and homology modeling | http://www.scfbio-iitd.res.in/bhageerath/bhageerath_h.jsp (accessed on 4 March 2024) |
SWISS-MODEL | Performs local similarity/fragment assembly for protein structure prediction | http://swissmodel.expasy.org/ (accessed on 29 Feburary 2024) |
Yasara | Performs ligand and oligomer modeling, template detection, alignment, and model fragment hybridization, and can be used in text mode (clusters) or with a graphical user interface | http://www.yasara.org/ (accessed on 2 March 2024) http://www.yasara.org/casp8.htm (accessed on 1 March 2024) |
AWSEM-Suite | Uses molecular dynamics simulation to understand co-evolutionarily history, template-guided, and optimized folding landscapes | http://awsem.rice.edu/ (accessed on 28 Feburary 2024) |
Gramene | With a user-friendly interface, allows users to filter and export attributes related to species, germplasm, name/synonym, library/source and more. | http://www.gramene.org/ (accessed on 5 March 2024) |
EnsemblPlants | Provides annotation, alignment, and visualization of plant genomes from biodiversity initiatives and collaborations | http://plants.ensembl.org/ (accessed on 1 March 2024) |
MapGene2Chromosome | Analyzes the heredity of gene families and performs map-based gene cloning | http://mg2c.iask.in/mg2c_v2.0/ (accessed on 26 Feburary 2024) |
MapChart | Produces charts of genetic linkage maps and QTL data | https://www.mapchart.net/ (accessed on 1 March 2024) |
GSDS 2.0 | Assists in visualizing annotated gene features and generating high-quality figures for publication | https://gsds.gao-lab.org/Gsds_help.php (accessed on 3 March 2024) |
IUPred | Provides a combined web interface that identifies disordered protein regions using IUPred2 and disordered binding regions using ANCHOR2 | https://iupred2a.elte.hu/ (accessed on 4 March 2024) |
DESeq2 | A fundamental task in RNA-seq count data analysis is detecting differentially expressed genes | https://bioconductor.org/packages/release/bioc/html/ (accessed on 26 Feburary 2024) |
StringTie | Employs efficient algorithms to reconstruct transcript structures and estimate expression levels from bulk RNA-Seq reads aligned to a reference genome | https://ccb.jhu.edu/software/stringtie/ (accessed on 3 March 2024) |
PLEXdb | A unified plant and associated pathogens gene expression resource that serves as a genotype-to-phenotype, hypothesis-building information warehouse. It leverages highly parallel expression data and provides access to pertinent genetic, physical, and pathway data | https://www.plexdb.org/ (accessed on 28 Feburary 2024) |
PlantGenIE | A comprehensive web resource designed for searching, visualizing, and analyzing genomics as well as transcriptomics data across multiple plant species | http://www.plantgenie.org/ (accessed on 7 March 2024) |
TAIR | A genetic and molecular biology database dedicated to A. thaliana | https://www.arabidopsis.org/ (accessed on 23 Feburary 2024) |
MaizeGDB | Functions as a community-focused, long-term informatics resource tailored for researchers studying Zea mays | https://www.maizegdb.org/ (accessed on 2 March 2024) |
Genevestigator | A tool for exploring public and private gene expression data from bulk tissue to single cells | https://genevestigator.com/ (accessed on 28 Feburary 2024) |
MetaboAnalyst | Offers various modules for statistical, biomarker, pathway, network, and functional analysis of metabolomics data | https://www.metaboanalyst.ca/ (accessed on 4 March 2024) |
XCMS | A framework designed for the processing and visualization of chromatographically separated and single-spectra mass spectral data | https://xcmsonline.scripps.edu/landing_page.php?pgcontent=mainPage (accessed on 4 March 2024) |
MetaboLights | A cross-species, cross-technique database that encompasses metabolite structures, spectra, roles, locations, concentrations, and experimental data | https://www.ebi.ac.uk/metabolights/ (accessed on 3 March 2024) |
PMN | Provides statistics on pathways, enzymes, reactions, and compounds, along with detailed descriptions | http://plantcyc.org/ (accessed on 27 Feburary 2024) |
MassBank | A metadata-centric, auto-curating repository designed for efficient storage and querying of mass spectral data | https://massbank.eu/MassBank/ (accessed on 2 March 2024) |
PlantCyc | Multi-species reference database of plant metabolic pathways in over 500 species | http://pmn.plantcyc.org/ (accessed on 27 Feburary 2024) |
Golm Metabolome Database | Enables the search and distribution of mass spectra for biologically active metabolites quantified through Gas chromatography–mass spectrometry (GC–MS) | http://gmd.mpimp-golm.mpg.de/ (accessed on 3 March 2024) |
COLOMBOS | Offers extensive organism-specific cross-platform gene expression datasets for various bacterial model organisms | http://colombos.net/ (accessed on 4 March 2024) |
OmicsNet | Facilitates the interpretation of multi-omics signatures through biological networks | http://www.omicsnet.ca/ (accessed on 29 Feburary 2024) |
OmicsDI | Open-source platform that integrates and disseminates omics datasets from various resources and studies | https://www.omicsdi.org/ (accessed on 5 March 2024) |
OMICTools | Provides a comprehensive list of tools and databases for genomics applications | https://omictools.com/ (accessed on 5 March 2024) |
Panorama | A server-based data repository application for targeted mass spectrometry assays that integrates with the Skyline mass spec workflow | https://panoramaweb.org/ (accessed on 28 Feburary 2024) |
CRISPR RGEN Tools | Offers standalone, downloadable predictive models that efficiently forecast potential off-target numbers in CRISPR applications | https://www.rgenome.net/Cas-designer (accessed on 3 March 2024) |
CRISPRscan | Generates tracks for genome browsers, designs sgRNAs for specific gene sites, and scans the entire genome for off-target effects | https://www.crisprscan.org/ (accessed on 27 Feburary 2024) |
CCTop | Identifies mismatches, forecasts off-target effects, and predicts sgRNA efficiency | https://cctop.cos.uni-heidelberg.de:8043/ (accessed on 4 March 2024) |
CRISTA | Provides a framework for ML, identifies off-targets, and evaluates targets | https://crista.tau.ac.il/ (accessed on 1 March 2024) |
CRISPR-GE | Creates vectors and designs primers for on-target amplification | https://skl.scau.edu.cn/ (accessed on 1 March 2024) |
CRISPR-P | Analyzes gRNA sequences and performs on-target and off-target screening | https://crispr.hzau.edu.cn/CRISPR2/ (accessed on 29 Feburary 2024) |
CRSeek | Locates both on- and off-target websites | https://github.com/DamLabResources/crseek (accessed on 2 March 2024) |
CRISPResso | Potential is found for both on- and off-targets | http://github.com/lucapinello/CRISPResso (accessed on 28 Feburary 2024) |
Cas-OFFinder | Identifies potential off-target sites and provides detailed information about their locations, orientations, and the number of mismatches | http://www.rgenome.net/cas-offinder/ (accessed on 1 March 2024) |
CasOT | Identifies potential off-target locations based on user-specified PAM types, mismatch rates, and genomes | http://eendb.zfgenetics.org/Casot/ (accessed on 28 Feburary 2024) |
CRISPRitz | Enumerates, annotates, and assesses the potential implications of putative off-target sequences on the functioning genome | https://github.com/pinellolab/CRISPRitz (accessed on 1 March 2024) |
CRISPRloci | Defines the CRISPR leaders for each locus, predicts the direction of each CRISPR array, and annotates Cas9 genes | https://rna.informatik.uni-freiburg.de (accessed on 28 Feburary 2024) |
CRISPRdigger | Enhances the accuracy of a query genome by detecting CRISPRs with improved direct repeat annotations | http://www.healthinformaticslab.org/supp/ (accessed on 2 March 2024) |
BATCH-GE | Identifies and documents precise genome editing events, such as indel mutations, and estimates the associated mutagenesis efficiencies | https://github.com/WouterSteyaert/BATCH-GE.git (accessed on 1 March 2024) |
CRISPR Plant v2 | For extremely specialized sgRNAs | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6330547/ (accessed on 1 March 2024) |
CrisprGE | A central repository for CRISPR/Cas9-based genome editing data | http://crdd.osdd.net/servers/crisprge/ (accessed on 29 Feburary 2024) |
Tools | Abiotic Stressor | Algorithm | Features and Description | Websites |
---|---|---|---|---|
ASRpro | Drought, salinity, light, high and low temperatures | SVM | Autocross covariance and K-aner composition identification of proteins. | https://iasri-sg.icar.gov.in/asrpro/ (accessed on 1 March 2024) |
AsmIR | Drought, salinity, high and low temperatures | SVM | Pseudo-K-tuple nucleotide composition; predicts abiotic stress miRNA. | https://iasri-sg.icar.gov.in/asmir/ (accessed on 1 March 2024) |
PlncPRO | Abiotic | RF | Predicts abiotic stress-responsive long non-coding RNA | http://ccbb.jnu.ac.in/plncpro/ (accessed on 1 March 2024) |
ASRmiRNA | Abiotic | SVM | Predicts abiotic responsive miRNA. | http://cabgrid.res.in:8080/asrmirna/dataset.html (accessed on 1 March 2024) |
ASLncR | Abiotic | SVM | Predicts abiotic stress-responsive long non-coding RNA. | https://iasri-sg.icar.gov.in/aslncr/ (accessed on 1 March 2024) |
Ir-HSP | High temperatures | SVM | Categorizes protein sequences into one of the heat-shock families | http://cabgrid.res.in:8080/ir-hsp/ (accessed on 1 March 2024) |
DeeperHSP | High temperatures | CNN | Identifies heat-shock proteins. | https://github.com/seonwoo-min/DeeperHSP (accessed on 1 March 2024) |
AFP-Pred | Cold | RF | Predicts anti-freeze protein properties. | https://www3.ntu.edu.sg/home/EPNSugan/index_files/AFP-Pred.htm (accessed on 1 March 2024) |
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Zhang, X.; Ibrahim, Z.; Khaskheli, M.B.; Raza, H.; Zhou, F.; Shamsi, I.H. Integrative Approaches to Abiotic Stress Management in Crops: Combining Bioinformatics Educational Tools and Artificial Intelligence Applications. Sustainability 2024, 16, 7651. https://doi.org/10.3390/su16177651
Zhang X, Ibrahim Z, Khaskheli MB, Raza H, Zhou F, Shamsi IH. Integrative Approaches to Abiotic Stress Management in Crops: Combining Bioinformatics Educational Tools and Artificial Intelligence Applications. Sustainability. 2024; 16(17):7651. https://doi.org/10.3390/su16177651
Chicago/Turabian StyleZhang, Xin, Zakir Ibrahim, Muhammad Bilawal Khaskheli, Hamad Raza, Fanrui Zhou, and Imran Haider Shamsi. 2024. "Integrative Approaches to Abiotic Stress Management in Crops: Combining Bioinformatics Educational Tools and Artificial Intelligence Applications" Sustainability 16, no. 17: 7651. https://doi.org/10.3390/su16177651