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Key research themes
1. How are multi-omics and integrative bioinformatics approaches advancing the understanding of plant responses and gene function prediction?
This research theme focuses on leveraging multi-omics data—genomics, transcriptomics, proteomics, metabolomics—and integrating them through bioinformatics platforms and computational models to decipher the complexity of plant molecular responses and gene functions. It covers how integrated datasets contribute to systems-level insights in gene function prediction, stress responses, and facilitate plant breeding.
Key finding: The paper highlights an integrative multilevel omics framework combining genomics, transcriptomics, proteomics, and metabolomics to unravel plant molecular mechanisms underpinning abiotic stress responses. It emphasizes the... Read more
Multi-Omics Approaches and Resources for Systems-Level Gene Function Prediction in the Plant Kingdom
Key finding: This study advances gene function prediction by combining multi-omics datasets with high-performance computing and machine learning models such as convolutional neural networks, outperforming traditional sequence-based... Read more
Key finding: The article provides empirical evidence that machine learning algorithms effectively analyze heterogeneous high-throughput omics data to improve plant agronomic traits. It details curated datasets, software tools, and... Read more
Key finding: The research identifies critical challenges in managing and integrating multi-scale omics and environmental datasets for AI application in plant sciences. It argues that robust data infrastructure and standards are... Read more
2. What bioinformatics platforms and databases are enabling large-scale plant genomic and phenomic data integration and exploration?
This theme addresses the development and deployment of specialized bioinformatics platforms and databases that provide comprehensive genomic, phenomic, and functional annotation data. It elucidates how these resources facilitate data accessibility, comparative genomics, gene annotation, co-expression analysis, and support large consortium efforts for crop and model species research.
Key finding: PlantGenIE.org integrates multi-species genomic and transcriptomic datasets using user-friendly interfaces, enabling visualization of expression networks and cross-species coexpression conservation. It supports genome... Read more
Key finding: Gramene hosts 39 fully assembled reference plant genomes with integrated ontologies, variation data, and metabolic pathway annotations using the Plant Reactome framework. It offers programmatic access and supports... Read more
Key finding: The Planteome project provides comprehensive reference and species-specific ontologies facilitating semantic integration of plant genomics and phenomics data across 95 taxa. It publishes over 21 million ontology-based... Read more
Key finding: This paper presents PlantAligDB, a curated database of aligned nucleotide sequences from six genomic regions across 223 plant families, facilitating accessible, quality-controlled sequence alignments and phylogenetic... Read more
Key finding: PGSB PlantsDB enhances comparative genomics by integrating fragmented, large cereal genomes with synteny visualization tools (CrowsNest) and RNA-Seq expression browsers, supporting species including barley, wheat, and rye. It... Read more
3. How are advances in genome assembly, annotation, and visualization tools addressing the complexities of plant genomes?
Given the intrinsic challenges posed by large, repetitive, polyploid plant genomes, this theme explores state-of-the-art computational methodologies and best practices for genome assembly, structural and functional annotation, and visualization. It includes evaluations of repeat masking, use of long- and short-read sequencing data, evidence-based predictions, and orthology-informed functional annotation enhancing annotation accuracy.
Welcome to the big leaves: best practices for improving genome annotation in non-model plant genomes
Key finding: Through comparative assessment across five diverse plant species, this study quantifies the impact of repeat masking, RNA-seq read type (short vs. long reads), and protein evidence integration on BRAKER- and MAKER-based gene... Read more
Key finding: This article reviews fundamental obstacles in plant genome assembly arising from high repeat content, large genome sizes, ploidy, and heterozygosity. It synthesizes advances in sequencing technologies and bioinformatic tools... Read more
Key finding: By identifying strict 1-to-1 ortholog cliques across ten plant species using reciprocal best BLAST hits from both genomic and proteomic data, this comparative genomics approach enriched wheat gene annotations by 65% over... Read more
Key finding: The Plant Orthology Browser (POB) provides an interactive web platform visualizing over one million orthologous gene relations among 20 plant species based on reciprocal best BLAST hits of protein and DNA sequences. It... Read more
Key finding: GeneSeqer@PlantGDB introduces a web-accessible spliced alignment tool optimized for plants, enabling accurate gene structure annotation using native EST/cDNA and protein evidence. The platform supports expert refinement of... Read more