ArticleThe New phytologist2020
TGFam-Finder: a novel solution for target-gene family annotation in plants.
Article in The New phytologist, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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18 citing papers in PubMed.
- Integrative sequence-structure analysis reveals hidden WD40 domains forming stable β-propeller folds with potential biological functions in plants.Plant communications · 2026Article
- The origin, evolution, and diversification of MADS-box transcription factors in green plants.Plant communications · 2025Article
- An overview of computational methods for gene prediction in eukaryotes: strengths, limitations, and future directions.Bioinformatics advances · 2025Review
- Haplotype-resolved genome assembly and resequencing analysis provide insights into genome evolution and allelic imbalance in Pinus densiflora.Nature genetics · 2024Article
- Identification and expression analyses of B3 genes reveal lineage-specific evolution and potential roles of REM genes in pepper.BMC plant biology · 2024Article
- Genomic basis of multiphase evolution driving divergent selection of zinc-finger homeodomain genes.Nucleic acids research · 2023Article
- Comparative and expression analyses of AP2/ERF genes reveal copy number expansion and potential functions of ERF genes in Solanaceae.BMC plant biology · 2023Article
- PHD finger proteins function in plant development and abiotic stress responses: an overview.Frontiers in plant science · 2023Review
- The state of Medusozoa genomics: current evidence and future challenges.GigaScience · 2022Review
- Identification of novel PHD-finger genes in pepper by genomic re-annotation and comparative analyses.BMC plant biology · 2022Article
- Building a foundation for gene family analysis in Rosaceae genomes with a novel workflow: A case study inFrontiers in plant science · 2022Article
- Two different domain architectures generate structural and functional diversity amongFrontiers in plant science · 2022Article
- PlantTribes2: Tools for comparative gene family analysis in plant genomics.Frontiers in plant science · 2022Article
- Recurrent mutations promote widespread structural and functional divergence of MULE-derived genes in plants.Nucleic acids research · 2021Article
- Genome assembly of the popular Korean soybean cultivar Hwangkeum.G3 (Bethesda, Md.) · 2021Article
- Comparative analysis of de novo genomes reveals dynamic intra-species divergence of NLRs in pepper.BMC plant biology · 2021Article
- Comparative Analysis of Re-Annotated Genes Provides Insight into Evolutionary Divergence and Expressions of Aquaporin Family in Pepper.Plants (Basel, Switzerland) · 2021Article
- Automatic Prediction and Annotation: There Are Strong Biases for Multigenic Families.Frontiers in genetics · 2021Article
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26 authors.
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Abstract
Whole-genome annotation error that omits essential protein-coding genes hinders further research. We developed Target Gene Family Finder (TGFam-Finder), an alternative tool for the structural annotation of protein-coding genes containing target domain(s) of interest in plant genomes. TGFam-Finder took considerably reduced annotation run-time and improved accuracy compared to conventional annotation tools. Large-scale re-annotation of 50 plant genomes identified an average of 150, 166 and 86 additional far-red-impaired response 1, nucleotide-binding and leucine-rich-repeat, and cytochrome P450 genes, respectively, that were missed in previous annotations. We detected significantly higher number of translated genes in the new annotations using mass spectrometry data from seven plant species compared to previous annotations. TGFam-Finder along with the new gene models can provide an optimized platform for comprehensive functional, comparative, and evolutionary studies in plants.
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