ArticlePlant physiology2004
Computational identification and characterization of novel genes from legumes.
Article in Plant physiology, 2004. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 76 papers.
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76 citing papers in PubMed, 178 citations in OpenAlex.
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- Role of Brassica orphan gene BrLFM on leafy head formation in Chinese cabbage (Brassica rapa).TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2023Article
- Orphan Genes in Crop Improvement: Enhancing Potato Tuber Protein without Impacting Yield.Plants (Basel, Switzerland) · 2022Article
- A deep learning approach for orphan gene identification in moso bamboo (Phyllostachys edulis) based on the CNN + Transformer model.BMC bioinformatics · 2022Article
- A variable gene family encoding nodule-specific cysteine-rich peptides in pea (Frontiers in plant science · 2022Article
- Research Advances and Prospects of Orphan Genes in Plants.Frontiers in plant science · 2022Review
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- Comparing Early Transcriptomic Responses of 18 Soybean (International journal of molecular sciences · 2021Article
- Analysis of a gene family for PDF-like peptides from Arabidopsis.Scientific reports · 2021Article
- Genome-Wide Identification, Characterization and Function Analysis of Lineage-Specific Genes in the Tea PlantFrontiers in genetics · 2021Article
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- Genome sequence and spore germination-associated transcriptome analysis of Corynespora cassiicola from cucumber.BMC microbiology · 2020Article
- Gene Expression in Nitrogen-Fixing Symbiotic Nodule Cells inThe Plant cell · 2020Review
- Mitochondrial Fostering: The Mitochondrial Genome May Play a Role in Plant Orphan Gene Evolution.Frontiers in plant science · 2020Article
- Plant Leucine-Rich Repeat Receptor Kinase (LRR-RK): Structure, Ligand Perception, and Activation Mechanism.Molecules (Basel, Switzerland) · 2019Review
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- Plant defensins: types, mechanism of action and prospects of genetic engineering for enhanced disease resistance in plants.3 Biotech · 2019Review
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16 more citing papers are in PubMed but not listed here.
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Authors and funding
4 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The Fabaceae, the third largest family of plants and the source of many crops, has been the target of many genomic studies. Currently, only the grasses surpass the legumes for the number of publicly available expressed sequence tags (ESTs). The quantity of sequences from diverse plants enables the use of computational approaches to identify novel genes in specific taxa. We used BLAST algorithms to compare unigene sets from Medicago truncatula, Lotus japonicus, and soybean (Glycine max and Glycine soja) to nonlegume unigene sets, to GenBank's nonredundant and EST databases, and to the genomic sequences of rice (Oryza sativa) and Arabidopsis. As a working definition, putatively legume-specific genes had no sequence homology, below a specified threshold, to publicly available sequences of nonlegumes. Using this approach, 2,525 legume-specific EST contigs were identified, of which less than three percent had clear homology to previously characterized legume genes. As a first step toward predicting function, related sequences were clustered to build motifs that could be searched against protein databases. Three families of interest were more deeply characterized: F-box related proteins, Pro-rich proteins, and Cys cluster proteins (CCPs). Of particular interest were the >300 CCPs, primarily from nodules or seeds, with predicted similarity to defensins. Motif searching also identified several previously unknown CCP-like open reading frames in Arabidopsis. Evolutionary analyses of the genomic sequences of several CCPs in M. truncatula suggest that this family has evolved by local duplications and divergent selection.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.