ArticleNucleic acids research2008
PlantTribes: a gene and gene family resource for comparative genomics in plants.
Article in Nucleic acids research, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 47 papers.
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47 citing papers in PubMed.
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- Alkaloid production and response to natural adverse conditions inBiotechnologia · 2022Article
- PlantTribes2: Tools for comparative gene family analysis in plant genomics.Frontiers in plant science · 2022Article
- Building a foundation for gene family analysis in Rosaceae genomes with a novel workflow: A case study inFrontiers in plant science · 2022Article
- Phylogenomic resolution of order- and family-level monocot relationships using 602 single-copy nuclear genes and 1375 BUSCO genes.Frontiers in plant science · 2022Article
- Convergent Biochemical Pathways for Xanthine Alkaloid Production in Plants Evolved from Ancestral Enzymes with Different Catalytic Properties.Molecular biology and evolution · 2021Article
- SHR4z, a novel decoy effector from the haustorium of the parasitic weed Striga gesnerioides, suppresses host plant immunity.The New phytologist · 2020Article
- Characterization of the AP2/ERF Transcription Factor Family and Expression Profiling of DREB Subfamily under Cold and Osmotic Stresses inPlants (Basel, Switzerland) · 2020Article
- Landscape of gene transposition-duplication within the Brassicaceae family.DNA research : an international journal for rapid publication of reports on genes and genomes · 2019Article
- A Target Capture-Based Method to Estimate Ploidy From Herbarium Specimens.Frontiers in plant science · 2019Article
- Fern genomes elucidate land plant evolution and cyanobacterial symbioses.Nature plants · 2018Article
- Overlapping Patterns of Gene Expression Between Gametophyte and Sporophyte Phases in the FernFrontiers in plant science · 2018Article
- Haustorium initiation in the obligate parasitic plant Phelipanche ramosa involves a host-exudated cytokinin signal.Journal of experimental botany · 2017Article
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- Computational Tools for Genomic Studies in Plants.Current genomics · 2016Article
- Convergent evolution of caffeine in plants by co-option of exapted ancestral enzymes.Proceedings of the National Academy of Sciences of the United States of America · 2016Article
- Local Auxin Biosynthesis Mediated by a YUCCA Flavin Monooxygenase Regulates Haustorium Development in the Parasitic Plant Phtheirospermum japonicum.The Plant cell · 2016Article
- A Phylogenomic Assessment of Ancient Polyploidy and Genome Evolution across the Poales.Genome biology and evolution · 2016Article
- Elucidating steroid alkaloid biosynthesis in Veratrum californicum: production of verazine in Sf9 cells.The Plant journal : for cell and molecular biology · 2015Article
Corrections and comments
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Authors and funding
6 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The PlantTribes database (http://fgp.huck.psu.edu/tribe.html) is a plant gene family database based on the inferred proteomes of five sequenced plant species: Arabidopsis thaliana, Carica papaya, Medicago truncatula, Oryza sativa and Populus trichocarpa. We used the graph-based clustering algorithm MCL [Van Dongen (Technical Report INS-R0010 2000) and Enright et al. (Nucleic Acids Res. 2002; 30: 1575-1584)] to classify all of these species' protein-coding genes into putative gene families, called tribes, using three clustering stringencies (low, medium and high). For all tribes, we have generated protein and DNA alignments and maximum-likelihood phylogenetic trees. A parallel database of microarray experimental results is linked to the genes, which lets researchers identify groups of related genes and their expression patterns. Unified nomenclatures were developed, and tribes can be related to traditional gene families and conserved domain identifiers. SuperTribes, constructed through a second iteration of MCL clustering, connect distant, but potentially related gene clusters. The global classification of nearly 200 000 plant proteins was used as a scaffold for sorting approximately 4 million additional cDNA sequences from over 200 plant species. All data and analyses are accessible through a flexible interface allowing users to explore the classification, to place query sequences within the classification, and to download results for further study.
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