| URL: | http://wheat.cau.edu.cn/TGT/ |
| Full name: | Triticeae-GeneTribe - a homology database for Triticeae |
| Description: | Triticeae-GeneTribe (TGT) is a homology database for Triticeae, which can perform gene evolution and function analysis by integrating available genome assemblies of Triticeae species. A series of versatile analysis and visualization tools, such as homologues, micro-collinearity, macro-collinearity analysis, gene description, and gene ontology enrichment, are supported. |
| Year founded: | 2020 |
| Last update: | |
| Version: | 1.0 |
| Accessibility: |
Accessible
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| Country/Region: | China |
| Data type: | |
| Data object: | |
| Database category: | |
| Major species: |
Triticum aestivum
Triticum spelta
Triticum turgidum
Triticum dicoccoides
Triticum urartu
Aegilops speltoides
Aegilops tauschii
Aegilops searsii
Aegilops bicornis
Aegilops longissima
Aegilops sharonensis
Thinopyrum elongatum
Secale cereale
Hordeum vulgare
Avena strigosa
Brachypodium distachyon
Oryza sativa
Zea mays
Arabidopsis thaliana
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| Keywords: |
| University/Institution: | China Agricultural University |
| Address: | |
| City: | Beijing |
| Province/State: | |
| Country/Region: | China |
| Contact name (PI/Team): | Yongming Chen |
| Contact email (PI/Helpdesk): | chen_yongming@126.com |
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A Collinearity-Incorporating Homology Inference Strategy for Connecting Emerging Assemblies in the Triticeae Tribe as a Pilot Practice in the Plant Pangenomic Era. [PMID: 32979565]
Plant genome sequencing has dramatically increased, and some species even have multiple high-quality reference versions. Demands for clade-specific homology inference and analysis have increased in the pangenomic era. Here we present a novel method, GeneTribe (https://chenym1.github.io/genetribe/), for homology inference among genetically similar genomes that incorporates gene collinearity and shows better performance than traditional sequence-similarity-based methods in terms of accuracy and scalability. The Triticeae tribe is a typical allopolyploid-rich clade with complex species relationships that includes many important crops, such as wheat, barley, and rye. We built Triticeae-GeneTribe (http://wheat.cau.edu.cn/TGT/), a homology database, by integrating 12 Triticeae genomes and 3 outgroup model genomes and implemented versatile analysis and visualization functions. With macrocollinearity analysis, we were able to construct a refined model illustrating the structural rearrangements of the 4A-5A-7B chromosomes in wheat as two major translocation events. With collinearity analysis at both the macro- and microscale, we illustrated the complex evolutionary history of homologs of the wheat vernalization gene Vrn2, which evolved as a combined result of genome translocation, duplication, and polyploidization and gene loss events. Our work provides a useful practice for connecting emerging genome assemblies, with awareness of the extensive polyploidy in plants, and will help researchers efficiently exploit genome sequence resources. |