ArticlePlant physiology2022
GGDB: A Grameneae genome alignment database of homologous genes hierarchically related to evolutionary events.
Article in Plant physiology, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 4 papers.
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Who cites it
4 citing papers in PubMed.
- Constructing a Prognostic Model for Clear Cell Renal Cell Carcinoma Based on Glycosyltransferase Gene and Verification of Key Gene Identification.International journal of molecular sciences · 2025Article
- An integrative 3D-genome database for plants.Plant communications · 2025Article
- Synthetic Retinoid Sulfarotene Selectively Inhibits Tumor-Repopulating Cells of Intrahepatic Cholangiocarcinoma via Disrupting Cytoskeleton by P-Selectin/PSGL1 N-Glycosylation Blockage.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2025Article
- Split-Cre mediated deletion of DNA no longer needed after site-specific integration in rice.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2022Article
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Authors and funding
6 authors.
Funding
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Abstract
The genomes of Gramineae plants have been preferentially sequenced owing to their economic value. These genomes are often quite complex, for example harboring many duplicated genes, and are the main source of genetic innovation and often the result of recurrent polyploidization. Deciphering these complex genome structures and linking duplicated genes to specific polyploidization events are important for understanding the biology and evolution of plants. However, efforts have been hampered by the complexity of analyzing these genomes. Here, we analyzed 29 well-assembled and up-to-date Gramineae genome sequences by hierarchically relating duplicated genes in collinear regions to specific polyploidization or speciation events. We separated duplicated genes produced by each event, established lists of paralogous and orthologous genes, and ultimately constructed an online database, GGDB (http://www.grassgenome.com/). Homologous gene lists from each plant and between plants can be displayed, searched, and downloaded from the database. Interactive comparison tools are deployed to demonstrate homology among user-selected plants and to draw genome-scale or local alignment figures and gene-based phylogenetic trees corrected by exploiting gene collinearity. Using these tools and figures, users can easily detect structural changes in genomes and explore the effects of paleo-polyploidy on crop genome structure and function. The GGDB will provide a useful platform for improving our understanding of genome changes and functional innovation in Gramineae plants.
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