GGDB: A Grameneae Genome Alignment Database of Homologous Genes Hierarchically Related to Evolutionary Events

Abstract

Owing to their economic values, Gramineae plants have been preferentially sequenced their genomes. These genomes are often quite complex, e.g., harboring many duplicated genes, which were the main source of genetic innovation and often the results of recurrent polyploidization. Deciphering the complex genome structure and linking duplicated genes to specific polyploidization events are important to understand the biology and evolution of plants. However, the effort has been held back due to its high complexity in analyzing these genomes. Here, by hierarchically relating duplicated genes in colinearity to each polyploidization or speciation event, we analyzed 29 well-assembled and up-to-date Gramineae genome sequences, separated duplicated genes produced by each event, established lists of paralogous and orthologous genes, and eventually constructed an on-line database, GGDB (http://www.grassgenome.com/). Homologous gene lists from each plant and between them can be displayed, searched, and downloaded from the database. Interactive comparison tools were deployed to demonstrate homology among user-selected plants, to draw genome-scale or local alignment figures, phylogenetic trees of genes corrected by exploiting gene colinearity, etc. Using these tools and figures, users can easily observe genome structural changes, and explore the effects of paleo-polyploidy on crop genome structure and function. The GGDB will be a useful platform to improve understanding the genome changes and functional innovation of Gramineae plants. Key pointsO_LIGGDB is the only portal hosting Grameneae colinear homologous genes hierarchically related to evolutionary events, especially polyploidization, which have occurred recursively. C_LIO_LIAllows systematic analysis of colinear gene relationships and function origination and/or divergence across Grameneae plants. C_LIO_LIServing the Grameneae research community, with new genomes, modules, tools, and analysis. C_LI