PlantCFG: Database of Candidate Flowering Genes in Plants
——A comprehensive database with web tools for analyzing candidate flowering genes in multiple plants
PlantCFG, a multi-species plant flowering gene database, include 112 species from 10 plant families. We performed a
careful literature survey and 459, 71, and 112 reported flowering genes were curated in Arabidopsis
thaliana, Glycine max, and Oryza sativa, respectively. The candidate flowering genes in
other species were identified by using a combination of sequence similarity and conserved domain based
approaches. It contains 82,597 candidate flowering genes, which were classified into 372 protein classes and 62 gene families. PlantCFG aims to
collect, organize, display and
compare flowering genes in multiple plants, including the following: (i) query the basic information of
candidate
flowering genes in 112 plants; (ii)
explore
the functions of genes involved in the ‘ABCDE’ model; (iii) carry out collinearity relationship, phylogenetic, sequence identity, and Ka/Ks analyses of candidate
flowering genes in different species; and (iv) browse, search and batch download flowering gene lists and
sequences. Furthermore, we provide a Submit module, where users can submit flowering gene, which will be
reviewed and periodically updated to the database.
The Top Menu. This is the navigation bar at the top of the PlantCFG database, which contains Search
(By species, By reported flowering genes, By gene
family , By Pfam family and By sequence),
Synteny
, ABCDE model, Evolution (Phylogenetic, Sequence
identity and Ka/Ks),
Download and Submit
module.
Brief Introduction. For quick search of flowering genes, the gene ID of 112 species, gene name of
Arabidopsis thaliana, Glycine max, and Oryza sativa, Pfam and Gene family are
supported.
Quick entry of function modules.
Species Summary. Provided the basic information, homologous of Ath/Osa/Gly flowering genes
,candidate flowering genes,pfam family and gene family of
each species.
PlantCFG contains 8,2104 flowering genes, obtained from 112 species of 10 plant families
(Gramineae,
Leguminosae, Brassicaceae, Cucurbitaceae, Asteraceae, Rosaceae, Solanaceae, Sterculiaceae, Oleaceae, and
Chenopodiaceae). In this page, users can query the basic information of 112 plants, including flowering gene
distribution, their protein classes and gene families.
Species Introduction.
Species Description.
Flowering gene list.
Gene Distribution.
We provided the Search Flowering gene page in the Search (By reported flowering genes) module to retrieve
the flowering genes information in Arabidopsis thaliana, Glycine max, and Oryza sativa
more conveniently.
Search Page.
Search flowering gene information
The 8,2104 flowering genes were classified into 372 protein classes and 62
gene families. All these
information and other features can be browsed in our user-friendly website.
The information of 62 gene family.
Statistics of 62 gene family.
Members of your selected gene family.
Gene number of your selected gene family in each species.
Gene details of your selected gene family.
The results of Pfam Family is similar to that of gene family.
On the “ Search by sequence ” pages, users can obtain the highest similarity of candidate flowering genes by
entering the unknown nucleic acid or protein sequences.
We used an interactive plugin to display homologous gene pairs by selecting different species and
chromosomes. Different colors of the circles represent different species, and the gray line represent a
homologous gene pair. By hovering the mouse, users can view the information of the homologous gene pair.
Genes related to flower development are a series of"homologous genes" because they determine the
characteristics of flower organs without changing their origin. According to their roles in floral
organogenesis, these genes can be divided into 5 groups: A, B, C, D and
E.
We designed an eFP browser for exploring genes involved in 'ABCDE' model.
We designed an eFP browser for exploring genes involved in 'ABCDE' model.
Illustration of 'ABCDE' model.
The number of genes in different models of the species your choose.
The phylogenetic module provides a cross-species comparison of the
phylogenetic relationships of flowering genes, and users can access a whole view of orthologues and
paralogues of a flowering gene.
Search Page.
Phylogenetic tree and Gene structure.
This page provided the evolutionary relationship of homologous genes based on Arabidopsis thaliana,
Glycine max, and Oryza sativa flowering genes, including multi alignment of homologus genes.
Search Page.
Multi alignment of homologus genes.
The Ka/Ks ratio was used to diagnose the form of sequence evolution.
The Ka/Ks module provides the comparison of
Ka/Ks of candidate flowering genes between 112 species. We also
provides multiple dynamic charts for users to visualize and investigate the
Ka/Ks distribution.
Search Page.
The distribution of Ka/Ks.
On the Download page, you can download the flowering gene sequence through Arabidopsis thaliana,
Glycine max, and Oryza sativa gene, Pfam family, Gene family, and ABCDE model.
Search Page.
Download flowering genes sequence.
Furthermore, as a comprehensive platform for plant flowering gene analysis, we provide a Submit module and
plan to continuously update the flowering gene, maintain and improve the database to better serve the
researchers.
Search Page.
Search Page.
