Abstract
BackgroundIntronless genes are a significant characteristic of prokaryotes. Systematic identification and annotation are primary and crucial steps for determining the functions of intronless genes and understanding their occurrence in eukaryotes.DescriptionIn this paper, we describe the construction of the Intronless Genes Database in Dicots (IGDD; available at http://bio.njfu.edu.cn/igdd/), which contains data for five well-annotated plants including Arabidopsis thaliana, Carica papaya, Populus trichocarpa, Salix suchowensis and Vitis vinifera. Using highly visual settings, IGDD displays the structural and functional annotations, the homolog groups, the syntenic relationships, the expression patterns, and the statistical characteristics of intronless genes. In addition, useful tools such as an advanced search and local BLAST are available through a user-friendly and intuitive web interface.ConclusionIn conclusion, the IGDD provides a comprehensive and up-to-date platform for researchers to assist the exploration of intronless genes in dicot plants.
Highlights
Intronless genes are a significant characteristic of prokaryotes
To build a centralized platform, we developed intronless genes database in dicotsWGD (IGDD)—a comprehensive and integrated database for intronless genes that covers five dicots, including Arabidopsis thaliana (Arabidopsis), Carica papaya, Populus trichocarpa, Salix suchowensis and Vitis vinifera
In IGDD, different categories of datasets are classified and compared within and among species with user-friendly graphics. Analytical tools such as BLAST are embedded in IGDD to help predict the putative orthologous groups of the intronless genes
Summary
Intronless genes are a significant characteristic of prokaryotes. Systematic identification and annotation are primary and crucial steps for determining the functions of intronless genes and understanding their occurrence in eukaryotes.Description: In this paper, we describe the construction of the Intronless Genes Database in Dicots (IGDD; available at http://bio.njfu.edu.cn/igdd/), which contains data for five well-annotated plants including Arabidopsis thaliana, Carica papaya, Populus trichocarpa, Salix suchowensis and Vitis vinifera. Intronless genes are a significant characteristic of prokaryotes. Systematic identification and annotation are primary and crucial steps for determining the functions of intronless genes and understanding their occurrence in eukaryotes. IGDD displays the structural and functional annotations, the homolog groups, the syntenic relationships, the expression patterns, and the statistical characteristics of intronless genes. Genes that are not interrupted by introns are called intronless genes or single-exon genes Depending on their structure, genes in eukaryotes fall into two categories: intronless genes and intron-containing genes. Intronless genes as a model, compared with intron-containing homologs, can enable an inverse approach to studying the considerable roles of introns, which are only found in eukaryotes [1]. IGD is derived from GenBank, which does not contain all the sequences available from genome projects; it does not provide representative intronless gene sets. Compared with IGD, PIGD has an improved methodology, but contains less evolutionary information in its gene annotations
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