Abstract
Sorghum (Sorghum bicolor [L.] Moench) has excellent agronomic traits and biological properties, such as heat and drought-tolerance. It is a C4 grass and potential bioenergy-producing plant, which makes it an important crop worldwide. With the sorghum genome sequence released, it is essential to establish a sorghum functional genomics data mining platform. We collected genomic data and some functional annotations to construct a sorghum functional genomics database (SorghumFDB). SorghumFDB integrated knowledge of sorghum gene family classifications (transcription regulators/factors, carbohydrate-active enzymes, protein kinases, ubiquitins, cytochrome P450, monolignol biosynthesis related enzymes, R-genes and organelle-genes), detailed gene annotations, miRNA and target gene information, orthologous pairs in the model plants Arabidopsis, rice and maize, gene loci conversions and a genome browser. We further constructed a dynamic network of multidimensional biological relationships, comprised of the co-expression data, protein–protein interactions and miRNA-target pairs. We took effective measures to combine the network, gene set enrichment and motif analyses to determine the key regulators that participate in related metabolic pathways, such as the lignin pathway, which is a major biological process in bioenergy-producing plants.Database URL: http://structuralbiology.cau.edu.cn/sorghum/index.html.
Highlights
Sorghum originated from Africa and is the 5th major cereal in terms of production and acreage throughout the world
We focused mainly on transcription factors/regulators (TFs/TRs) and seven other super families, carbohydrate-active enzymes (CAZymes), protein kinases (PKs), UBs, cytochrome P450 members (CYPs), monolignol biosynthesis (MBs), R-genes and organellegenes
We have shown seven integrated genomic features, nuclear genome coding genes, miRNAs, expressed sequence tags (ESTs), organelle genome information, repeat elements, mRNA-seq data and miRNA-seq data, in genome browser’ (Gbrowse)
Summary
Sorghum originated from Africa and is the 5th major cereal in terms of production and acreage throughout the world It occupies 8 million hectares of farmland and provides food, feed, fiber and fuel. Grain sorghum has a high content of starch and can supply nutrition to humans and animals; forage sorghum is highly digestible and used as animal feed or as a cover crop; Sweet sorghum has a high content of sugar These three kinds of sorghum can be used as raw materials for the industrial production of ethanol or other specialty chemicals
Sign-in/Register to view highlights & summary Sign-in/Register to access full text options 
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a call
