MilletRancidDB
Database for Rancidity associated genes identified in genomes of Pearl millet, Foxtail millet, Finger millet, Rice and Arabadopsis along with 82 transcriptome datasets of Pearl millet.
Welcome to the Millet Rancidity Database (MilletRancidDB)
Various transcriptomic investigations have been executed on pearl millet to scrutinize its gene expression under diverse stressful situations. Though, not much focus is given over identification of rancidity associated enzymes/transcripts in pearl millet. Also, different genomic resources have been established for foxtail millet and other millets and crops. However, such resources are currently lacking for pearl millet.
This database provide information about rancidity associated enzymes, lipase, lipoxygenase (LOX), polyphenol oxidase, and peroxidase, in 82 different publically available transcriptome datasets of Pearl millet. These datasets belong to different species of Pearl millet corresponding to different tissues and stress conditions. Details about these datasets can be obtained from Transcriptome page .
For identification of lipase, lipoxygenase (LOX), polyphenol oxidase, and peroxidase in transcriptome datasets of pearl millet, initially these enzymes or corresponding genes were taken from 11 different Pennisetum glaucum (pearl millet) species, 01 species of Eleusine coracana (finger millet), 01 species of Setaria italica (foxtail millet), Oryza sativa(rice) and Arabidopsis thaliana. Details about them can be obtained from Genome page. All these genes/enzymes obtained from these 15 species was used to mine rancidity associated enzymes or corresponding transcripts in 82 transcriptome dataset. A total of 15 different plant species were considered, which include:
- 01 species of Pennisetum glaucum (Tift 23D2B1-P1-P5) from ICRISAT
- 10 species of Pennisetum glaucum along with 01 species of Setaria italica and Eleusine coracana from MilletDB
- Rice from RAP-DB
- Arabidopsis thaliana from TAIR
For all these species, except Pennisetum glaucum (Tift 23D2B1-P1-P5), annotation details were avilable and thus genes were taken on that basis. Though, for Pennisetum glaucum (Tift 23D2B1-P1-P5) annotation detail was not available and thus for this particular species, genome sequences were aligned against rancidity associated genes sequence of rest of 10 species of Pennisetum glaucum and genes showing significant alignment were taken for further analysis.
Literature review was carried out to identify different transcriptome studies carried out over pearl millet. On the basis of these studies, eighty-two publically available transcriptome data of different cultivar of Pearl millet were considered. They belong to different tissues like root, leaf etc and also to different stress condition, e.g. heat, drought etc with control conditions. Raw reads were taken for each dataset and after reference based assembly, they were aligned against the rancidity genes/enzymes obtained from 15 different plant species leading to identification of four rancidity associated enzymes, Lipase, Lipoxygenase, Polyphenol Oxidase and Peroxidase in these transcriptome datasets.