Study : Sinapis alba strain:B1D Transcriptome or Gene expression


Sinapis alba strain:B1D Transcriptome or Gene expression
Alternaria brassicicola is a necrotrophic fungus that is known to be the primary causal agent of a disease called the Black spot disease in almost all known species and varieties of the Brassicaceae family. A majority of crop yield is destroyed because of the impact of this disease. Therefore, remedies are required to be developed in order to check such devastating loss in crop yield. This is only possible after proper understanding of the mechanism by which the disease progression takes place. Due to the lack of any resistant background within the Brassica germplasm, Sinapis alba (which is a close relative of Brassica juncea) has been taken as the model to study the resistance mechanism. In this respect understanding of the transcripts that are expressed and differentially regulated upon infection with the given fungal pathogen is a stark requirement. Thus, we have undertaken the exercise of performing a comparative transcriptomics or profiling of all the transcripts that are differentially regulated upon challenge with Alternaria brassiciola (in both the susceptible and resistant backgrounds). This not only provides information about the transcripts that express as a defense response but also provides useful insights into the different pathways that are initiated or up-regulated as a response to the infection. This is very useful to obtain an idea about the probable and promising points where the defense regulation can be arising from. Thus looking into these areas makes the process of reaching to some interesting and pivotal areas very programmed and directed. It gives a meaningful direction to looking for the promising areas that regulate the defense response. In this project we have carried out the next generation sequencing of the transcriptome of the above mentioned samples using Illumina HiSeq2000 paired end sequencing. For the Brassica juncea samples about 10.16GB of data was obtained from the control samples and 13.07GB from treated samples. For the Sinapis alba samples 9.16GB data was obtained from control and 10.13GB from treated samples. An average of 45 million reads were obtained from each sample. The reads were subjected to high quality screening to remove the adapter contamination and low quality reads. These HQ reads were assembles into contigs and transcripts using velvet and oases softwares respectively. These were then annotated with the TAIR (Arabidopsis thaliana). Almost 80% of the transcripts were annotated. These were then subjected to DESeq (Digital expression) analysis. This was followed by an extensive analysis of the differential regulation of the genes and their classification.
Data files


Accession number Name Taxon