Pathogen Identification in Plant using NGS
Pathogens since ages has been linked to different types of diseases including those of human beings, animals or even plants. Deadly effects of these organisms have been reported in different scientific articles that necessitates the process of identification and analysing. Methods for identification has been many, but the most widely applied is the method of sequencing. The article will focus on how the sequencing technologies can be applied in identifying pathogens in the Plant kingdom.
Pathogens in Agriculture
Agriculture tends to be one of the most important sectors for a sustainable future. However, the crop productivity can be affected by the impact of various pathogens such as bacteria, fungi, viruses etc. Different factors responsible for the leading cause of infections by these organisms have been reported. Molecular biology techniques such as RT-PCR has been used for identifying the pathogens, but these techniques are useful when known microorganisms are on focus. To overcome this, the next generation sequencing technologies are now used which can be applied on a wide variety of microorganisms. Different analysis platforms have been developed considering specifically the plant pathogens. Below discussed are a few of the major applied methods for the identification of pathogens in plants.
16S sequencing in pathogen identification.
For a better pathogenic identification, traditional methods have been replaced with sequencing of the microorganism such as the 16S rRNA sequence. Even for the rarely isolated, and the novel pathogens, this method stands as one of the preferred techniques of pathogen identification. Another interchangeable term used for this is 16S rDNA. One of the main reasons behind the use of 16S rRNA sequence is the presence of highly conserved regions along with the variable regions. Development of databases have provided an easy storage of large number of 16S rRNA sequence for a wide variety of microorganisms. Another applicability of the methods is establishing a phylogenetic relationship between the sequences. 16S sequences are reported to be universal within the bacterial genome. Therefore, the differences at the genetic level can be analysed.
Virus and their virome
Plant infections are not only restricted to the bacteria and fungi, but many cases have focused on the viral infections. Treatment of viral infections are still limited and hence it is of utmost concern to identify these pathogens at an early stage. Next Generation Sequencing technologies have provided the way to analyse the virome of an infected plant. The advantage of using NGS based technology in identifying pathogens from a virome is its ability to detect those viral transcripts whose frequency is even lesser than one in a million. Also, with multiple batches of sequencing in parallel, multiple viruses can be detected simultaneously.