Bhumika Dubay

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917454848867

Shiv Nadar University, India

Universidad Politechnica de Madrid, Spain

CBGP (UPM-INIA), Madrid, Spain

Understanding host range evolution in plant RNA viruses: In the era of global transformations, the challenge is to understand the pattern of small changes that are occurring. One such challenge is in understanding, how to survive? How to continue the food supplies? How to save our ecosystems from invaders? Yet how to sustain the natural ecology? To answer such ninety-nine questions the best approach is to understand the mechanisms of the change. And for this, we need to study at a large scale (at the scale of big data). Our focus was mainly on crop lands, forests, wasteland and edges. With the help of this research work, I demonstrated a metagenomics approach where I studied these plaant viruses directly taken from their natural habitat, on a larger scale. The dimensions of this thesis work covered the establishment of protocols to be able to maximize our reach to these plant viruses. I focused on plant RNA viruses because they are the biggest group of invaders to the plant in our researched locations. I studied different ways of getting the virus sequences including extraction of virion associated nucleotide particles, random priming PCR, size-based chromatographic purification of viral nucleic acid, total RNA extractions, etc. Out of these, plant total RNA was most suited for sequencing and then, I started testing different protocols for extraction and pooling. My experiment suggests the column based RNA extraction protocol using Direct-zol kit from Zymo research to be the most versatile as well as time effective solution for data acquisition. To set a pipeline for post sequencing analysis, I created the artificial wild plant genome with sequence simulations and tried different ways of species prediction in our genome. The alignment results suggest that clustering the sequence reads using traditional binning approaches are not a good idea prior to its alignment. I used reference base alignment, and the reference genomes were selected using Basic Local Alignment Search Tool (BLAST). I also tested our protocols on plant samples collected in the field from Melon crop fields and from Oak wood habitats from the South Madrid region of Central Spain. I had 70% success rate in the sequencing of field samples. The pipeline established, suggested 30 different viruses to be present in 14 different host species. This project opens up the way to further sequence and analyses of more plant species from  more habitats using the knowledge obtained, in order to describe patterns of evolution of the viruses so  obtained

Workshop on New Frontiers in Plant Biology- 2016

PhD student, EPIDIVERSE project(Horizon 2020), Institute of Applied Genomics-TS, Udine, Italy