Reemergence of tomato spotted wilt virus (TSWV) and exploring genome-based management options for thrips and TSWV in peanut production

Two PhD students are leading this effort. Ms. Pin-Chu Lai is examining the prevalence of 
virulent strains of TSWV in recent years, and Mr. Michael Catto is involved in sequencing and annotating the tobacco thrips, Frankliniella fusca, genome. 
Our previous work (Sunadaraj et al. 2014, Phytopathology) examined multiple TSWV isolates from TSWV-resistant and susceptible cultivars, and found that there was no evidence for 
selection against TSWV leading to development of highly-virulent strains. However, that study was based on just the coat protein gene sequencing. Other parts of the viral genome could be 
involved in suppressing plant defenses, and hence could experience increased selection pressure against them, especially in resistant cultivars. Ms. Pin-Chu Lai sequenced multiple virus isolates from 2016 to 2019 from TSWV-susceptible and resistant cultivars and examined them in detail. Results of that effort will be detailed in this report. 
On the genome aspect of the project, we initially partnered with the Georgia Genomics Facility and used an Illumina l OX sequencing platform to generate a draft genome. Annotations of the draft genome indicated that the assembly was lacking in several areas. We have now resorted to using a state of the art (PacBio) platform to generate sequences for the genome annotation. We believe that both methods may not be independently sufficient, and a hybrid assembly of both methods would be necessary. For this purpose, we are collaborating with researchers from both Auburn University and from North Carolina State University. We hope this to be a multiyear effort, and hope to have a draft genome for thrips available by the end of 2020.