High Throughput Sequencing-Aided Survey Reveals Widespread Mixed Infections of Whitefly-Transmitted Viruses in Cucurbits in Georgia, USA.

Saritha Raman Kavalappara,Hayley Milner,Cecilia Mcgregor,Alton N Sparks,Sudeep Bag,Kaelyn Morgan,William M Wintermantel,Albert K Culbreath,Naga Charan Konakalla

doi:10.3390/v13060988

Abstract

Viruses transmitted by the sweet potato whitefly (Bemisia tabaci) have been detrimental to the sustainable production of cucurbits in the southeastern USA. Surveys were conducted in the fall of 2019 and 2020 in Georgia, a major cucurbit-producing state of the USA, to identify the viruses infecting cucurbits and their distribution. Symptomatic samples were collected and small RNA libraries were prepared and sequenced from three cantaloupes, four cucumbers, and two yellow squash samples. An analysis of the sequences revealed the presence of the criniviruses cucurbit chlorotic yellows virus (CCYV), cucurbit yellow stunting disorder virus (CYSDV), and the begomovirus cucurbit leaf crumple virus (CuLCrV). CuLCrV was detected in 76%, CCYV in 60%, and CYSDV in 43% of the total samples (n = 820) tested. The level of mixed infections was high in all the cucurbits, with most plants tested being infected with at least two of these viruses. Near-complete genome sequences of two criniviruses, CCYV and CYSDV, were assembled from the small RNA sequences. An analysis of the coding regions showed low genetic variability among isolates from different hosts. In phylogenetic analysis, the CCYV isolates from Georgia clustered with Asian isolates, while CYSDV isolates clustered with European and USA isolates. This work enhances our understanding of the distribution of viruses on cucurbits in South Georgia and will be useful to develop strategies for managing the complex of whitefly-transmitted viruses in the region.

Highlights

Introduction published maps and institutional affilVegetables are the fourth largest commodity group grown in Georgia by value, and cucurbits (Cucurbitaceae Juss.) contribute a total of USD 322 million towards the Georgia farm gate value [1]
Using the unbiased small RNA sequencing and de-novo assembly, we identified the whitefly-transmitted viruses infecting cucurbits in the region and showed that they are more widely distributed than previously assumed
There is no actual estimate of losses in dollars due to the complexity of whiteflytransmitted virus diseases, but the amount is believed to be in the tens of millions of dollars [2]

Summary

Introduction

Introduction published maps and institutional affilVegetables are the fourth largest commodity group grown in Georgia by value, and cucurbits (Cucurbitaceae Juss.) contribute a total of USD 322 million towards the Georgia farm gate value [1]. Cantalupensis Naudin), cucumber (Cucumis sativus L.), and yellow squash and zucchini (Cucurbita pepo L.), is concentrated in southern Georgia. Cucurbit production has become very challenging due to unusually high populations of whiteflies (Bemicia tabaci complex), and an associated heavy incidence of whitefly-transmitted viruses, primarily in the fall. Based on crop loss estimates in 2016 and 2017, several millions of dollars were lost due to whiteflies and the viruses they transmit in cucurbits (cantaloupe, yellow squash, and zucchini) and beans (Phaseolus vulgaris L.) [2]. Whitefly-transmitted viruses reported from the state, and infecting cucurbits include cucurbit leaf crumple virus (CuLCrV) [3], cucurbit yellow stunting disorder virus (CYSDV) [4], sida golden mosaic iations

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