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Viruses 2017, 9(4), 92; doi:10.3390/v9040092

Deep Sequencing Analysis of RNAs from Citrus Plants Grown in a Citrus Sudden Death-Affected Area Reveals Diverse Known and Putative Novel Viruses

1
Instituto de Biociências da Universidade Estadual Paulista (Unesp), Botucatu, SP, 18615-689, Brazil
2
Centro de Citricultura Sylvio Moreira, Instituto Agronômico de Campinas, Cordeirópolis, SP, 13490-970, Brazil
3
Department of Plant Pathology, University of California, Davis, CA 9561608751, USA
4
Institute for Sustainable Plant Protection (IPSP), CNR, Turin, 10135, Italy
*
Author to whom correspondence should be addressed.
Received: 6 March 2017 / Revised: 18 April 2017 / Accepted: 20 April 2017 / Published: 24 April 2017
(This article belongs to the Section Viruses of Plants, Fungi and Protozoa)
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Abstract

Citrus sudden death (CSD) has caused the death of approximately four million orange trees in a very important citrus region in Brazil. Although its etiology is still not completely clear, symptoms and distribution of affected plants indicate a viral disease. In a search for viruses associated with CSD, we have performed a comparative high-throughput sequencing analysis of the transcriptome and small RNAs from CSD-symptomatic and -asymptomatic plants using the Illumina platform. The data revealed mixed infections that included Citrus tristeza virus (CTV) as the most predominant virus, followed by the Citrus sudden death-associated virus (CSDaV), Citrus endogenous pararetrovirus (CitPRV) and two putative novel viruses tentatively named Citrus jingmen-like virus (CJLV), and Citrus virga-like virus (CVLV). The deep sequencing analyses were sensitive enough to differentiate two genotypes of both viruses previously associated with CSD-affected plants: CTV and CSDaV. Our data also showed a putative association of the CSD-symptomatic plants with a specific CSDaV genotype and a likely association with CitPRV as well, whereas the two putative novel viruses showed to be more associated with CSD-asymptomatic plants. This is the first high-throughput sequencing-based study of the viral sequences present in CSD-affected citrus plants, and generated valuable information for further CSD studies. View Full-Text
Keywords: citrus sudden death; CSDaV; CTV; plant viruses; high-throughput sequencing citrus sudden death; CSDaV; CTV; plant viruses; high-throughput sequencing
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This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. (CC BY 4.0).

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MDPI and ACS Style

Matsumura, E.E.; Coletta-Filho, H.D.; Nouri, S.; Falk, B.W.; Nerva, L.; Oliveira, T.S.; Dorta, S.O.; Machado, M.A. Deep Sequencing Analysis of RNAs from Citrus Plants Grown in a Citrus Sudden Death-Affected Area Reveals Diverse Known and Putative Novel Viruses. Viruses 2017, 9, 92.

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