Identification of viruses belonging to the familyPartitiviridaefrom plant transcriptomes

Abstract

1Viruses in the family Partitiviridae consist of non-enveloped viruses with bisegmented double-2 stranded RNA genomes. Viruses in this family have been identified from plants and fungi. In 3 this study, we identified several viruses belonging to the family Partitiviridae using plant 4 transcriptomes. From 11 different plant species, we identified a total of 74 RNA segments 5 representing 23 partitiviruses. Of 74 RNA segments, 28 RNA segments encode RNA-6 dependent RNA polymerases (RdRp) while 46 RNA segments encode coat proteins (CPs). 7According to ICTV demarcation for the family Partitiviridae, 25 RNAs encoding RdRp and 8 41 RNAs encoding CP were novel RNA segments. In addition, we identified eight RNA 9 segments (three for RdRp and five for CP) belonging to the known partitivruses. Taken together, 10 this study provides the largest number of partitiviruses from plant transcriptomes in a single 11 study. Viruses in the family Partitiviridae consist of non-enveloped viruses with bisegmented double-2 stranded (ds) RNA genomes [1]. Each RNA segment of the viruses in the family Partitiviridae 3 encodes a single protein including RNA-dependent RNA polymerase (RdRp) or coat protein 4 (CP). Members in the family Partitiviridae can be divided into five different genera according 5 to the host. For example, viruses in the genera Alphapartitivirus and Betapartitivirus are 6 identified from either plants or fungi while viruses in the genus Gammapartitivirus and 7 Deltapartitivirus are derived from only fungi and plants, respectively [1]. In addition, viruses 8 in the genus Cryspovirus are identified from protozoa. Transmission of partitiviruses is 9 occurred by seeds (plants), cell division and sporogenesis (fungi), and oocytes (protozoa) [1]. 10 To date, there are more than 45 partitivirus species. In particular, there are five deltapartitivirus 11 species infecting plants including Pepper cryptic virus 1 (PCV-1) [2], Pepper cryptic virus 2 12 (PCV-2), Fig cryptic virus (FCV) [3], Beet cryptic virus 2 (BCV2), and Beet cryptic virus 3 13 (BCV3) [4] according to International Committee on Taxonomy of Viruses (ICTV). 14 To identify novel partitiviruses with dsRNA genomes, dsRNA extraction followed by 15 next-generation sequencing (NGS) is an efficient approach. Based on those approaches, several 16 partitiviruses have been identified. For example, Melon necrotic spot virus was identified from 17 watermelon plant (Citrullus lanatus Thunb) using SOLiD NGS analysis [5]. Pittosporum 18 cryptic virus 1 was identified from an Italian pittosporum plant by NGS with extracted dsRNA 19 [6]. Similarly, application of NGS to extracted dsRNA has resulted in identification of 20 Trichoderma atroviride partitivirus 1 from the fungal species Trichoderma atroviride [7]. 21 Moreover, instead of traditional molecular cloning methods, in silico data analyses has 22 resulted in identification of diverse dsRNA viruses from expressed sequence tag (EST) 23 database [8] and plant transcriptomes [9-13]. Moreover, 120 mycoviruses infecting fungi have...