First natural crossover recombination of intact ORFs between two distinct species of the familyClosteroviridae

Abstract

18Lettuce chlorosis virus-SP (LCV-SP) (family Closteroviridae, genus Crinivirus), is a 19 new strain of LCV which is able to infect green bean plants and incapable of infecting 20 lettuce crops. In the present study, high throughput and Sanger sequencing of RNA 21 was used to obtain the LCV-SP full-length sequence. The LCV-SP genome comprises 22 8825 nt and 8672 nt equivalent with RNA1 and RNA2 respectively. RNA1 of LCV-SP 23 contains four ORFs, the proteins encoded by the ORF1a and ORF1b are closely related 24 to LCV RNA1 from California (FJ380118) whereas the 3´ end encodes proteins which 25 share high amino acid sequence identity with RNA1 of BnYDV (EU191904). The 26 genomic sequence of RNA2 consists of 8 ORFs, instead of 10 ORFs contained in LCV-27 California isolate. The distribution of vsiRNA (virus-derived small interfering RNA) along 28 the LCV-SP genome suggested the presence of subgenomic RNAs corresponding with 29 HSP70, P6.4 and P60. Results of the analysis using RDP4 and Simplot programs are the 30 proof of the evidence that LCV-SP is the first recombinant of the family Closteroviridae 31 by crossover recombination of intact ORFs, being the LCV RNA1 (FJ380118) and BnYDV 32 RNA1 (EU191904) the origin of the new LCV strain. Genetic diversity values of virus 33 isolates in the recombinant region obtained after sampling LCV-SP infected green bean 34 between 2011 and 2017 might suggest that the recombinant virus event occurred in 35 the area before this period. The presence of LCV-SP shows the role of recombination 36 as a driving force of evolution within the genus Crinivirus, a globally distributed, 37 emergent genus. 38 39 Introduction 3 40 Lettuce chlorosis virus (LCV) belongs to the genus Crinivirus, family 41 Closteroviridae. Viruses included in this family are the largest among the known plant 42 viruses and present ssRNA, positive-sense genome [1]. Family Closteroviridae has been 43 classified in three genera based on vector transmission and phylogenetic relationships: 44 Closterovirus, Ampelovirus, and Crinivirus. Recently, a new genus named Velarivirus 45 has been proposed [2]. All members of genus Crinivirus include segmented genomes, 46 are whitefly-transmitted and limited to the phloem [3]. 47 Many members of genus Crinivirus are considered emerging epidemics worldwide [4]. 48 LCV was described in the 1990´s in California, transmitted by the whitefly Bemisia 49 tabaci and affecting lettuce and sugar beet crops [5]. The complete sequence and the 50 genomic organization of LCV were described in 2009 by [6] and comprises a bipartite 51 genome formed by RNA1 and RNA2. LCV RNA1 contains the replication module (ORFs 52 1a and 1b), which encodes conserved domains of a papain-like leader proteinase (P-53 PRo), a methyltransferase (MTR), helicase (HEL) and RNA-dependent RNA polymerase 54 (RdRp), ORF2 encodes a putative 8-kDa protein (P8), and ORF3 encodes a 22.9-kDa 55 protein (P23) recently described as viral suppressor of RNA silencing [7]. LCV RNA2 56 contains the hallmark Closterovirus gene array ...