Identification of a single-stranded DNA virus associated with citrus chlorotic dwarf disease, a new member in the family Geminiviridae

Abstract

In the attempt to identify the causal agent of Citrus chlorotic dwarf disease (CCDD), a virus-like disorder of citrus, the small RNA fraction and total DNA from symptomatic citrus plants were subjected to high-throughput sequencing. DNA fragments deriving from an apparently new geminivirus-like agent were found and assembled by NGS to re-construct the entire viral genome. The newly identified virus has a circular single-stranded DNA genome comprising five open reading frames (ORFs) with sequence homologies with those encoded by geminiviruses. PCR and qPCR assays were successfully used for determining its presence in the CCDD-affected plants obtained by graft propagation. The larger genome size (3.64 vs. 2.5-3.0 kb) and a number of differences in its structural organization, identified this virus as a highly divergent member of the family Geminiviridae, to which the provisional name of Citrus chlorotic dwarf-associated virus (CCDaV) is assigned.

Identification and molecular characterization of a novel monopartite geminivirus associated with mulberry mosaic dwarf disease

“…Sequencing of eleven independent clones identified very low nucleotide variability in the circular DNA, substantially consisting of silent mutations in the prevailing variants. Searches in databases for similar sequences and comparisons with other viruses (Tables 1 and S4) were consistent with the possibility that such a circular DNA molecule was the genomic component of a geminivirus related to CCDaV, a divergent geminivirus recently identified in citrus (Loconsole et al, 2012).…”

“…In the last few years, identification of divergent geminiviruses infecting citrus, grapevine and Jatropha multifida (Al Rwahnih et al, 2013;Krenz et al, 2012;Loconsole et al, 2012;Polston et al, 2014;Poojari et al, 2013) has shown that the host range of geminiviruses is not limited to herbaceous plants. In this study we report the identification and characterization of a novel geminivirus infecting mulberry trees, as an addition to the list of woody plants infected by geminiviruses in nature.…”

“…S1), suggesting a possible role in virus trafficking also for the MMDaV V3 protein. Interestingly, extension of these analyses to the genome of other divergent geminiviruses, including Eragrostis curvula streak virus (ECSV, genus Eragrovirus) (Varsani et al, 2009), GRBaV (Al Rwahnih et al, 2013;Krenz et al, 2012) and CCDaV (Loconsole et al, 2012) identified in the same genomic position of these viruses a TM domain in a putative protein encoded by an unreported ORF (Table 2 and Fig. S1).…”

“…Members of the genera Mastrevirus and Becurtovirus differ from the others because of the expression strategy of two replication-associated proteins (Rep), which relies on the alternative splicing of the complementary-sense transcripts (Varsani et al, 2014a;Wright et al, 1997). A few highly divergent and still unclassified geminiviruses have recently been described from Euphorbia (Euphorbia caput-medusae-associated virus, EcmLV) (Bernardo et al, 2013), citrus (citrus chlorotic dwarf-associated virus, CCDaV) (Loconsole et al, 2012), grapevine (grapevine red blotch-associated virus, GRBaV) (Al Rwahnih et al, 2013;Krenz et al, 2012;Poojari et al, 2013). Viral RNAs, including those of geminiviruses (Seguin et al, 2014), are targeted by host defence mechanisms based on RNA silencing and, through the activity of Dicer-like enzymes (DCLs), become the source of virus-derived small RNAs of [21][22][23][24].…”

Establishment of three new genera in the family Geminiviridae: Becurtovirus, Eragrovirus and Turncurtovirus

“…1): 1) Becurtovirus: Including the species Beet curly top Iran virus and Spinach curly top Arizona virus (Table 1) [14,18,19,33,39] 2) Eragrovirus: Including the species Eragrostis curvula streak virus (Table 2) [35] 3) Turncurtovirus: Including the species Turnip curly top virus (Table 3) [5,29,30] We additionally acknowledge the need for further new genera to accommodate three other highly divergent groups of geminiviruses that have recently been found infecting grapevines in the USA [22,28] and citrus plants in Turkey [23], as well as two closely related viruses (*72 % genomewide pairwise sequence identity) infecting Euphorbia caputmedusae in South Africa [4] and French beans in India.…”