Catharanthus mosaic virus: A potyvirus from a gymnosperm, Welwitschia mirabilis

Koh, Shu Hui; Li, Hua; Admiraal, Ryan; Jones, Michael G. K.; Wylie, Stephen J.

doi:10.1016/j.virusres.2015.03.007

Cited by 14 publications

(7 citation statements)

References 35 publications

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“…However, one novel putative varicosavirus, Pinus flexilis virus 1, was associated with a gymnosperm host. Few viruses were identified previously from gymnosperms [ 12 , 56 , 57 , 58 , 59 ]. Interestingly, a putative RdRp sequence was identified in the gymnosperm Sciadopitys verticillata and proposed to belong to a varicosavirus [ 14 ].…”

Section: Discussionmentioning

confidence: 99%

Illuminating the Plant Rhabdovirus Landscape through Metatranscriptomics Data

Bejerman

Dietzgen

Debat

2021

Viruses

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Rhabdoviruses infect a large number of plant species and cause significant crop diseases. They have a negative-sense, single-stranded unsegmented or bisegmented RNA genome. The number of plant-associated rhabdovirid sequences has grown in the last few years in concert with the extensive use of high-throughput sequencing platforms. Here, we report the discovery of 27 novel rhabdovirus genomes associated with 25 different host plant species and one insect, which were hidden in public databases. These viral sequences were identified through homology searches in more than 3000 plant and insect transcriptomes from the National Center for Biotechnology Information (NCBI) Sequence Read Archive (SRA) using known plant rhabdovirus sequences as the query. The identification, assembly and curation of raw SRA reads resulted in sixteen viral genome sequences with full-length coding regions and ten partial genomes. Highlights of the obtained sequences include viruses with unique and novel genome organizations among known plant rhabdoviruses. Phylogenetic analysis showed that thirteen of the novel viruses were related to cytorhabdoviruses, one to alphanucleorhabdoviruses, five to betanucleorhabdoviruses, one to dichorhaviruses and seven to varicosaviruses. These findings resulted in the most complete phylogeny of plant rhabdoviruses to date and shed new light on the phylogenetic relationships and evolutionary landscape of this group of plant viruses. Furthermore, this study provided additional evidence for the complexity and diversity of plant rhabdovirus genomes and demonstrated that analyzing SRA public data provides an invaluable tool to accelerate virus discovery, gain evolutionary insights and refine virus taxonomy.

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Section: Discussionmentioning

confidence: 99%

Illuminating the Plant Rhabdovirus Landscape through Metatranscriptomics Data

Bejerman

Dietzgen

Debat

2021

Viruses

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“…However, one novel putative varicosavirus, Pinus flexilis virus 1, was associated with a gymnosperm host. Few viruses were identified previously from gymnosperms (Alvarez-Quinto et al, 2020; Han et al, 2002; Koh et al, 2015; Lauber et al, 2019; Nibert et al, 2014). Interestingly, a putative RdRp sequence was identified in the gymnosperm Sciadopitys verticillata and proposed to belong to a varicosavirus (Mushegian et al, 2016).…”

Section: Discussionmentioning

confidence: 99%

Illuminating the plant rhabdovirus landscape through metatranscriptomics data

Bejerman

Dietzgen

Debat

2021

Preprint

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Rhabdoviruses infect a large number of plant species and cause significant crop diseases. They have a negative-sense, single-stranded unsegmented or bisegmented RNA genome. The number of plant-associated rhabdovirid sequences has grown in the last few years in concert with the extensive use of high-throughput sequencing platforms. Here we report the discovery of 26 novel rhabdovirus genomes associated with 24 different host plant species and one insect, which were hidden in public databases. These viral sequences were identified through homology searches in more than 3,000 plant and insect transcriptomes from the NCBI Sequence Read Archive (SRA) using known plant rhabdovirus sequences as query. Identification, assembly and curation of raw SRA reads resulted in sixteen viral genome sequences with full-length coding regions and ten partial genomes. Highlights of the obtained sequences include viruses with unique and novel genome organizations among known plant rhabdoviruses. Phylogenetic analysis showed that thirteen of the novel viruses were related to cytorhabdoviruses, one to alphanucleorhabdoviruses, five to betanucleorhabdoviruses, one to dichorhaviruses, and six to varicosaviruses. These findings resulted in the most complete phylogeny of plant rhabdoviruses to date and shed new light on the phylogenetic relationships and evolutionary landscape of this group of plant viruses. Furthermore, this study provides additional evidence for the complexity and diversity of plant rhabdovirus genomes and demonstrates that analyzing SRA public data provides an invaluable tool to accelerate virus discovery, gain evolutionary insights and refine virus taxonomy.

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“…It might be that the greater molecular repertoire of monocots, asterids, and rosids, which have resulted from repeated genome duplication [51], allow viruses to form functioning relationships with them. It is noteworthy that few potyviruses have been reported from caryophyllids and very few from basal angiosperms, such as the ranunculids, although hibbertia virus Y is from a Gunnerid, and catharanthus mosaic virus was isolated from Welwitschia mirabilis (a gymnosperm; [52]). Two poty-like metagenomes have recently been reported from unexpected hosts (snails and a "dipteran mix") and are discussed below.…”

Section: Phylogeneticsmentioning

confidence: 99%

The Potyviruses: An Evolutionary Synthesis Is Emerging

Gibbs

Hajizadeh

Ohshima

et al. 2020

Viruses

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In this review, encouraged by the dictum of Theodosius Dobzhansky that “Nothing in biology makes sense except in the light of evolution”, we outline the likely evolutionary pathways that have resulted in the observed similarities and differences of the extant molecules, biology, distribution, etc. of the potyvirids and, especially, its largest genus, the potyviruses. The potyvirids are a family of plant-infecting RNA-genome viruses. They had a single polyphyletic origin, and all share at least three of their genes (i.e., the helicase region of their CI protein, the RdRp region of their NIb protein and their coat protein) with other viruses which are otherwise unrelated. Potyvirids fall into 11 genera of which the potyviruses, the largest, include more than 150 distinct viruses found worldwide. The first potyvirus probably originated 15,000–30,000 years ago, in a Eurasian grass host, by acquiring crucial changes to its coat protein and HC-Pro protein, which enabled it to be transmitted by migrating host-seeking aphids. All potyviruses are aphid-borne and, in nature, infect discreet sets of monocotyledonous or eudicotyledonous angiosperms. All potyvirus genomes are under negative selection; the HC-Pro, CP, Nia, and NIb genes are most strongly selected, and the PIPO gene least, but there are overriding virus specific differences; for example, all turnip mosaic virus genes are more strongly conserved than those of potato virus Y. Estimates of dN/dS (ω) indicate whether potyvirus populations have been evolving as one or more subpopulations and could be used to help define species boundaries. Recombinants are common in many potyvirus populations (20%–64% in five examined), but recombination seems to be an uncommon speciation mechanism as, of 149 distinct potyviruses, only two were clear recombinants. Human activities, especially trade and farming, have fostered and spread both potyviruses and their aphid vectors throughout the world, especially over the past five centuries. The world distribution of potyviruses, especially those found on islands, indicates that potyviruses may be more frequently or effectively transmitted by seed than experimental tests suggest. Only two meta-genomic potyviruses have been recorded from animal samples, and both are probably contaminants.

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Catharanthus mosaic virus: A potyvirus from a gymnosperm, Welwitschia mirabilis

Cited by 14 publications

References 35 publications

Illuminating the Plant Rhabdovirus Landscape through Metatranscriptomics Data

Illuminating the Plant Rhabdovirus Landscape through Metatranscriptomics Data

Illuminating the plant rhabdovirus landscape through metatranscriptomics data

The Potyviruses: An Evolutionary Synthesis Is Emerging

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