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Remarkable diversity of endogenous viruses in a crustacean genome.

Thézé J, Leclercq S, Moumen B, Cordaux R, Gilbert C - Genome Biol Evol (2014)

Bottom Line: These fragments result from endogenization, that is, integration of the viral genome into the host germline genome followed by vertical inheritance.We show that viral endogenization occurred recurrently during the evolution of isopods and that A. vulgare viral lineages were involved in multiple host switches that took place between widely divergent taxa.More generally, our results underline the power of paleovirology in characterizing the viral diversity currently infecting eukaryotic taxa.

View Article: PubMed Central - PubMed

Affiliation: Université de Poitiers, UMR CNRS 7267 Ecologie et Biologie des Interactions, Equipe Ecologie Evolution Symbiose, Poitiers, France.

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Mapping of the 54 Armadillidium vulgare EVEs on representative virus genomes. Light gray rectangles represent virus genes with their genomic positions, including conserved domains in dark gray. Numbered black lines represent A. vulgare EVEs. Numbers below these black lines indicate the position of A. vulgare EVEs on the above viral genome. Numbers in red correspond to EVEs that were PCR amplified and sequenced. Numbers in blue correspond to EVEs for which recognizable flanking regions were identified (4: 3'-flanking region contains a host gene of unknown function approximately 700 bp away from the EVE, 19 and 42: 3'-flanking regions contain nonlong terminal repeat retrotransposon-like reverse transcriptases approximately 8,600 bp and 250 bp away from the EVEs, respectively). Dots and vertical bars represent stop codons and frameshifts found in A. vulgare EVEs, respectively. The Rift Valley fever virus (NC_014395, NC_014396, NC_014397; Bunyaviridae), Midway virus (NC_012702; Mononegavirales), Armigeres subalbatus virus SaX06-AK20 (NC_014609; Totiviridae), Dragonfly orbiculatus virus (NC_023854; Circoviridae like), and infectious hypodermal and hematopoietic necrosis virus (NC_002190; Parvoviridae) were the representative virus genomes used for the mapping.
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evu163-F1: Mapping of the 54 Armadillidium vulgare EVEs on representative virus genomes. Light gray rectangles represent virus genes with their genomic positions, including conserved domains in dark gray. Numbered black lines represent A. vulgare EVEs. Numbers below these black lines indicate the position of A. vulgare EVEs on the above viral genome. Numbers in red correspond to EVEs that were PCR amplified and sequenced. Numbers in blue correspond to EVEs for which recognizable flanking regions were identified (4: 3'-flanking region contains a host gene of unknown function approximately 700 bp away from the EVE, 19 and 42: 3'-flanking regions contain nonlong terminal repeat retrotransposon-like reverse transcriptases approximately 8,600 bp and 250 bp away from the EVEs, respectively). Dots and vertical bars represent stop codons and frameshifts found in A. vulgare EVEs, respectively. The Rift Valley fever virus (NC_014395, NC_014396, NC_014397; Bunyaviridae), Midway virus (NC_012702; Mononegavirales), Armigeres subalbatus virus SaX06-AK20 (NC_014609; Totiviridae), Dragonfly orbiculatus virus (NC_023854; Circoviridae like), and infectious hypodermal and hematopoietic necrosis virus (NC_002190; Parvoviridae) were the representative virus genomes used for the mapping.

Mentions: To identify EVEs in whole-genome sequences of the isopod crustacean A. vulgare, we first performed a TBLASTX search using all complete viral genomes publicly available in GenBank and EMBL (January 2014) as queries (n = 2,048). We then used all hits resulting from this search (n = 10,727) as queries to carry out a reciprocal BLASTX on the nonredundant protein database of the NCBI. This approach yielded a total of 54 A. vulgare genome sequences of unambiguous viral origin, ranging from 42 to 588 aa in length (average = 173 aa) and showing 46–78% aa similarity (average = 58%) to their most closely related exogenous viral protein sequences (fig. 1 and supplementary table S1, Supplementary Material online). The 54 EVEs were assigned to four different families (Bunyaviridae, Circoviridae, Parvoviridae, and Totiviridae) and one order (Mononegavirales), representing three of the seven types of viral genomes (-ssRNA, dsRNA, and ssDNA). Among those families/order, the Circoviridae and Totiviridae families are not currently reported by the ICTV (King et al. 2011) to infect arthropods (but see e.g., Wu et al. 2010; Rosario et al. 2012). The diversity of EVEs discovered in the A. vulgare genome is remarkable in that most previously published paleovirology studies have reported less than 20 EVEs and/or less than 4 different viral families in a given genome (Feschotte and Gilbert 2012).Fig. 1.—


Remarkable diversity of endogenous viruses in a crustacean genome.

Thézé J, Leclercq S, Moumen B, Cordaux R, Gilbert C - Genome Biol Evol (2014)

Mapping of the 54 Armadillidium vulgare EVEs on representative virus genomes. Light gray rectangles represent virus genes with their genomic positions, including conserved domains in dark gray. Numbered black lines represent A. vulgare EVEs. Numbers below these black lines indicate the position of A. vulgare EVEs on the above viral genome. Numbers in red correspond to EVEs that were PCR amplified and sequenced. Numbers in blue correspond to EVEs for which recognizable flanking regions were identified (4: 3'-flanking region contains a host gene of unknown function approximately 700 bp away from the EVE, 19 and 42: 3'-flanking regions contain nonlong terminal repeat retrotransposon-like reverse transcriptases approximately 8,600 bp and 250 bp away from the EVEs, respectively). Dots and vertical bars represent stop codons and frameshifts found in A. vulgare EVEs, respectively. The Rift Valley fever virus (NC_014395, NC_014396, NC_014397; Bunyaviridae), Midway virus (NC_012702; Mononegavirales), Armigeres subalbatus virus SaX06-AK20 (NC_014609; Totiviridae), Dragonfly orbiculatus virus (NC_023854; Circoviridae like), and infectious hypodermal and hematopoietic necrosis virus (NC_002190; Parvoviridae) were the representative virus genomes used for the mapping.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

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getmorefigures.php?uid=PMC4231630&req=5

evu163-F1: Mapping of the 54 Armadillidium vulgare EVEs on representative virus genomes. Light gray rectangles represent virus genes with their genomic positions, including conserved domains in dark gray. Numbered black lines represent A. vulgare EVEs. Numbers below these black lines indicate the position of A. vulgare EVEs on the above viral genome. Numbers in red correspond to EVEs that were PCR amplified and sequenced. Numbers in blue correspond to EVEs for which recognizable flanking regions were identified (4: 3'-flanking region contains a host gene of unknown function approximately 700 bp away from the EVE, 19 and 42: 3'-flanking regions contain nonlong terminal repeat retrotransposon-like reverse transcriptases approximately 8,600 bp and 250 bp away from the EVEs, respectively). Dots and vertical bars represent stop codons and frameshifts found in A. vulgare EVEs, respectively. The Rift Valley fever virus (NC_014395, NC_014396, NC_014397; Bunyaviridae), Midway virus (NC_012702; Mononegavirales), Armigeres subalbatus virus SaX06-AK20 (NC_014609; Totiviridae), Dragonfly orbiculatus virus (NC_023854; Circoviridae like), and infectious hypodermal and hematopoietic necrosis virus (NC_002190; Parvoviridae) were the representative virus genomes used for the mapping.
Mentions: To identify EVEs in whole-genome sequences of the isopod crustacean A. vulgare, we first performed a TBLASTX search using all complete viral genomes publicly available in GenBank and EMBL (January 2014) as queries (n = 2,048). We then used all hits resulting from this search (n = 10,727) as queries to carry out a reciprocal BLASTX on the nonredundant protein database of the NCBI. This approach yielded a total of 54 A. vulgare genome sequences of unambiguous viral origin, ranging from 42 to 588 aa in length (average = 173 aa) and showing 46–78% aa similarity (average = 58%) to their most closely related exogenous viral protein sequences (fig. 1 and supplementary table S1, Supplementary Material online). The 54 EVEs were assigned to four different families (Bunyaviridae, Circoviridae, Parvoviridae, and Totiviridae) and one order (Mononegavirales), representing three of the seven types of viral genomes (-ssRNA, dsRNA, and ssDNA). Among those families/order, the Circoviridae and Totiviridae families are not currently reported by the ICTV (King et al. 2011) to infect arthropods (but see e.g., Wu et al. 2010; Rosario et al. 2012). The diversity of EVEs discovered in the A. vulgare genome is remarkable in that most previously published paleovirology studies have reported less than 20 EVEs and/or less than 4 different viral families in a given genome (Feschotte and Gilbert 2012).Fig. 1.—

Bottom Line: These fragments result from endogenization, that is, integration of the viral genome into the host germline genome followed by vertical inheritance.We show that viral endogenization occurred recurrently during the evolution of isopods and that A. vulgare viral lineages were involved in multiple host switches that took place between widely divergent taxa.More generally, our results underline the power of paleovirology in characterizing the viral diversity currently infecting eukaryotic taxa.

View Article: PubMed Central - PubMed

Affiliation: Université de Poitiers, UMR CNRS 7267 Ecologie et Biologie des Interactions, Equipe Ecologie Evolution Symbiose, Poitiers, France.

Show MeSH
Related in: MedlinePlus