In and Outs of Chuviridae Endogenous Viral Elements: Origin of a Potentially New Retrovirus and Signature of Ancient and Ongoing Arms Race in Mosquito Genomes

Abstract

Background: Endogenous viral elements (EVEs) are sequences of viral origin integrated into the host genome. EVEs have been characterized in various insect genomes, including mosquitoes. A large EVE content has been found in Aedes aegypti and Aedes albopictus genomes among which a recently described Chuviridae viral family is of particular interest, owing to the abundance of EVEs derived from it, the discrepancy among the chuvirus endogenized gene regions and the frequent association with retrotransposons from the BEL-Pao superfamily. In order to better understand the endogenization process of chuviruses and the association between chuvirus glycoproteins and BEL-Pao retrotransposons, we performed a comparative genomics and evolutionary analysis of chuvirus-derived EVEs found in 37 mosquito genomes. Results: We identified 428 EVEs belonging to the Chuviridae family confirming the wide discrepancy among the chuvirus genomic regions endogenized: 409 glycoproteins, 18 RNA-dependent RNA polymerases and one nucleoprotein region. Most of the glycoproteins (263 out of 409) are associated specifically with retroelements from the Pao family. Focusing only on well-assembled Pao retroelement copies, we estimated that 263 out of 379 Pao elements are associated with chuvirus-derived glycoproteins. Seventy-three potentially active Pao copies were found to contain glycoproteins into their LTR boundaries. Thirteen out of these were classified as complete and likely autonomous copies, with a full LTR structure and protein domains. We also found 116 Pao copies with no trace of glycoproteins and 37 solo glycoproteins. All potential autonomous Pao copies, contained highly similar LTRs, suggesting a recent/current activity of these elements in the mosquito genomes. Conclusion: Evolutionary analysis revealed that most of the glycoproteins found are likely derived from a single or few glycoprotein endogenization events associated with a recombination event with a Pao ancestral element. A potential functional Pao-chuvirus hybrid (named Anakin) emerged and the glycoprotein was further replicated through

Dissecting the Species-Specific Virome in Culicoides of Thrace

“…In our study, we did not identify any contigs corresponding to Galbut virus or any other related viruses. Chuviridae is a family of arthropod viruses often found only in metagenomic studies with variable genomic structure ( Dezordi et al, 2020 ). The close proximity of haranti chuvirus and cataneii chu-like virus with Wuchang cockroach virus 3 within the phylogenetic tree and their distance from Tacheng tick virus 5 and Bole tick virus 3 favored a segmented genome structure depiction (type II) as proposed by Li et al (2015 ; Figure 6 ).…”

“…The close proximity of haranti chuvirus and cataneii chu-like virus with Wuchang cockroach virus 3 within the phylogenetic tree and their distance from Tacheng tick virus 5 and Bole tick virus 3 favored a segmented genome structure depiction (type II) as proposed by Li et al (2015 ; Figure 6 ). Moreover, chuviruses have been linked to endogenous viral elements (EVEs) that include either small or larger fragments of insect-specific viruses incorporated into insect genomes ( Aguiar et al, 2015 ; Dezordi et al, 2020 ). It is possible that viruses represented by a partial fragment or a single segment may actually be EVEs as even sequences of well-established viral families such as Flaviviridae have been shown to form EVEs ( Lequime and Lambrechts, 2017 ).…”

Soybean Thrips (Thysanoptera: Thripidae) Harbor Highly Diverse Populations of Arthropod, Fungal and Plant Viruses

“…Finally, it is possible that some partial and low abundance contigs could be derived from virus-like sequences integrated into the soybean thrips genome. Virus-like sequences have been detected in the genomes of multiple arthropod species [77][78][79][80][81]. Most frequently, the detected sequences are related to parvoviruses and GPs of negative-stranded RNA viruses [82].…”

Exploration of RNA-Seq data to identify a potential pathogen of the leaf-mining moth, Stomphastis thraustica (Meyrick, 1908) (Lepidoptera: Gracillariidae)

“…We identified several partial sequences of insect-specific viruses from family Rhabdoviridae, Metaviridae , and Chuviridae but this data is not conclusive to consider those viruses as the cause of disease in the larvae ( Tables 3 and S1). Some of those sequences might represent Endogenous Viral Elements (EVEs) which could be part of the S. thraustica genome [1] . These S. thraustica larval RNA-Seq data provided no evidence for the presence of detectable Microsporidia-like Nosema sp., which is a well-known cause of mortality in other lepidopteran larvae [ 2 , 3 ].…”