Improved reference genome of the arboviral vector <i>Aedes albopictus</i>

Palatini, Umberto; Masri, Reem A.; Cosme, Luciano V.; Koren, Sergey; Thibaud‐Nissen, Françoise; Biedler, James K.; Krsticevic, Flávia; Johnston, J. Spencer; Halbach, Rebecca; Crawford, Jacob E.; Antoshechkin, Igor; Failloux, Anna‐Bella; Pischedda, Elisa; Marconcini, Michele; Ghurye, Jay; Rhie, Arang; Sharma, Atashi; Карагодин, Д. А.; Jenrette, James; Gamez, Stephanie; Miesen, Pascal; Caccone, Adalgisa; Sharakhova, Maria V.; Tu, Zhijian; Papathanos, Philippos Aris; Rij, Ronald P. van; Akbari, Omar S.; Powell, Jeffrey R.; Phillippy, Adam M.; Bonizzoni, Mariangela

doi:10.1101/2020.02.28.969527

Cited by 19 publications

(57 citation statements)

References 60 publications

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“…We run ViR on WGS data of Ae. albopictus and identified a total of seven candidate viral integrations absent in the reference genome assemblies, AloF1 and AalbF2 (27,28). PCR primers were designed on the basis of these candidates (Table 1) and used on DNA extracted from different mosquitoes than those used as source of WGS data.…”

Section: Molecular Validation Of Vir-predicted Integration Sitesmentioning

confidence: 99%

“…albopictus. Aedes albopictus has the largest mosquito genome sequenced to date, the majority of which is repetitive DNA (27,28). For…”

Section: Benchmarking Virmentioning

confidence: 99%

“…Ae. albopictus, three genome assemblies are available, which differ greatly in the number of scaffolds and are all larger than the expected size of the genome based on cytofluorimetric estimates, suggesting duplications (27,28,37). We selected to run ViR using two assemblies, AaloF1 and AalbF2, which have 154782 and 2197 scaffolds, respectively.…”

Section: Benchmarking Virmentioning

confidence: 99%

“…We selected to run ViR using two assemblies, AaloF1 and AalbF2, which have 154782 and 2197 scaffolds, respectively. Hundreds of EVEs from various taxonomic viral categories are annotated in AaloF1 and AalbF2 (23,28), giving further complexity.…”

Section: Benchmarking Virmentioning

confidence: 99%

“…To ameliorate this issue, we have developed ViR, a new bioinformatics pipeline which improves the characterization of integration sites by solving the dispersion of reads in genome sequences that are rich of repetitive DNA. We benchmarked ViR with low-and high-coverage WGS data from Aedes albopictus, to date the mosquito species with the largest genome size and highest TE content among Culicinae (27,28). We extensively evaluated ViR performance using WGS data from both single and pooled DNA samples, followed by molecular validation of predicted insertion sites.…”

Section: Introductionmentioning

confidence: 99%

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ViR: a tool to account for intrasample variability in the detection of viral integrations

Pischedda

Crava

Carlassara

et al. 2020

Preprint

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Lateral gene transfer (LT) from viruses to eukaryotic cells is a well-recognized phenomenon. Somatic integrations of viruses have been linked to persistent viral infection and genotoxic effects, including various types of cancer. As a consequence, several bioinformatic tools have been developed to identify viral sequences integrated into the human genome. Viral sequences that integrate into germline cells can be transmitted vertically, be maintained in host genomes and be co-opted for host functions. Endogenous viral elements (EVEs) have long been known, but the extent of their widespread occurrence has only been recently appreciated. Modern genomic sequencing analyses showed that eukaryotic genomes may harbor hundreds of EVEs, which derive not only from DNA viruses and retroviruses, but also from nonretroviral RNA viruses and are mostly enriched in repetitive regions of the genome. Despite being increasingly recognized as important players in different biological processes such as regulation of expression and immunity, the study of EVEs in non-model organisms has rarely gone beyond their characterization from annotated reference genomes because of the lack of computational methods suited to solve signals for EVEs in repetitive DNA. To fill this gap, we developed ViR, a pipeline which ameliorates the detection of integration sites by solving the dispersion of reads in genome assemblies that are rich of repetitive DNA. Using paired-end whole genome sequencing (WGS) data and a user-built database of viral genomes, ViR selects the best candidate couples of reads supporting an integration site by solving the dispersion of reads resulting from intrasample variability. We benchmarked ViR to work with sequencing data from both single and pooled DNA samples and show its applicability using WGS data of a non-model organism, the arboviral vector Aedes albopictus. Viral integrations predicted by ViR were molecularly validated supporting the accuracy of ViR results. Additionally, ViR can be readily adopted to detect any LT event providing ad hoc non-host sequences to interrogate.

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Section: Molecular Validation Of Vir-predicted Integration Sitesmentioning

confidence: 99%

“…albopictus. Aedes albopictus has the largest mosquito genome sequenced to date, the majority of which is repetitive DNA (27,28). For…”

Section: Benchmarking Virmentioning

confidence: 99%

Section: Benchmarking Virmentioning

confidence: 99%

Section: Benchmarking Virmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 3 more Smart Citations

ViR: a tool to account for intrasample variability in the detection of viral integrations

Pischedda

Crava

Carlassara

et al. 2020

Preprint

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Multiple introductions and overwintering shape the progressive invasion of Aedes albopictus beyond the Alps

Vavassori

Honnen

Saarman

et al. 2022

Ecology and Evolution

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Aedes albopictus originates from Southeast Asia and is considered one of the most invasive species globally. This mosquito is a nuisance and a disease vector of significant public health relevance. In Europe, Ae. albopictus is firmly established and widespread south of the Alps, a mountain range that forms a formidable biogeographic barrier to many organisms. Recent reports of Ae. albopictus north of the Alps raise questions of (1) the origins of its recent invasion, and (2) if this mosquito has established overwintering populations north of the Alps. To answer these questions, we analyzed population genomic data from >4000 genome‐wide SNPs obtained through double‐digest restriction site‐associated DNA sequencing. We collected SNP data from specimens from six sites in Switzerland, north and south of the Alps, and analyzed them together with specimens from other 33 European sites, five from the Americas, and five from its Asian native range. At a global level, we detected four genetic clusters with specimens from Indonesia, Brazil, and Japan as the most differentiated, whereas specimens from Europe, Hong Kong, and USA largely overlapped. Across the Alps, we detected a weak genetic structure and high levels of genetic admixture, supporting a scenario of rapid and human‐aided dispersal along transportation routes. While the genetic pattern suggests frequent re‐introductions into Switzerland from Italian sources, the recovery of a pair of full siblings in two consecutive years in Strasbourg, France, suggests the presence of an overwintering population north of the Alps. The suggestion of overwintering populations of Ae. albopictus north of the Alps and the expansion patterns identified points to an increased risk of further northward expansion and the need for increased surveillance of mosquito populations in Northern Europe.

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The diversity of endogenous viral elements in insects

Gilbert

Belliardo

2022

Current Opinion in Insect Science

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Improved reference genome of the arboviral vector Aedes albopictus

Cited by 19 publications

References 60 publications

ViR: a tool to account for intrasample variability in the detection of viral integrations

ViR: a tool to account for intrasample variability in the detection of viral integrations

Multiple introductions and overwintering shape the progressive invasion of Aedes albopictus beyond the Alps

The diversity of endogenous viral elements in insects

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