Biology subjects

Debat, H. J.

Publications and source records attributed to Debat, H. J..

7 recordsLinked to original sources

bioRxiv2018

Molecular characterization of effector protein SAP54 in Bellis Virescence Phytoplasma (16SrIII-J)

Phytoplasmas are wall-less bacteria, with a parasitic life style responsible for numerous plant diseases worldwide. The genomic landscape of phytoplasmas has been scarcely studied. Nevertheless, since the introduction of next generation sequencing technologies, genome wide studies of these pathogens are flourishing and a handful of phytoplasmas genomes are available in public databases. In South America, phytoplasmas from 16SrIII group (X-disease) are the most widely distributed, and only a draft genome from a phytoplasmas 16SrIII-J infected periwinkle from Chile has been generated (Phytoplasma Vc33). Here, in grafting experiments we characterized the phenotypic signatures of an Argentinian daisy derived isolate of a 16SrIII-J phytoplasma (Bellis Virescence Phytoplasma) infecting periwinkle. Moreover, we applied a pipeline for genome wide annotation of the Vc33 genome and identified the effector protein SAP54. We then employed the obtained data to amplify, clone, sequence and characterize a SAP54 orthologue protein of Bellis Virescence Phytoplasma. Structural and phylogenetic analyses suggested that the identified SAP54 is highly conserved, and that its co-divergence among phytoplasma is not directly consistent with the evolutionary trajectories derived from rRNA analyses. The results gathered here could provide the basis for reverse genetics experiments using 16SrIII-J SAP54 proteins to assess their eventual influence in pathogenesis.

molecular biology↗

bioRxiv2018

Identification of novel RNA viruses associated to bird’s-foot trefoil (Lotus corniculatus)

Birds-foot trefoil (Lotus corniculatus) is a nutritious forage crop, employed for livestock foraging around the world. Here, we report the identification and characterization of two novel viruses associated with birds-foot trefoil. Virus sequences with affinity to enamoviruses (ssRNA (+); Luteoviridae; Enamovirus) and nucleorhabdoviruses (ssRNA (-); Rhabdoviridae; Nucleorhabdovirus) were detected in L. corniculatus transcriptome data. The tentatively named birds-foot trefoil associated virus 1 (BFTV-1) genome organization is characterized by 13,626 nt long negative-sense ssRNA. BFTV-1 presents in its antigenome orientation six predicted gene products in the canonical order 3'-N-P-P3-M-G-L-5'. The proposed birds-foot trefoil associated virus 2 (BFTV-2) 5,736 nt virus sequence presents a typical 5'-PO-P1-2-IGS-P3-P5-3' enamovirus genome structure. Phylogenetic analysis suggests that BFTV-1 is closely related to Datura yellow vein nucleorhabdovirus, and that BFTV-2 clusters into a monophyletic cluster of legumes-associated enamoviruses. This sub-clade of highly related and co-divergent legume associated viruses provides insights on the evolutionary history of the enamoviruses. The bioinformatic reanalysis of SRA libraries deposited in the NCBI database constitutes an emerging approach to the discovery of novel plant viruses which should be important for both quarantine purposes and disease management.

plant biology↗

bioRxiv2018

Evidence of a Novel Vitivirus in Grapevine cv Riesling

Vitivirus are ssRNA(+) viruses in the family Betaflexiviridae (subfamily Trivirinae). There are currently ten ICTV recognized virus species in the genus; nevertheless, the extended use of NGS technologies is rapidly expanding their diversity and six more have been proposed recently. Here, we present the characterization of a novel virus from grapevines, which fits the genomic architecture and evolutionary constraints to be classifiable within the Vitivirus genus. The detected virus sequence is 7,607 nt long, including a typical genome organization of ORFs encoding a replicase (RP), a 22 kDa protein, a movement protein, a coat protein (CP) and a nucleic acid binding protein. Here, we present the characterization of a novel virus from grapevines. Phylogenetic analyses based on the predicted RP and CP protein unequivocally places the new virus within the Vitivirus genus. Multiple independent RNAseq data confirmed the presence of the detected virus in berries at diverse developmental stages. Additionally, we detected, confirmed, and assembled virus sequences from grapevine samples of distinct cultivars from America, Europe, Asia and Oceania, sharing 74.9%-97.9% nt identity, suggesting that the identified virus is widely distributed and diverse. We propose the name grapevine virus L (GVL) to the detected Vitivirus.

plant biology↗

bioRxiv2018

Expanding the size limit of RNA viruses: Evidence of a novel divergent nidovirus in California sea hare, with a ~35.9 kb virus genome

While RNA viruses thrive with massive structural and functional diversity, their genomes size variation is particularly low, ranging only from ~2-to-33 kb. Here, I present the characterization of RNA sequences corresponding to the first virus associated with Aplysia californica. Genome structure and domain architecture suggest that the identified virus is a novel member of Nidovirales. The proposed aplysia californica nido-like virus (AcNV), with a genome sequence of ca.35,906 nt, represents the longest ever recorded RNA virus yet. Phylogenetic insights indicate that AcNV clusters in a major phylloclade of unclassified invertebrate nidoviruses, Roniviridae, and Mesoniviridae. Basal branching in this emerging cluster could indicate that AcNV is a member of a novel divergent clade within Nidovirales. Further, virus RNA detection in multiple independent studies suggests that AcNV is neurotropic with a broad cell/tissue/organ tropism, supported by AcNV occurrence in diverse organs, including the first detection of a Nidovirales in single specific neurons.\n\nHighlights-RNA virus genomes reported in the literature are limited at ca. 33.4 kb\n-A novel nidovirus was identified in the gastropod mollusk Aplysia californica\n-The aplysia californica nido-like virus (AcNV) presents a 35.9 kb RNA genome\n-AcNV has a broad tropism, is enriched in the CNS, and accumulates in neurons\n-The unique features of A. californica enables single-neuron virus dynamics of AcNV

microbiology↗

bioRxiv2017

Firefly genomes illuminate the origin and evolution of bioluminescence

Fireflies are among the best-studied of the bioluminescent organisms. Despite longterm interest in the biochemistry, neurobiology, and evolution of firefly flash signals and the widespread biotechnological applications of firefly luciferase, only a limited set of genes related to this complex trait have been described. To investigate the genetic basis of firefly bioluminescence, we generated a high-quality reference genome for the Big Dipper firefly Photinus pyralis, from which the first laboratory luciferase was cloned, using long-read (PacBio), short-read (Illumina), and Hi-C sequencing technologies. To facilitate comparative genomics, we also generated short-read genome assemblies for a Japanese firefly Aquatica lateralis and a bioluminescent click beetle, Ignelater luminosus. Analyses of these genomic datasets supports at least two independent gains of luminescence in beetles, and provides new insights into the evolution of beetle bioluminescence and chemical defenses that likely co-evolved over their 100 million years of evolution.

genomics↗

bioRxiv2017

Molecular Identification and Characterization of Two Rubber Dandelion Amalgaviruses

The Amalgaviridae family comprise persistent viruses that share the genome architecture of Totiviridae and gene evolutionary resemblance to Partitiviridae. Two genera have been assigned to this family, including genus Amalgavirus consisting in nine recognized species, corresponding to plant infecting viruses with dsRNA monosegmented genomes of ca. 3.4 kb. Here, we present the molecular characterization of two novel viruses detected in rubber dandelion (Taraxacum kok-saghyz). The sequenced viruses are 3,409 and 3,413 nt long, including two partially overlapping ORFs encoding a putative coat protein and an RNA-dependent RNA polymerase (RdRP). Phylogenetic insights based on the RdRP suggest them to be members of two new species within the Amalgavirus genus. Multiple independent RNAseq data suggest that the identified viruses have a dynamic distribution and low relative RNA levels in infected plants. Virus presence was not associated with any apparent symptoms on the plant hosts. We propose the names rubber dandelion latent virus 1 & 2 to the detected amalgaviruses; the first viruses to be associated to this emergent and sustainable natural rubber crop.

microbiology↗

bioRxiv2017

An RNA Virome Associated To The Golden Orb-Weaver Spider Nephila clavipes

The golden orb-weaver spider Nephila clavipes, known for its sexual size dimorphism, is abundant and widespread in the New World. The first annotated genome of orb-weaver spiders, exploring N. clavipes, has recently been reported. The study, focused primarily on the diversity of silk specific genes, shed light into the complex evolutionary history of spiders. Furthermore, a robust transcriptome analysis provided a massive resource for N. clavipes RNA survey. Here, I present evidence of viral sequences corresponding to the first 10 extant virus species associated to N. clavipes and indeed, nephilids. The putatively new species are linked to ssRNA positive-strand viruses, such as Picornavirales, and to ssRNA negative-strand and dsRNA viruses. In addition, I detected sequence data of new strains of two recently reported arthropod viruses, which complemented and extended the corresponding sequence references. The identified viruses appear to be complete, potentially functional, and presenting the typical architecture and consistent viral domains. The intrinsic nature of the detected sequences and their absence in the recently generated genome assembly, suggest that they correspond to bona fide RNA virus sequences. The available RNA data allowed for the first time to address a tissue/organ specific analysis of virus loads/presence in spiders, suggesting a complex spatial and differential distribution of the tentative viruses, encompassing the spider brain and also silk and venom glands. Until recently, the virus landscape associated to spiders remained elusive. The discovered viruses described here provide only a fragmented glimpse of the potential magnitude of the Aranea virosphere. Future studies should focus not only on complementing and expanding these findings, but also on addressing the potential ecological role of these viruses, which might influence the biology of these outstanding arthropod species.\n\nFunding statementThe author received no specific funding for this study.\n\nEthics statements(Authors are required to state the ethical considerations of their study in the manuscript, including for cases where the study was exempt from ethical approval procedures)

microbiology↗