Biology subjects

Dietzgen, R. G.

Publications and source records attributed to Dietzgen, R. G..

3 recordsLinked to original sources

bioRxiv2025

Expanding the known nucleorhabdovirus world: the final chapter in a trilogy exploring the hidden diversity of plant-associated rhabdoviruses

Nucleorhabdoviruses, classified into four distinct genera within the family Rhabdoviridae (subfamily Betarhabdovirinae), are plant-infecting viruses, characterized by nucleus-associated, enveloped, bacilliform virions. Nucleorhabdoviruses possess an unsegmented, single-stranded, negative-sense RNA genome (ca. 12-15.2 kb) that encodes six to eight proteins. Here, by exploring large publicly available metatranscriptomics datasets, we report the identification and genomic characterization of 47 novel viruses with genetic and evolutionary hallmarks of nucleorhabdoviruses. These viruses are associated with 45 distinct host plant species and were previously hidden in public database. Our findings significantly broaden the known host range of nucleorhabdoviruses, including the first nucleorhabdovirus associated with ferns and the first gammanucleorhabdoviruses linked to dicot hosts. Genetic divergence and evolutionary analyses suggest that all these novel viruses likely represent members of novel species. Phylogenetic reconstruction indicates that ten novel viruses are related to alphanucleorhabdoviruses, 25 to betanucleorhabdoviruses, eight to deltanucleorhabdoviruses and four to gammanucleorhabdoviruses. This study constitutes the final chapter in a trilogy chronicling a data mining expedition into the cryptic diversity of plant-associated rhabdoviruses, a journey that began with varicosaviruses and continued with cytorhabdoviruses. These new findings yield the most comprehensive phylogeny of nucleorhabdoviruses to date, significantly expanding our genomic understanding and illuminating the phylogenetic relationships and evolutionary dynamics of this virus group. Further, this work underscores the value of large-scale sequence data mining in advancing our understanding of the hidden world of plant rhabdoviruses.

microbiology↗

bioRxiv2020

Genome-enabled insights into the biology of thrips as crop pests

BackgroundThe western flower thrips, Frankliniella occidentalis (Pergande), is a globally invasive pest and plant virus vector on a wide array of food, fiber and ornamental crops. While there are numerous studies centered on thrips pest and vector biology, feeding behaviors, ecology, and insecticide resistance, the underlying genetic mechanisms of the processes governing these areas of research are largely unknown. To address this gap, we present the F. occidentalis draft genome assembly and official gene set. ResultsWe report on the first genome sequence for any member of the insect order Thysanoptera. Benchmarking Universal Single-Copy Ortholog (BUSCO) assessments of the genome assembly (size = 415.8 Mb, scaffold N50 = 948.9 Kb) revealed a relatively complete and well-annotated assembly in comparison to other insect genomes. The genome is unusually GC-rich (50%) compared to other insect genomes to date. The official gene set (OGS v1.0) contains 16,859 genes, of which [~]10% were manually verified and corrected by our consortium. We focused on manual annotation, phylogenetic and expression evidence analyses for gene sets centered on primary themes in the life histories and activities of plant-colonizing insects. Highlights include: 1) divergent clades and large expansions in genes associated with environmental sensing (chemosensory receptors) and detoxification (CYP4, CYP6 and CCE enzymes) of substances encountered in agricultural environments; 2) a comprehensive set of salivary gland-associated genes supported by enriched expression; 3) apparent absence of members of the IMD innate immune defense pathway; and 4) developmental- and sex-specific expression analyses of genes associated with progression from larvae to adulthood through neometaboly, a distinct form of maturation compared to complete metamorphosis in the Holometabola. ConclusionsAnalysis of the F. occidentalis genome offers insights into the polyphagous behavior of this insect pest to find, colonize and survive on a widely diverse array of plants. The genomic resources presented here enable a more complete analysis of insect evolution and biology, providing a missing taxon for contemporary insect genomics-based analyses. Our study also offers a genomic benchmark for molecular and evolutionary investigations of other thysanopteran species.

genomics↗

bioRxiv2020

Molecular characterization of a novel cytorhabdovirus with a unique genomic organization infecting yerba mate (Ilex paraguariensis) in Argentina

The genome of a novel rhabdovirus was detected in yerba mate (Ilex paraguariensis St. Hil.). The newly identified virus, tentatively named yerba mate virus A (YmVA), has a genome of 14,961 nucleotides. Notably, eight open reading frames were identified in the antigenomic orientation of the negative-sense, single-stranded viral RNA, including two novel accessory genes, in the order 3-N-P-3-4-M-G-L-8-5. Sequence identity of the encoded proteins as well as phylogenetic analysis suggest that YmVA is a new member of the genus Cytorhabdovirus, family Rhabdoviridae. YmVA unique genomic organization and phylogenetic relationships indicate that this virus likely represents a distinct evolutionary lineage within the cytorhabdoviruses.

microbiology↗