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The Discovery and Classification of Novel Viruses from the Giant Virus Phylum Nucleocytoviricota (NCV)

Authors: Vivek, Manya;

The Discovery and Classification of Novel Viruses from the Giant Virus Phylum Nucleocytoviricota (NCV)

Abstract

The phylum Nucleocytoviricota (NCV), encompassing a diverse array of large and giant viruses, primarily comprises double-stranded DNA viruses that infect a wide range of eukaryotic organisms. Emerging evidence suggests a significant role of Horizontal Gene Transfer (HGT) within members of the NCV phylum, potentially enhancing their adaptability through the acquisition of novel genes and functions. However, the functional implications of these transferred genes remain poorly understood, necessitating further research. My project used recent metagenome-assembled genomes (MAGs) from the Barre Woods site at Harvard Forest. MAGs were formed using two different methods involving assembly of individual metagenomes and the combined assembly of all 6 metagenomes. The comparison between individual and co-assembled data revealed that the integration of both datasets provides a more comprehensive depiction of the genomic landscape. I developed a pipeline to help predict potential HGT events to better understand genetic exchange mechanisms within the NCV phylum. I identified horizontal gene transfer candidates related to the new viral MAGs from Barre Woods. Matches of the viral MAGs to bacterial genomes in NCBI involved many instances of misclassification of viral genomes as bacteria or viral - bacterial horizontal gene transfer candidates were not further analyzed. The Perivirus MAG has large contiguous matches to genome projects of the snail, Elysia margianta and fungus, Rhizophagus. The Perivirus genes matching the snail genome were on small contigs with a different read depth than the main chromosomal regions of the snail suggesting that a Perivirus relative may have been infecting the snail at the time DNA was isolated. This provides evidence that one possible host for the Perivirus are snails commonly found in forests. The Perivus genes matched genome regions from several Rhizophagus species, suggesting large-scale virus gene integration in an ancestor of these species. The pipeline identified a significant number of ANK genes in a Pimascovirales NCV MAGs that have homology matches to two genes from aphids. I proposed that the ANK gene in the NCV is a result of a HGT from the aphids to the NCV, followed by a gene duplication event that leads to the repeats of the ANK gene.

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selected citations
These citations are derived from selected sources.
This is an alternative to the "Influence" indicator, which also reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
BIP!Citations provided by BIP!
popularity
This indicator reflects the "current" impact/attention (the "hype") of an article in the research community at large, based on the underlying citation network.
BIP!Popularity provided by BIP!
influence
This indicator reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
BIP!Influence provided by BIP!
impulse
This indicator reflects the initial momentum of an article directly after its publication, based on the underlying citation network.
BIP!Impulse provided by BIP!
0
Average
Average
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