2023
DOI: 10.1371/journal.pgen.1010998
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Revisiting evolutionary trajectories and the organization of the Pleolipoviridae family

Tomas Alarcón-Schumacher,
Dominik Lücking,
Susanne Erdmann

Abstract: Archaeal pleomorphic viruses belonging to the Pleolipoviridae family represent an enigmatic group as they exhibit unique genomic features and are thought to have evolved through recombination with different archaeal plasmids. However, most of our understanding of the diversity and evolutionary trajectories of this clade comes from a handful of isolated representatives. Here we present 164 new genomes of pleolipoviruses obtained from metagenomic data of Australian hypersaline lakes and publicly available metage… Show more

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Cited by 4 publications
(2 citation statements)
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“…Additionally, 38 ‘incomplete’ pR1SE-like elements were detected, with a minimum of 3 of the 6 proteins detected ( Table S3 ). Of the 40 complete pR1SE-like entities, 35 were retrieved from NCBI, while five additional contigs were detected in the metagenomes of Australian salt lakes [ 10 ], and none could be detected in the IMG/VR database. We will refer to the detected pR1SE-like entities as apHPVs, for archaeal plasmids of haloarchaea potentially transferred in plasmid vesicles, while ‘H’ can be replaced by the abbreviation for the host (e.g., HR for Halorubrum ; apHRPV1 for pR1SE) as common for virus names.…”
Section: Resultsmentioning
confidence: 99%
See 1 more Smart Citation
“…Additionally, 38 ‘incomplete’ pR1SE-like elements were detected, with a minimum of 3 of the 6 proteins detected ( Table S3 ). Of the 40 complete pR1SE-like entities, 35 were retrieved from NCBI, while five additional contigs were detected in the metagenomes of Australian salt lakes [ 10 ], and none could be detected in the IMG/VR database. We will refer to the detected pR1SE-like entities as apHPVs, for archaeal plasmids of haloarchaea potentially transferred in plasmid vesicles, while ‘H’ can be replaced by the abbreviation for the host (e.g., HR for Halorubrum ; apHRPV1 for pR1SE) as common for virus names.…”
Section: Resultsmentioning
confidence: 99%
“…DNA sequencing libraries were prepared (FS DNA Library, NEBNext ® Ultra™) and sequenced (2 × 250 bp paired end, Illumina HiSeq2500, Rapid Mode) at the Max-Planck Genome-Centre Cologne (Germany). The data have previously been described in Alarcón-Schumacher et al [ 10 ], and raw data are available at ENA-EMBL under project number PRJEB61734. Reads were trimmed with Cutadapt (v4.6) [ 11 ], removing low-quality, short, or unpaired reads (parameters: -q 30 -m 30).…”
Section: Methodsmentioning
confidence: 99%