Genomic Sequence and Analysis of EhV-99B1, a New Coccolithovirus from the Norwegian Fjords

Abstract

Coccolithoviruses are giant dsDNA viruses that infect Emiliania huxleyi, the most ubiquitous marine microalga. Here, we present the genome of the latest coccolithovirus strain to be sequenced, EhV-99B1, and compare it with two other coccolithovirus genomes (EhV-86 and EhV-163). EhV-99B1 shares a pairwise nucleotide identity of 98% with EhV-163 (the two strains were isolated from the same Norwegian fjord but in different years), and just 96.5% with EhV-86 (isolated in the same spring as EhV-99B1 but in the English Channel). We confirmed and extended the list of relevant genomic differences between these EhVs from the Norwegian fjord and EhVs from the English Channel, namely the removal/insertions of: a phosphate permease, an endonuclease, a transposase, and two specific tRNAs. As a whole, this study provided new clues and insights into the diversity and mechanisms driving the evolution of these large oceanic viruses, in particular those processes involving selfish genetic elements.

Coccolithoviruses: A Review of Cross-Kingdom Genomic Thievery and Metabolic Thuggery

“…Similarly, Pagarete et al [44] report differences in the type of tRNAs encoded by EhV-86 and EhV-99B1. However, after an in-depth study of the different codon frequencies of the genomes of EhV-86 and EhV-99B1, they concluded that the difference in tRNAs does not correspond to the respective codon frequencies in each genome and that it is more likely that strain-specific tRNA differences represent adaptations to different host strains.…”

“…This transporter is encoded by all EhV isolates from the English Channel and the Scottish coast, but absent in the Norwegian isolate EhV-99B1 ([44]; and this study) and the partially sequenced genome of the Norwegian isolate EhV-163 (not included in this study) [43]. Instead, a 75-bp scar remnant of the transporter gene is still present at the 3′ end of this gene in both Norwegian isolates, and is replaced by a putative endonuclease [43].…”

“…Instead, a 75-bp scar remnant of the transporter gene is still present at the 3′ end of this gene in both Norwegian isolates, and is replaced by a putative endonuclease [43]. This indicates that the Norwegian fjord EhVs once possessed the gene [44] and have since lost it. Such genes are common in E. huxleyi , which has six inorganic phosphate transporters and an alkaline phosphatase that enable it to thrive in low phosphorous conditions [66].…”

“…Annotated EhV genomes [1,44,45,46,47,48,49] were used to build genomic alignments. Prior to analysis, the gaps between the assembled annotated contigs of each draft genome were made the same length by adding a known length of ambiguous nucleotides (i.e., a series of 10 Ns).…”

“…Since the sequencing of the EhV-86 genome, an additional 12 EhV strains have been isolated and their genomes sequenced [43,44,45,46,47,48,49]. This makes EhVs one of the largest collections of Phycodnaviridae viruses in culture with complete or near-complete genome sequences available.…”