Draft Genome Sequence of Four Coccolithoviruses: Emiliania huxleyi Virus EhV-88, EhV-201, EhV-207, and EhV-208

Abstract

The Coccolithoviridae are a group of viruses which infect the marine coccolithophorid microalga Emiliania huxleyi. The Emiliania huxleyi viruses (known as EhVs) described herein have 160-to 180-nm diameter icosahedral structures, have genomes of approximately 400 kbp, and consist of more than 450 predicted coding sequences (CDSs). Here, we describe the genomic features of four newly sequenced coccolithoviruses (EhV-88, EhV-201, EhV-207, and EhV-208) together with their draft genome sequences and their annotations, highlighting the homology and heterogeneity of these genomes to the EhV-86 model reference genome.T he coccolithoviruses infect Emiliania huxleyi, a globally distributed bloom-forming marine microalga. The abundance of Emiliania huxleyi viruses (EhVs) in natural seawater can typically reach 10 7 ml Ϫ1 in bloom conditions and 10 8 to 10 9 ml Ϫ1 under laboratory culture (6). Following the full sequencing of the model virus EhV-86 (isolated in 1999 from the English Channel) and the partial sequencing of EhV-163 (isolated from a Norwegian fjord the following year), we have recently undertaken to sequence the remaining English Channel isolates currently contained within the Plymouth Virus Collection (PVC) (1). The draft genomes of EhV-84, EhV-203, and EhV-202 have been described previously (4, 5). Here, we present the draft genomes of the remaining four coccolithoviruses in the PVC: EhV-88, EhV-201, EhV-207, and EhV-208.EhV-88 was isolated from the English Channel (50°15=N/ 04°13=W) from a depth of 5 m in 1999, while were isolated from the English Channel (49°56=N/ 04°19=W, 50°15=N/04°13=W, and 50°15=N/04°13=W, respectively) from a depth of 2 to 15 m in 2001 (1, 8). Their icosahedral virion structure and morphology are similar to those of other coccolithoviruses and of phycodnaviruses in general (9). Phylogenetic analysis of available major capsid protein (MCP) and DNA pol gene sequences indicates that the closest relatives to EhV-88 are EhV-84 and EhV-86 (4, 7), while EhV-201, EhV-207, and EhV-208 are closely related to 8).Genome sequencing, finishing, and annotation were performed by the Broad Institute. The genomes were sequenced using the 454 FLX pyrosequencing technology platform (Roche/454, Branford, CT). Library construction and sequencing were performed as previously described (2). General protocols for library construction can be found at http://www.broadinstitute.org /annotation/viral/Phage/Protocols.html. De novo genome assembly of resulting reads was performed using the Newbler v2.3 assembly software package (2). A total of 74,782, 78,268, 33,894, and 85,422 reads were produced and assembled into 8,7, 16, and 17 contigs, comprising 396,598 bp, 406,701 bp, 420,391 bp, and 409,403 bp,, respectively. Genes were identified using the Broad Institute's Automated Phage Annotation Protocol (2). Additional gene prediction analysis and functional annotation was performed within the Integrated Microbial Genomes-Expert Review (IMG-ER) platform (3).General features of the genomes include nucleotide compo...

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

“…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.…”

Rewiring Host Lipid Metabolism by Large Viruses Determines the Fate of Emiliania huxleyi, a Bloom-Forming Alga in the Ocean

“…In total, we sequenced around 410 million short reads of 100 bp from six libraries (Supplemental Data Set 1). Reads were aligned to viral genomes (Allen et al, 2006a;Nissimov et al, 2012), to an E. huxleyi transcriptome, which was constructed based on genomic data (Read et al, 2013), and a de novo transcriptome assembly (see Methods and Feldmesser et al, 2014). Gene expression normalization was performed independently to the host and viral genomes and transcript abundance estimation was performed using RSEM (Li and Dewey, 2011).…”

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

“…A 75-bp scar remnant of the phosphate permease gene is still present at the 3′ end of this genome region in both viruses indicating that the fjord EhVs did once possess the phosphate permease gene. However, ehv117 is encoded by, and retained in, all the 9 EhV strains isolated from the English Channel [6,7,8,9,10]. The involvement of the gene product in the active transport of phosphate could provide a crucial advantage for the production of new nucleotides during replication of the viral genome.…”

“…Due to the highly repetitive nature of the genomes, just one coccolithovirus (EhV-86) has been fully sequenced, in which 472 CDSs were identified [6], while a further eight strains (EhV-163, EhV-201, EhV-202, EhV-203, EhV-207, EhV-208, EhV-84 and EhV-88) have been partially sequenced [7,8,9,10,11]. EhV-86 was originally isolated from the English Channel in 1999, the same year as EhV-99B1, while EhV-163 was isolated from the same Norwegian fjord as EhV-99B1 a year later in 2000 [12].…”