Endogenous CRESS virus (ECV) data

Sequences derived from CRESS DNA viruses commonly occur in metazoan genomes. These endogenous cress virus (ECV) provide unique information about the evolution and biology of the Cressdnaviricota, being similar in some ways to 'viral fossils'. ECV sequences have revealed a wealth of new information about CRESS DNA virus evolution. CRESS-GLUE represents and organises the fossil record of CRESS DNA viruses.

Species with endogenous CRESS DNA viruses

Some of the species in which we identified EVEs that are derived from CRESS DNA viruses, left to right: icefish (Chaenocephalus aceratus), wels catfish CRESS DNA virus (Siluris glanis), black & white tegu (Salvator merianae), Sunda flying lemur (Galeopterus variegatus).

These web pages provide a description of CRESS-GLUE's paleovirus component, and quick links to specific data items.

Relevance to virology

Endogenous viral sequences can inform our understanding of contemporary viruses in a wide variety of ways. Perhaps most importantly, EVEs allow calibration of the long-term evolutionary history of virus groups, which greatly influences how we understand their biology.

Importantly, once time calibrations have been established, a far richer range of comparative genomic studies can be performed. By examining variation in the light of a known evolutionary history, these studies can provide invaluable insights into the biological mechanisms through which viruses replicate and spread.

In some cases, studies of paleoviruses can go a step further - EVE sequences can be used to guide the reconstitution of functional nucleic acids and proteins via gene synthesis, so that their biological properties may be empirically investigated. This in turn, can greatly expand the scope of comparative/theoretical approaches in paleovirology.

Circovirus host species

Some more of the species in which we identified EVEs derived from CRESS DNA viruses, left to right: inshore hagfish (Eptatretus burgeri), Ryukyu mouse (Mus caroli), dust mites (Tropilaelaps mercedesae), Pseudomyrmex ants.

Relevance to viral metagenomics

The ECV sequences in CRESS-GLUE can provide a useful resource for those interested in identifying and characterising CRESS DNA viruses in metagenomic datasets.

Firstly, these sequences be used to exclude any potential 'false positive' hits (i.e. sequences that seem to represent new CRESS DNA viruses but in fact derive from genomic DNA).

In addition, when new CRESS DNA virus species are identified, inclusion of EVEs in phylogenetic analyses can often provide useful information about their broader ecology and evolution, including (uniquely) their long-term evolution. For example, see Dennis et al. (2018), and Kinsella et al. (2020).

Relevance to genomics

ECVs are not only useful genetic markers, several lines of evidence indicate they may have, or have had, functional roles as host alleles. The prevalence of multicopy ECV lineages in some species suggests that germline incorporation of CRESS DNA virus sequences might have influenced the evolution of host genomes in important ways.

Where do the ECV data come from?

EVE sequences were recovered from whole genome sequence (WGS) assemblies via database-integrated genome screening (DIGS) using the DIGS tool.

All data pertaining to this screen are included in this repository, or in the associated "DIGS-for-EVEs" project.

Nomenclature for ECVs

We have applied a systematic approach to naming ECV, following a convention developed for endogenous retroviruses (ERVs). Each element was assigned a unique identifier (ID) constructed from a defined set of components.

ECV Nomenclature

The first component is the classifier ‘ECV’ (endogenous CRESS virus).

The second component is a composite of two distinct subcomponents separated by a period: (i) the name of ECV group; (ii) a numeric ID that uniquely identifies the insertion. The numeric ID is an integer that identifies a unique insertion locus that arose as a consequence of an initial germline infection. Thus, orthologous copies in different species are given the same number.

Where an ECV sequence is thought to have been duplicated within the germline following it's initial incorporation (e.g. via segmental duplication or transposition) we have appended an additional 'duplicate id' to the numeric ID, separated by a period. Please note that we have not yet resolved the orthologous relationships among sets of eHBV sequences belonging to multicopy ECV lineages. We have therefore assigned unique duplicate IDs to each sequence within these lineages.

The third component of the ID defines the set of host species in which the ortholog occurs, or did occur prior to being deleted.

ECV reference sequences and data

We constructed reference sequences for using alignments of ECV sequences derived from the same initial germline colonisation event - i.e. orthologous elements in distinct species, and paralogous elements that have arisen via intragenomic duplication of ECV sequences.

Reference sequence data in tabular format can be found at the following links:

Nucleotide level data:

Taxonomic group Tabular data Full-length ECV nucleotides Full-length ECV
Genus Circovirus 2020-07-15 FASTA MSA Individual FASTA
Genus Cyclovirus 2020-07-15 FASTA MSA Individual FASTA
Unclassified CRESS 2020-07-15 - Individual FASTA

Protein level data:

Taxonomic group Rep protein Rep protein Cap protein Cap protein
Genus Circovirus FASTA MSA Individual FASTA FASTA MSA Individual FASTA
Genus Cyclovirus FASTA MSA Individual FASTA FASTA MSA Individual FASTA

Multiple sequence alignments

Multiple sequence alignment constructed in this study are linked together using GLUE's ‘alignment tree’ data structure. Alignments in the project include:

  1. A single ‘root’ alignment constructed to represent proposed homologies between representative members of major CRESS virus lineages (including extinct lineages represented only by ECVs).
  2. Genus-level’ alignments for each CRESS DNA virus family. These alignments have been constructed to represent homologies between the genomes of representative members of specific CRESS virus genera and ECV reference sequences.
  3. Tip’ alignments in which all taxa are derived from a single ECV lineage.

Phylogenetic trees

We used GLUE to implement an automated process for deriving midpoint rooted, annotated trees from the alignments included in our project.

Trees were constructed at distinct taxonomic levels:

  1. Recursively populated root phylogeny (Rep)
  2. Genus-level phylogenies
  3. ECV lineage-level phylogenies

Raw ECV sequences and data

These are the raw data generated by database-integrated genome screening (DIGS). The tabular files contain information about the genomic location of each EVE. EVEs were classified by comparison to a polypeptide sequence reference library designed to represent the known diversity of CRESS viruses - this includes extinct lineages represented only by endogenous viral elements (EVEs).

These data were obtained via DIGS performed in vertebrate genome assemblies downloaded from NCBI genomes (2020-07-15).

Taxonomic Group ECV locus data in tabular format Individual FASTA files
Genus Circovirus 2020-07-15 2020-07-15
Genus Cyclovirus 2020-07-15 2020-07-15
Unclassified CRESS 2020-07-15 2020-07-15

Paleovirus-specific schema extensions

The paleovirus component of CRESS-GLUE extends GLUE's core schema to allow the capture of EVE-specific data. These schema extensions are defined in this file and comprise two additional tables: 'locus_data' and 'refcon_data'. Both tables are linked to the main 'sequence' table via the 'sequenceID' field.

The 'locus_data' table contains information pertaining to individual EVE sequences: e.g. species in which they occur, genome assembly version, genomic location(i.e. scaffold, location coordinates, and orientation).

The 'refcon_data' table contains information pertaining to our ECV reference sequences, which we have constructed in an effort to reconstruct, as closely as possible, the sequences of the progenitor viruses that gave rise to EVEs.

Related Publications

Kinsella CM, Bart A, Deijs M, Broekhuizen P, Kaczorowska J, Jebbink MF, van Gool T, Cotten M, and L van der Hoek. (2020)
Entamoeba and Giardia parasites implicated as hosts of CRESS viruses.
Nat Commun. Sep 15;11(1):4620. doi: 10.1038/s41467-020-18474-w. [view]

Dennis TPW, de Souza WM, Marsile-Medun S, Singer JB, Wilson SJ, and RJ Gifford (2019)
The evolution, distribution and diversity of endogenous circoviral elements in vertebrate genomes.
Virus Research [view]

Dennis TPW, Flynn PJ, de Souza WM, Singer JB, Moreau CS, Wilson SJ, and RJ Gifford (2018)
Insights into CRESS DNA virus host range from the genomic fossil record.
Journal of Virology [view]

Singer JB, Thomson EC, McLauchlan J, Hughes J, and RJ Gifford (2018)
GLUE: A flexible software system for virus sequence data.
BMC Bioinformatics [view]

Zhu H, Dennis T, Hughes J, and RJ Gifford (2018)
Database-integrated genome screening (DIGS): exploring genomes heuristically using sequence similarity search tools and a relational database. [preprint]

Gifford RJ, Blomberg B, Coffin JM, Fan H, Heidmann T, Mayer J, Stoye J, Tristem M, and WE Johnson (2018)
Nomenclature for endogenous retrovirus (ERV) loci.
Retrovirology [view]

Katzourakis A. and RJ. Gifford (2010)
Endogenous viral elements in animal genomes.
PLoS Genetics [view]