Posted by RJG on March 25th, 2014 • An in silico genome screening pipeline using PERL, BLAST and MySQL.
Release of a tool for in silico genome screening
The Database-Integrated Genome Screening (DIGS) tool supports systematic in silico screening of sequence databases.
The screening strategy implemented in the DIGS tool is based on the use of FASTA-formatted sequence libraries to perform similarity searches with the BLAST+ program suite. Data obtained through screening is captured in a MySQL database. The screening process is coordinated using a PERL program. MySQL can be used to monitor progress and analyze data recovered by screening.
Version 1.0 of the DIGS tool is available for LINUX/UNIX and Mac operating systems. The DIGS tool is an open source project hosted on GitHub. Obtain the latest version of DIGS here (link to download zip file is bottom left).
A long-tailed chinchilla
Parvovirus-related EVEs in South American rodentsParvoviruses (family Parvoviridae) are single stranded DNA-viruses that infect animals. Pathogenic parvoviruses of humans include the B19 virus which causes fifth disease ('slapped cheek syndrome') in children. Among mammals, pathogenic parvovirus infections have been identified in cats, dogs, mink and cattle.
In recent years, we and others have reported sequences derived from parvoviruses in animal genomes [1-4]. Certain parvoviruses are known to integrate into the genome of cells they infect. For example, human adeno-associated virus (AAV) integrates at a specific site on chromosome 19, and is of interest as gene therapy vector. The relatively widespread occurrence of parvovirus-related endogenous viral elements (parvo-EVEs) indicates that this process can sometimes introduce sequences derived from parvoviruses into the host germline.
Although parvoviruses can integrate into host genomes, integration it is not an essential step in their replication cycle, as it is for retroviruses. Accordingly, parvo-EVEs are orders of magnitude less common than endogenous retroviruses (ERVs).
A recent in silico screen of mammalian genomes identified novel parvovirus-related EVEs in the genomes of two South American rodent species; the long-tailed chinchilla (Chinchilla lanigera), and the degu (Octodon degus).
Eye of a chicken with Marek's disease (click here to see comparison with a normal chicken eye).
Reticuloendotheliosis virus in a Marek's disease vaccine.Marek's disease (MD) is one of the most common diseases affecting poultry flocks worldwide. MD is caused by infection with gallid herpesvirus 2 (GHV-2), a virus that belongs to the same subfamily (Alphaherpesvirinae) as varicella zoster virus, which causes chickenpox in humans.
MD was first described by Professor Josef Marek in 1907. Over recent decades the disease has substantially increased in severity of symptoms, evolving from an endemic infection causing a mild paralytic syndrome, into a globally distributed and highly contagious neoplastic disease . MD is estimated to cause annual losses of over $1 billion to the global poultry industry .
The first MD vaccines were developed in the late 1960s. One of the most successful vaccines was based on herpesvirus of turkeys (HVT), which is distinct from, but closely related to GHV-2. Widespread use of HVT vaccines in the early 1970s saw a drastic reduction in losses from MD . Over subsequent years, however, the effectiveness of these vaccines declined. Newer vaccines were developed in response, but the effectiveness of these vaccines was also short-lived. This pattern is ongoing, with GHV-2 repeatedly countering new vaccines, while simultaneously increasing in virulence.
Reticuleoendotheliosis virus (REV) is a retrovirus that has been isolated from poultry and wild birds. REV has been found as a contaminant in MD vaccines on multiple occasions, dating back to the early 1970s. We previously presented evidence that REV is not a natural infection of birds, but is in fact a mammalian retrovirus that was accidentally transmitted to birds in the early 20th century . We propose that REV subsequently contaminated avian cell culture systems, and that this likely accounts for the presence of DNA sequences derived from REV in the genomes of some GHV-2 strains. REV sequences have also been identified in the genome of another large DNA virus that infects birds - fowlpox virus (FWPV).
Shortly after the our paper was published, a new REV genome sequence was reported, derived from a strain (REV-MD2) contaminating an HVT-based MD vaccine . We examined this new sequence in the context of our hypothesis of REV origin.
Illustration of a golden-collared toucanet
An unusual group of recombinant ERVs identified in avian genomesThe evolutionary relationships of endogenous retroviruses (ERVs) are commonly studied through phylogenetic analysis of the highly conserved polymerase (pol) gene, focusing particularly on the region that encodes the reverse transcriptase (RT) protein. However, the envelope (env) gene, which encodes the glycoprotein used by retroviruses to bind and enter cells, also contains regions of relatively high sequence conservation, and can be used to study the evolutionary relationships of diverse retroviruses [1,2].
Env glycoproteins stud the surface of retroviral particles. They typically comprise two subunits: a surface (SU) subunit that binds a receptor on the exterior surface of a target cell, and a transmembrane (TM) subunit that mediates entry into the interior of that cell. The TM subunit typically exhibits evolutionarily conserved features, and like RT, can be used to construct phylogenetic trees representing the evolutionary relationships between retroviruses.
Combined phylogenetic analysis of the RT and TM domains of retroviral genomes can reveal how diverse retroviruses have 'recombined' during their evolution, swapping genes to generate chimeric retroviruses with novel properties. Recombination can greatly influence the evolutionary trajectories of viruses. For example, a novel env gene acquired through recombination may enable a retrovirus to infect cell types and host species it previously could not.
In a paper published in Journal of Virology this month , we describe a novel group of recombinant ERVs in the genomes of birds (class Aves). This group, referred to here as 'Aves ERV-F', is relatively rare, and has an unusual genome structure that appears to have arisen via an ancient recombination event involving highly divergent retroviruses.