CiteULike | Further Information

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Mendeley | Further Information

{"title"=>"Endogenous viral elements in animal genomes", "type"=>"journal", "authors"=>[{"first_name"=>"Aris", "last_name"=>"Katzourakis", "scopus_author_id"=>"6505851563"}, {"first_name"=>"Robert J.", "last_name"=>"Gifford", "scopus_author_id"=>"56049718700"}], "year"=>2010, "source"=>"PLoS Genetics", "identifiers"=>{"issn"=>"15537390", "pui"=>"360082647", "pmid"=>"21124940", "isbn"=>"1553-7404 (Electronic)\\r1553-7390 (Linking)", "doi"=>"10.1371/journal.pgen.1001191", "sgr"=>"78649718268", "scopus"=>"2-s2.0-78649718268"}, "id"=>"0eee05ed-3d58-347c-830e-75c86272d1f8", "abstract"=>"Integration into the nuclear genome of germ line cells can lead to vertical inheritance of retroviral genes as host alleles. For other viruses, germ line integration has only rarely been documented. Nonetheless, we identified endogenous viral elements {(EVEs)} derived from ten non-retroviral families by systematic in silico screening of animal genomes, including the first endogenous representatives of double-stranded {RNA,} reverse-transcribing {DNA,} and segmented {RNA} viruses, and the first endogenous {DNA} viruses in mammalian genomes. Phylogenetic and genomic analysis of {EVEs} across multiple host species revealed novel information about the origin and evolution of diverse virus groups. Furthermore, several of the elements identified here encode intact open reading frames or are expressed as {mRNA.} For one element in the primate lineage, we provide statistically robust evidence for exaptation. Our findings establish that genetic material derived from all known viral genome types and replication strategies can enter the animal germ line, greatly broadening the scope of paleovirological studies and indicating a more significant evolutionary role for gene flow from virus to animal genomes than has previously been recognized.", "link"=>"http://www.mendeley.com/research/endogenous-viral-elements-animal-genomes", "reader_count"=>328, "reader_count_by_academic_status"=>{"Unspecified"=>8, "Professor > Associate Professor"=>17, "Librarian"=>1, "Researcher"=>64, "Student > Doctoral Student"=>21, "Student > Ph. D. Student"=>94, "Student > Postgraduate"=>16, "Student > Master"=>37, "Other"=>12, "Student > Bachelor"=>40, "Lecturer"=>3, "Lecturer > Senior Lecturer"=>3, "Professor"=>12}, "reader_count_by_user_role"=>{"Unspecified"=>8, "Professor > Associate Professor"=>17, "Librarian"=>1, "Researcher"=>64, "Student > Doctoral Student"=>21, "Student > Ph. D. Student"=>94, "Student > Postgraduate"=>16, "Student > Master"=>37, "Other"=>12, "Student > Bachelor"=>40, "Lecturer"=>3, "Lecturer > Senior Lecturer"=>3, "Professor"=>12}, "reader_count_by_subject_area"=>{"Unspecified"=>15, "Agricultural and Biological Sciences"=>210, "Arts and Humanities"=>1, "Philosophy"=>1, "Veterinary Science and Veterinary Medicine"=>6, "Computer Science"=>7, "Earth and Planetary Sciences"=>4, "Engineering"=>2, "Environmental Science"=>2, "Biochemistry, Genetics and Molecular Biology"=>43, "Mathematics"=>1, "Medicine and Dentistry"=>21, "Pharmacology, Toxicology and Pharmaceutical Science"=>2, "Physics and Astronomy"=>2, "Social Sciences"=>1, "Immunology and Microbiology"=>9, "Chemistry"=>1}, "reader_count_by_subdiscipline"=>{"Medicine and Dentistry"=>{"Medicine and Dentistry"=>21}, "Social Sciences"=>{"Social Sciences"=>1}, "Physics and Astronomy"=>{"Physics and Astronomy"=>2}, "Mathematics"=>{"Mathematics"=>1}, "Unspecified"=>{"Unspecified"=>15}, "Environmental Science"=>{"Environmental Science"=>2}, "Pharmacology, Toxicology and Pharmaceutical Science"=>{"Pharmacology, Toxicology and Pharmaceutical Science"=>2}, "Arts and Humanities"=>{"Arts and Humanities"=>1}, "Engineering"=>{"Engineering"=>2}, "Chemistry"=>{"Chemistry"=>1}, "Earth and Planetary Sciences"=>{"Earth and Planetary Sciences"=>4}, "Immunology and Microbiology"=>{"Immunology and Microbiology"=>9}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>210}, "Computer Science"=>{"Computer Science"=>7}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>43}, "Philosophy"=>{"Philosophy"=>1}, "Veterinary Science and Veterinary Medicine"=>{"Veterinary Science and Veterinary Medicine"=>6}}, "reader_count_by_country"=>{"United States"=>17, "Japan"=>3, "United Kingdom"=>6, "Portugal"=>1, "Russia"=>1, "Spain"=>1, "India"=>1, "Venezuela"=>2, "Austria"=>1, "Netherlands"=>1, "Belgium"=>1, "Taiwan"=>1, "Brazil"=>7, "Italy"=>3, "Mexico"=>2, "Israel"=>1, "France"=>2, "Chile"=>1, "Australia"=>1, "Germany"=>2}, "group_count"=>8}

ORCID | Further Information

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• {"url"=>"http%3A%2F%2Fjournals.plos.org%2Fplosgenetics%2Farticle%3Fid%3D10.1371%252Fjournal.pgen.1001191", "share_count"=>1, "like_count"=>0, "comment_count"=>2, "click_count"=>0, "total_count"=>3}

Journal Comments | Further Information

• {"type"=>"COMMENT", "annotationUri"=>"info:doi/10.1371/annotation/aff255f1-823b-4319-93f2-f3c5e627e258", "title"=>"Extensive viral/human protein homology at the pentapeptide level", "body"=>"This is a key paper with major implications. Hundreds of viruses appear to have infiltrated the human genome. The important consequence of this is that the proteins of today's viruses resemble our own. Numerous BLASTs of translated viral DNA vs. the human proteome are shown at this site named Pandora's box for obvious reasons http://www.polygenicpathways.co.uk/BLASTS.htm . Small contiguous amino acid stretches of 5 or more amino acids within human proteins exactly match those in the current virome (Vatches = viral matches). Upon infection these viral proteins are likely to seed havoc within the host's protein networks, acting as dummy ligands, decoy receptors or by interactome interference. This has major implications for understanding how viruses contribute to disease and several examples are shown. For example it would appear that such viral insertions, repeated over evolutionary time, are responsible for the creation of gene families. HSV-1 and HSV-2 express proteins that are homologous to many kinases, and the cytomegalovirus to many chemokine receptors.\n\nThe viruses implicated as risk factors in Alzheimer's disease, schizophrenia and Parkinson's disease all express proteins that are homologous to hundreds of susceptibility gene products in these diseases. This suggests that genes and risk factors act together, and that each may be a risk factor precisely because of such matches. The viral/human DNA homology also suggests that some gene association studies, using blood samples, may have been tracking infection as well as identifying susceptibility genes. \n\nSome of these observations are available at NaturePrecedings http://precedings.nature.com/users/c8e325bfe6bd1d4fc6e006ff204b5f19\n\n\n\n", "isRemoved"=>false, "created"=>"2010-11-19T18:00:35Z", "lastModified"=>"2010-11-19T18:00:35Z", "creator"=>{"userId"=>"157231"}, "highlightedText"=>"", "competingInterestStatement"=>{"creatorWasPrompted"=>true, "hasCompetingInterests"=>false}, "parentArticle"=>{"doi"=>"info:doi/10.1371/journal.pgen.1001191", "state"=>"published", "journals"=>{"PLoSGenetics"=>{"journalKey"=>"PLoSGenetics", "eIssn"=>"1553-7404", "title"=>"PLOS Genetics"}}}, "replyTreeSize"=>0, "mostRecentActivity"=>"2010-11-19T18:00:35Z", "replies"=>[]}
• {"type"=>"COMMENT", "annotationUri"=>"info:doi/10.1371/annotation/c68fbe2b-cb0d-4abf-bd20-d7805b7f222c", "title"=>"Copy of distributed press release", "body"=>"Paleovirology expanded: non-retroviral virus fragments found in animal genomes\n\nUnderstanding the evolution of life-threatening viruses like influenza, Ebola and dengue fever, could help us to minimize their impact. New research points the way to a fossil record of viruses that have insinuated themselves into the genomes of insects and other animals, providing clues about their evolutionary history. The findings, published online on November 18 in the open-access journal PLoS Genetics, could enable scientists to elucidate general principles in virus evolution from their genetic “fossils”, which in turn could inform approaches for controlling disease.\n\nRobert Gifford( Rockefeller University), and colleague Aris Katzourakis (Oxford University) used the rapidly advancing technology for genetic screening to analyze a database of insect, bird and mammal DNA for fragments of virus genomes, which they named endogenous viral elements (EVEs). The pair discovered representatives of ten families of viruses, including hepatitis B, Ebola, rabies, and dengue and yellow fevers integrated into the genomes studied. \n\n“In some cases, we’ve got the first evidence of an ancient origin for some of these virus groups”, said Gifford. While scientists have been aware of genetic signatures for retroviruses in animal genomes since the 1970s, much remains to be learned about these newly-discovered EVEs from non-retroviral viruses, including exactly how these virus fragments find their way into nuclear DNA. \n\nMost of the fragments documented by Gifford are no longer functional, appearing like what is commonly referred to as “junk DNA.” However, the findings suggest that some of these virus fragments may have been co-opted by their hosts at some point in their evolutionary history, perhaps as a defense against related infections. In particular, Gifford says that finding EVEs in insect genomes promises to reveal a new dimension in paleovirology, allowing scientists to probe the relationship and evolution of the virus, its vector and its host, potentially providing insight into the complex ecological relationships that underpin insect-borne diseases. \n", "isRemoved"=>false, "created"=>"2010-11-26T15:49:56Z", "lastModified"=>"2010-11-26T15:49:56Z", "creator"=>{"userId"=>"131543"}, "highlightedText"=>"", "competingInterestStatement"=>{"creatorWasPrompted"=>true, "hasCompetingInterests"=>false}, "parentArticle"=>{"doi"=>"info:doi/10.1371/journal.pgen.1001191", "state"=>"published", "journals"=>{"PLoSGenetics"=>{"journalKey"=>"PLoSGenetics", "eIssn"=>"1553-7404", "title"=>"PLOS Genetics"}}}, "replyTreeSize"=>1, "mostRecentActivity"=>"2010-11-26T15:53:25Z", "replies"=>[{"type"=>"REPLY", "parentID"=>17679, "annotationUri"=>"info:doi/10.1371/reply/bb50cbeb-6847-4ac6-aead-bc6f584a3581", "title"=>"Further media coverage", "body"=>"This article gained much attention in the science community.\n\nnature.com featured the findings (http://blogs.nature.com/news/thegreatbeyond/2010/11/viruses_tk.html), as did Discover Magazine (http://blogs.discovermagazine.com/loom/2010/11/18/your-inner-viruses-the-trickle-becomes-the-flood/).", "isRemoved"=>false, "created"=>"2010-11-26T15:53:25Z", "lastModified"=>"2010-11-26T15:53:25Z", "creator"=>{"userId"=>"131543"}, "highlightedText"=>"", "competingInterestStatement"=>{"creatorWasPrompted"=>true, "hasCompetingInterests"=>false}, "parentArticle"=>{"doi"=>"info:doi/10.1371/journal.pgen.1001191", "state"=>"published", "journals"=>{"PLoSGenetics"=>{"journalKey"=>"PLoSGenetics", "eIssn"=>"1553-7404", "title"=>"PLOS Genetics"}}}, "replyTreeSize"=>0, "mostRecentActivity"=>"2010-11-26T15:53:25Z", "replies"=>[]}]}
• {"type"=>"COMMENT", "annotationUri"=>"info:doi/10.1371/annotation/6c98d7cc-d406-41f4-86e1-f50c3548ab07", "title"=>"Recent dates for viral origins", "body"=>"Key phrase from paper: \"These findings also indicate that more recent dates of origin obtained for other virus families using molecular clock-based extrapolations are artifacts [30].\"\n\nDoesn't the detection of these very ancient but clearly recognizable integrated viral genomes invalidates the common methods of calculating the time to most recent common ancestor with results typically in the tens of thousands of years ? Could all these early dates be wrong ? ", "isRemoved"=>false, "created"=>"2011-09-01T18:35:55Z", "lastModified"=>"2011-09-01T18:35:55Z", "creator"=>{"userId"=>"10331"}, "highlightedText"=>"", "competingInterestStatement"=>{"creatorWasPrompted"=>true, "hasCompetingInterests"=>false}, "parentArticle"=>{"doi"=>"info:doi/10.1371/journal.pgen.1001191", "state"=>"published", "journals"=>{"PLoSGenetics"=>{"journalKey"=>"PLoSGenetics", "eIssn"=>"1553-7404", "title"=>"PLOS Genetics"}}}, "replyTreeSize"=>0, "mostRecentActivity"=>"2011-09-01T18:35:55Z", "replies"=>[]}

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• {"id"=>"1338480143388594176", "text"=>"@jbloom_lab You won't catch me arguing that non-retroviral viruses in general can't integrate, ever:\n\nhttps://t.co/eToISMfN65", "created_at"=>"2020-12-14T13:45:08Z", "user"=>"ArisKatzourakis", "user_name"=>"Aris Katzourakis", "user_profile_image"=>"http://pbs.twimg.com/profile_images/1200530896132222977/Mg89eKq9_normal.jpg"}
• {"id"=>"1347700729205706760", "text"=>"3. https://t.co/cAB48xkG1N https://t.co/Vrv5TxUc5U", "created_at"=>"2021-01-09T00:24:27Z", "user"=>"G05Vi", "user_name"=>"Vic. Citosina-Guanina???", "user_profile_image"=>"http://pbs.twimg.com/profile_images/1346272999197048833/--pzQCMI_normal.jpg"}
• {"id"=>"601774718102843392", "text"=>"@PLOSGenetics Endogenous Viral Elements in Animal Genomes \nby @ArisKatzourakis & @Paleovirologist \nhttp://t.co/idxgrjyfux", "created_at"=>"2015-05-22T15:40:47Z", "user"=>"CedricFeschotte", "user_name"=>"Cedric Feschotte", "user_profile_image"=>"http://pbs.twimg.com/profile_images/569002115591204864/yj39gyOv_normal.jpeg"}
• {"id"=>"681792816402554880", "text"=>"@arztdiego @neil_bodie EVEs and Ebola: first paper is here https://t.co/k8wpIGKOd8", "created_at"=>"2015-12-29T11:04:09Z", "user"=>"edrybicki", "user_name"=>"Ed Rybicki", "user_profile_image"=>"http://pbs.twimg.com/profile_images/946568031/ed_2010_normal.jpg"}
• {"id"=>"681818942541725697", "text"=>"RT @edrybicki: @arztdiego @neil_bodie EVEs and Ebola: first paper is here https://t.co/k8wpIGKOd8", "created_at"=>"2015-12-29T12:47:58Z", "user"=>"neil_bodie", "user_name"=>"Dr Neil Bodie", "user_profile_image"=>"http://pbs.twimg.com/profile_images/649319320024027136/qlk84JWD_normal.jpg"}
• {"id"=>"708184469438476289", "text"=>"Retroviruses. \"The vast majority of EVE insertions never reach fixation.\"\nhttps://t.co/DSDYxH8jmc", "created_at"=>"2016-03-11T06:55:09Z", "user"=>"TenFleming", "user_name"=>"Nigel Ten Fleming", "user_profile_image"=>"http://pbs.twimg.com/profile_images/549466594175619073/smi3zKQq_normal.jpeg"}
• {"id"=>"708184662762389504", "text"=>"Retroviruses: \"there are likely many unfixed EVEs present within species gene pools at a given time.\"\nhttps://t.co/DSDYxH8jmc", "created_at"=>"2016-03-11T06:55:55Z", "user"=>"TenFleming", "user_name"=>"Nigel Ten Fleming", "user_profile_image"=>"http://pbs.twimg.com/profile_images/549466594175619073/smi3zKQq_normal.jpeg"}
• {"id"=>"708185241815359488", "text"=>"Unfixed Retroviruse examples: Israeli acute paralysis virus (IAPPV) insertions in honey bees.\"\nhttps://t.co/DSDYxH8jmc", "created_at"=>"2016-03-11T06:58:13Z", "user"=>"TenFleming", "user_name"=>"Nigel Ten Fleming", "user_profile_image"=>"http://pbs.twimg.com/profile_images/549466594175619073/smi3zKQq_normal.jpeg"}
• {"id"=>"708185362716184576", "text"=>"Unfixed Retroviruse examples: koala endogenous retrovirus (KoRV) in koala bears.\nhttps://t.co/DSDYxH8jmc", "created_at"=>"2016-03-11T06:58:42Z", "user"=>"TenFleming", "user_name"=>"Nigel Ten Fleming", "user_profile_image"=>"http://pbs.twimg.com/profile_images/549466594175619073/smi3zKQq_normal.jpeg"}
• {"id"=>"708185451119529984", "text"=>"Unfixed Retroviruse examples: human herpesvirus 6 (HHV-6); HERV-K HML-2 insertions in humans.\nhttps://t.co/DSDYxH8jmc", "created_at"=>"2016-03-11T06:59:03Z", "user"=>"TenFleming", "user_name"=>"Nigel Ten Fleming", "user_profile_image"=>"http://pbs.twimg.com/profile_images/549466594175619073/smi3zKQq_normal.jpeg"}
• {"id"=>"708186063634698240", "text"=>"\"Viral infection of germ line cells...can lead to viral genes...inherited as host alleles.\"\nhttps://t.co/DSDYxH8jmc", "created_at"=>"2016-03-11T07:01:29Z", "user"=>"TenFleming", "user_name"=>"Nigel Ten Fleming", "user_profile_image"=>"http://pbs.twimg.com/profile_images/549466594175619073/smi3zKQq_normal.jpeg"}
• {"id"=>"708186355562455041", "text"=>"Viral infection in germ line cells are called endogenous viral elements (EVEs)\nhttps://t.co/DSDYxH8jmc", "created_at"=>"2016-03-11T07:02:39Z", "user"=>"TenFleming", "user_name"=>"Nigel Ten Fleming", "user_profile_image"=>"http://pbs.twimg.com/profile_images/549466594175619073/smi3zKQq_normal.jpeg"}
• {"id"=>"708186511003418624", "text"=>"EVEs \"are usually eliminated from the host gene pool within a small number of generations.\"\nhttps://t.co/DSDYxH8jmc", "created_at"=>"2016-03-11T07:03:16Z", "user"=>"TenFleming", "user_name"=>"Nigel Ten Fleming", "user_profile_image"=>"http://pbs.twimg.com/profile_images/549466594175619073/smi3zKQq_normal.jpeg"}
• {"id"=>"708186604490240001", "text"=>"EVEs \"can also increase in frequency, and some eventually reach fixation.\"\nhttps://t.co/DSDYxH8jmc", "created_at"=>"2016-03-11T07:03:38Z", "user"=>"TenFleming", "user_name"=>"Nigel Ten Fleming", "user_profile_image"=>"http://pbs.twimg.com/profile_images/549466594175619073/smi3zKQq_normal.jpeg"}
• {"id"=>"709245152146100225", "text"=>"Endogenous viral elements (EVEs).\nhttps://t.co/DSDYxGQIuE", "created_at"=>"2016-03-14T05:09:56Z", "user"=>"TenFleming", "user_name"=>"Nigel Ten Fleming", "user_profile_image"=>"http://pbs.twimg.com/profile_images/549466594175619073/smi3zKQq_normal.jpeg"}
• {"id"=>"709245343511257088", "text"=>"\"In animal genomes, the majority of EVEs are derived from reverse transcribing RNA (rtRNA) viruses.\"\nhttps://t.co/DSDYxGQIuE", "created_at"=>"2016-03-14T05:10:41Z", "user"=>"TenFleming", "user_name"=>"Nigel Ten Fleming", "user_profile_image"=>"http://pbs.twimg.com/profile_images/549466594175619073/smi3zKQq_normal.jpeg"}
• {"id"=>"709245730720972800", "text"=>"\"Retroviruses are the only animal viruses that integrate into the genome of the host cell as an obligate step.\"\nhttps://t.co/DSDYxGQIuE", "created_at"=>"2016-03-14T05:12:14Z", "user"=>"TenFleming", "user_name"=>"Nigel Ten Fleming", "user_profile_image"=>"http://pbs.twimg.com/profile_images/549466594175619073/smi3zKQq_normal.jpeg"}
• {"id"=>"709245832806207489", "text"=>"\"Retroviruses...are thus predisposed to enter the host germ line.\"\nhttps://t.co/DSDYxGQIuE", "created_at"=>"2016-03-14T05:12:38Z", "user"=>"TenFleming", "user_name"=>"Nigel Ten Fleming", "user_profile_image"=>"http://pbs.twimg.com/profile_images/549466594175619073/smi3zKQq_normal.jpeg"}
• {"id"=>"709246558794096640", "text"=>"\"We identified a large and diverse population of sequences in animal genomes...derived from non-retroviral viruses.\"\nhttps://t.co/DSDYxGQIuE", "created_at"=>"2016-03-14T05:15:31Z", "user"=>"TenFleming", "user_name"=>"Nigel Ten Fleming", "user_profile_image"=>"http://pbs.twimg.com/profile_images/549466594175619073/smi3zKQq_normal.jpeg"}
• {"id"=>"709246766365941760", "text"=>"\"Non-retroviral genome invasion ranging back to at least the late Mesozoic Era (?93 million years ago).\"\nhttps://t.co/DSDYxGQIuE", "created_at"=>"2016-03-14T05:16:20Z", "user"=>"TenFleming", "user_name"=>"Nigel Ten Fleming", "user_profile_image"=>"http://pbs.twimg.com/profile_images/549466594175619073/smi3zKQq_normal.jpeg"}
• {"id"=>"709247657286488064", "text"=>"\"Non-retroviral mammalian virus groups occur as endogenous elements in the genomes of...vectors.\"\nhttps://t.co/DSDYxGQIuE", "created_at"=>"2016-03-14T05:19:53Z", "user"=>"TenFleming", "user_name"=>"Nigel Ten Fleming", "user_profile_image"=>"http://pbs.twimg.com/profile_images/549466594175619073/smi3zKQq_normal.jpeg"}
• {"id"=>"709247801641803776", "text"=>"\"We describe the first EVEs derived from the rtDNA and dsRNA groups.\"\nhttps://t.co/DSDYxGQIuE", "created_at"=>"2016-03-14T05:20:27Z", "user"=>"TenFleming", "user_name"=>"Nigel Ten Fleming", "user_profile_image"=>"http://pbs.twimg.com/profile_images/549466594175619073/smi3zKQq_normal.jpeg"}
• {"id"=>"709248160506454016", "text"=>"\"The complete range of known animal virus replication strategies are represented\" by EVEs in animal genomes.\nhttps://t.co/DSDYxGQIuE", "created_at"=>"2016-03-14T05:21:53Z", "user"=>"TenFleming", "user_name"=>"Nigel Ten Fleming", "user_profile_image"=>"http://pbs.twimg.com/profile_images/549466594175619073/smi3zKQq_normal.jpeg"}
• {"id"=>"709248906111148034", "text"=>"\"The functionality of one of these sequences has been maintained in the host genome over many millions of years.\"\nhttps://t.co/DSDYxGQIuE", "created_at"=>"2016-03-14T05:24:51Z", "user"=>"TenFleming", "user_name"=>"Nigel Ten Fleming", "user_profile_image"=>"http://pbs.twimg.com/profile_images/549466594175619073/smi3zKQq_normal.jpeg"}
• {"id"=>"709249081059753984", "text"=>"\"The possibility that captured viral sequences may have played a larger than expected role in host evolution.\"\nhttps://t.co/DSDYxGQIuE", "created_at"=>"2016-03-14T05:25:32Z", "user"=>"TenFleming", "user_name"=>"Nigel Ten Fleming", "user_profile_image"=>"http://pbs.twimg.com/profile_images/549466594175619073/smi3zKQq_normal.jpeg"}
• {"id"=>"709249420072783873", "text"=>"\"Endogenous retroviruses have shaped vertebrate genome evolution.\"\nhttps://t.co/DSDYxGQIuE", "created_at"=>"2016-03-14T05:26:53Z", "user"=>"TenFleming", "user_name"=>"Nigel Ten Fleming", "user_profile_image"=>"http://pbs.twimg.com/profile_images/549466594175619073/smi3zKQq_normal.jpeg"}
• {"id"=>"709249691716886528", "text"=>"Endogenous retroviruses have acted \"as genetic parasites\"\nhttps://t.co/DSDYxGQIuE", "created_at"=>"2016-03-14T05:27:58Z", "user"=>"TenFleming", "user_name"=>"Nigel Ten Fleming", "user_profile_image"=>"http://pbs.twimg.com/profile_images/549466594175619073/smi3zKQq_normal.jpeg"}
• {"id"=>"709249839226351616", "text"=>"Endogenous retroviruses have introduced \"useful genetic novelty.\" \nhttps://t.co/DSDYxGQIuE", "created_at"=>"2016-03-14T05:28:33Z", "user"=>"TenFleming", "user_name"=>"Nigel Ten Fleming", "user_profile_image"=>"http://pbs.twimg.com/profile_images/549466594175619073/smi3zKQq_normal.jpeg"}
• {"id"=>"709607485116694528", "text"=>"\"The diverse EVE sequences...demonstrate an extensive history of gene flow from virus to animal genomes.\"\nhttps://t.co/DSDYxGQIuE", "created_at"=>"2016-03-15T05:09:42Z", "user"=>"TenFleming", "user_name"=>"Nigel Ten Fleming", "user_profile_image"=>"http://pbs.twimg.com/profile_images/549466594175619073/smi3zKQq_normal.jpeg"}
• {"id"=>"709607562409336832", "text"=>"\"Animal genomes are a living document of virus and host interaction.\" \nhttps://t.co/DSDYxGQIuE", "created_at"=>"2016-03-15T05:10:01Z", "user"=>"TenFleming", "user_name"=>"Nigel Ten Fleming", "user_profile_image"=>"http://pbs.twimg.com/profile_images/549466594175619073/smi3zKQq_normal.jpeg"}
• {"id"=>"709608231124013056", "text"=>"EVEs \"that are neutral or only slightly deleterious in their hosts may fortuitously drift or hitchhike to fixation.\"\nhttps://t.co/DSDYxGQIuE", "created_at"=>"2016-03-15T05:12:40Z", "user"=>"TenFleming", "user_name"=>"Nigel Ten Fleming", "user_profile_image"=>"http://pbs.twimg.com/profile_images/549466594175619073/smi3zKQq_normal.jpeg"}
• {"id"=>"709608351794130944", "text"=>"\"EVE insertions may confer an advantageous phenotype on the host and spread through the population by selection.\"\nhttps://t.co/DSDYxGQIuE", "created_at"=>"2016-03-15T05:13:09Z", "user"=>"TenFleming", "user_name"=>"Nigel Ten Fleming", "user_profile_image"=>"http://pbs.twimg.com/profile_images/549466594175619073/smi3zKQq_normal.jpeg"}
• {"id"=>"709609053627027457", "text"=>"\"In animal genomes, the majority of EVEs are derived from reverse transcribing...retroviruses.\"\nhttps://t.co/DSDYxGQIuE", "created_at"=>"2016-03-15T05:15:56Z", "user"=>"TenFleming", "user_name"=>"Nigel Ten Fleming", "user_profile_image"=>"http://pbs.twimg.com/profile_images/549466594175619073/smi3zKQq_normal.jpeg"}
• {"id"=>"709609230253297664", "text"=>"\"Retroviruses are the only animal viruses that integrate into the genome of the host cell as an obligate step.\"\nhttps://t.co/DSDYxGQIuE", "created_at"=>"2016-03-15T05:16:39Z", "user"=>"TenFleming", "user_name"=>"Nigel Ten Fleming", "user_profile_image"=>"http://pbs.twimg.com/profile_images/549466594175619073/smi3zKQq_normal.jpeg"}
• {"id"=>"709609337925345280", "text"=>"\"Retroviruses...are thus predisposed to enter the host germ line.\"\nhttps://t.co/DSDYxGQIuE", "created_at"=>"2016-03-15T05:17:04Z", "user"=>"TenFleming", "user_name"=>"Nigel Ten Fleming", "user_profile_image"=>"http://pbs.twimg.com/profile_images/549466594175619073/smi3zKQq_normal.jpeg"}
• {"id"=>"710328559592669187", "text"=>"\"A broad range of viruses are represented by EVEs in animal genomes.\"\nhttps://t.co/DSDYxGQIuE", "created_at"=>"2016-03-17T04:55:00Z", "user"=>"TenFleming", "user_name"=>"Nigel Ten Fleming", "user_profile_image"=>"http://pbs.twimg.com/profile_images/549466594175619073/smi3zKQq_normal.jpeg"}
• {"id"=>"710328725804601345", "text"=>"\"Viral ‘molecular fossils’ can provide the basis for robust, time-scaled, macroevolutionary studies.\"\nhttps://t.co/DSDYxGQIuE", "created_at"=>"2016-03-17T04:55:40Z", "user"=>"TenFleming", "user_name"=>"Nigel Ten Fleming", "user_profile_image"=>"http://pbs.twimg.com/profile_images/549466594175619073/smi3zKQq_normal.jpeg"}
• {"id"=>"711787196055994368", "text"=>"\"Retroviruses are unique amongst animal viruses in that integration occurs as an obligate step in replication.\"\nhttps://t.co/DSDYxGQIuE", "created_at"=>"2016-03-21T05:31:06Z", "user"=>"TenFleming", "user_name"=>"Nigel Ten Fleming", "user_profile_image"=>"http://pbs.twimg.com/profile_images/549466594175619073/smi3zKQq_normal.jpeg"}
• {"id"=>"711787377983930372", "text"=>"\"For all other animal viruses integration occurs anomalously.\"\nhttps://t.co/DSDYxGQIuE", "created_at"=>"2016-03-21T05:31:49Z", "user"=>"TenFleming", "user_name"=>"Nigel Ten Fleming", "user_profile_image"=>"http://pbs.twimg.com/profile_images/549466594175619073/smi3zKQq_normal.jpeg"}
• {"id"=>"711787605076123648", "text"=>"\"For all other animal viruses integration occurs...through interaction with cellular retroelements such as LINEs.\"\nhttps://t.co/DSDYxGQIuE", "created_at"=>"2016-03-21T05:32:44Z", "user"=>"TenFleming", "user_name"=>"Nigel Ten Fleming", "user_profile_image"=>"http://pbs.twimg.com/profile_images/549466594175619073/smi3zKQq_normal.jpeg"}
• {"id"=>"711787702497243136", "text"=>"\"For all other animal viruses integration occurs...via non-homologous recombination with genomic DNA.\"\nhttps://t.co/DSDYxGQIuE", "created_at"=>"2016-03-21T05:33:07Z", "user"=>"TenFleming", "user_name"=>"Nigel Ten Fleming", "user_profile_image"=>"http://pbs.twimg.com/profile_images/549466594175619073/smi3zKQq_normal.jpeg"}
• {"id"=>"715397869612572673", "text"=>"\"The presence of retrovirus sequences in animal genomes has been recognized since the 1970s.\"\nhttps://t.co/DSDYxH8jmc", "created_at"=>"2016-03-31T04:38:38Z", "user"=>"TenFleming", "user_name"=>"Nigel Ten Fleming", "user_profile_image"=>"http://pbs.twimg.com/profile_images/549466594175619073/smi3zKQq_normal.jpeg"}
• {"id"=>"715398276980219905", "text"=>"\"A large and diverse population of sequences in animal genomes that are derived from non-retroviral viruses.\"\nhttps://t.co/DSDYxH8jmc", "created_at"=>"2016-03-31T04:40:15Z", "user"=>"TenFleming", "user_name"=>"Nigel Ten Fleming", "user_profile_image"=>"http://pbs.twimg.com/profile_images/549466594175619073/smi3zKQq_normal.jpeg"}
• {"id"=>"730178170503172098", "text"=>"An endogenous viral element (EVE) is a genomic DNA sequence derived from a virus. https://t.co/eYGXDvtrqa", "created_at"=>"2016-05-10T23:30:16Z", "user"=>"DIGS_for_EVEs", "user_name"=>"DIGS for EVEs", "user_profile_image"=>"http://pbs.twimg.com/profile_images/730003035196432384/ZgzSPH5k_normal.jpg"}
• {"id"=>"730455166294605825", "text"=>"Seems the bornavirus matrix EVE in the aye-aye is orthologous to the one previously described in the mouse lemur... https://t.co/eYGXDvtrqa", "created_at"=>"2016-05-11T17:50:57Z", "user"=>"DIGS_for_EVEs", "user_name"=>"DIGS for EVEs", "user_profile_image"=>"http://pbs.twimg.com/profile_images/730003035196432384/ZgzSPH5k_normal.jpg"}
• {"id"=>"731067310971228160", "text"=>"A #circovirus-derived EVE in the genomes of carnivores has been reported previously: https://t.co/66bT5pnVGK https://t.co/7yBVVPs1SR", "created_at"=>"2016-05-13T10:23:24Z", "user"=>"DIGS_for_EVEs", "user_name"=>"DIGS for EVEs", "user_profile_image"=>"http://pbs.twimg.com/profile_images/730003035196432384/ZgzSPH5k_normal.jpg"}

Wikipedia | Further Information

• {"title"=>"Paleovirology", "url"=>"http://en.wikipedia.org/wiki/Paleovirology", "timestamp"=>"2018-10-09T08:53:26Z"}
• {"title"=>"Endogenous viral element", "url"=>"http://en.wikipedia.org/wiki/Endogenous_viral_element", "timestamp"=>"2019-02-21T13:04:46Z"}
• {"title"=>"Mononegavirales", "url"=>"http://en.wikipedia.org/wiki/Mononegavirales", "timestamp"=>"2019-02-11T23:53:21Z"}
• {"title"=>"Filoviridae", "url"=>"http://en.wikipedia.org/wiki/Filoviridae", "timestamp"=>"2019-02-06T22:33:23Z"}
• {"title"=>"Paléovirologie", "url"=>"http://fr.wikipedia.org/wiki/Paléovirologie", "timestamp"=>"2018-06-01T17:09:12Z"}
• {"title"=>"Elemento viral endógeno", "url"=>"http://es.wikipedia.org/wiki/Elemento_viral_endógeno", "timestamp"=>"2017-09-01T00:52:56Z"}
• {"title"=>"Paleovirología", "url"=>"http://es.wikipedia.org/wiki/Paleovirología", "timestamp"=>"2017-08-31T23:22:30Z"}
• {"title"=>"Célula germinal", "url"=>"http://es.wikipedia.org/wiki/Célula_germinal", "timestamp"=>"2019-03-02T17:49:10Z"}
• {"title"=>"内在性ウイルス様配列", "url"=>"http://ja.wikipedia.org/wiki/内在性ウイルス様配列", "timestamp"=>"2019-01-20T02:02:56Z"}
• {"title"=>"عنصر فيروسي ذاتي", "url"=>"http://ar.wikipedia.org/wiki/عنصر_فيروسي_ذاتي", "timestamp"=>"2018-04-10T08:01:22Z"}
• {"title"=>"File:Endogenous-Viral-Elements-in-Animal-Genomes-pgen.1001191.g007.jpg", "url"=>"http://commons.wikimedia.org/wiki/File:Endogenous-Viral-Elements-in-Animal-Genomes-pgen.1001191.g007.jpg", "timestamp"=>"2018-01-04T04:53:18Z"}
• {"title"=>"File:Endogenous-Viral-Elements-in-Animal-Genomes-pgen.1001191.g003.jpg", "url"=>"http://commons.wikimedia.org/wiki/File:Endogenous-Viral-Elements-in-Animal-Genomes-pgen.1001191.g003.jpg", "timestamp"=>"2018-01-04T04:53:14Z"}
• {"title"=>"File:Endogenous-Viral-Elements-in-Animal-Genomes-pgen.1001191.g002.jpg", "url"=>"http://commons.wikimedia.org/wiki/File:Endogenous-Viral-Elements-in-Animal-Genomes-pgen.1001191.g002.jpg", "timestamp"=>"2018-01-04T04:53:13Z"}
• {"title"=>"File:Endogenous-Viral-Elements-in-Animal-Genomes-pgen.1001191.g006.jpg", "url"=>"http://commons.wikimedia.org/wiki/File:Endogenous-Viral-Elements-in-Animal-Genomes-pgen.1001191.g006.jpg", "timestamp"=>"2018-01-04T04:53:17Z"}
• {"title"=>"File:Endogenous-Viral-Elements-in-Animal-Genomes-pgen.1001191.g004.jpg", "url"=>"http://commons.wikimedia.org/wiki/File:Endogenous-Viral-Elements-in-Animal-Genomes-pgen.1001191.g004.jpg", "timestamp"=>"2018-02-14T20:02:59Z"}
• {"title"=>"File:Endogenous-Viral-Elements-in-Animal-Genomes-pgen.1001191.g005.jpg", "url"=>"http://commons.wikimedia.org/wiki/File:Endogenous-Viral-Elements-in-Animal-Genomes-pgen.1001191.g005.jpg", "timestamp"=>"2018-01-04T04:53:16Z"}
• {"title"=>"File:Endogenous-Viral-Elements-in-Animal-Genomes-pgen.1001191.g001.jpg", "url"=>"http://commons.wikimedia.org/wiki/File:Endogenous-Viral-Elements-in-Animal-Genomes-pgen.1001191.g001.jpg", "timestamp"=>"2018-01-04T04:53:12Z"}

Wordpress.com | Further Information

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Figshare

• {"files"=>["https://ndownloader.figshare.com/files/407586", "https://ndownloader.figshare.com/files/407634", "https://ndownloader.figshare.com/files/407717", "https://ndownloader.figshare.com/files/407791", "https://ndownloader.figshare.com/files/407817", "https://ndownloader.figshare.com/files/407853", "https://ndownloader.figshare.com/files/407908", "https://ndownloader.figshare.com/files/407928", "https://ndownloader.figshare.com/files/407949", "https://ndownloader.figshare.com/files/407977"], "description"=>"<div><p>Integration into the nuclear genome of germ line cells can lead to vertical inheritance of retroviral genes as host alleles. For other viruses, germ line integration has only rarely been documented. Nonetheless, we identified endogenous viral elements (EVEs) derived from ten non-retroviral families by systematic <em>in silico</em> screening of animal genomes, including the first endogenous representatives of double-stranded RNA, reverse-transcribing DNA, and segmented RNA viruses, and the first endogenous DNA viruses in mammalian genomes. Phylogenetic and genomic analysis of EVEs across multiple host species revealed novel information about the origin and evolution of diverse virus groups. Furthermore, several of the elements identified here encode intact open reading frames or are expressed as mRNA. For one element in the primate lineage, we provide statistically robust evidence for exaptation. Our findings establish that genetic material derived from all known viral genome types and replication strategies can enter the animal germ line, greatly broadening the scope of paleovirological studies and indicating a more significant evolutionary role for gene flow from virus to animal genomes than has previously been recognized.</p></div>", "links"=>[], "tags"=>["endogenous", "viral", "elements", "genomes"], "article_id"=>140521, "categories"=>["Evolutionary Biology", "Cancer"], "users"=>["Aris Katzourakis", "Robert J. Gifford"], "doi"=>["https://dx.doi.org/10.1371/journal.pgen.1001191.s001", "https://dx.doi.org/10.1371/journal.pgen.1001191.s002", "https://dx.doi.org/10.1371/journal.pgen.1001191.s003", "https://dx.doi.org/10.1371/journal.pgen.1001191.s004", "https://dx.doi.org/10.1371/journal.pgen.1001191.s005", "https://dx.doi.org/10.1371/journal.pgen.1001191.s006", "https://dx.doi.org/10.1371/journal.pgen.1001191.s007", "https://dx.doi.org/10.1371/journal.pgen.1001191.s008", "https://dx.doi.org/10.1371/journal.pgen.1001191.s009", "https://dx.doi.org/10.1371/journal.pgen.1001191.s010"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Endogenous_Viral_Elements_in_Animal_Genomes/140521", "title"=>"Endogenous Viral Elements in Animal Genomes", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2010-11-18 00:08:41"}
• {"files"=>["https://ndownloader.figshare.com/files/816906"], "description"=>"<p>Animal viruses exhibit a range of genome types and replication strategies. While all viruses must produce mRNA in order to express proteins, steps between entry into the cell and the expression of mRNA vary greatly. Examples of the known animal virus replication strategies are shown to the left of the figure, with the representative families listed for each case. Arrows indicate steps in replication. Red lines indicate pathways that lead to viral genetic material becoming integrated into the nuclear genome of the host cell. Retroviruses are unique amongst animal viruses in that integration occurs as an obligate step in replication. For all other animal viruses integration occurs anomalously, through interaction with cellular retroelements such as LINEs, or via non-homologous recombination with genomic DNA. If integration occurs in a germ line cell that goes on to develop into a viable host organism, an EVE is formed. Green lines show the evolution of an EVE in its host lineage. In the example given, the EVE reaches genetic fixation at the point indicated, and is inherited by all descendant hosts thereafter. Assuming that insertion occurs randomly, the presence of related EVEs at the same locus in both descendant species A and B indicates that insertion occurred prior to their divergence, allowing a minimum age for the insertion to be inferred from the estimated timescale of their evolution. Conversely, the presence of an empty insertion site in species C provides a maximum age for the insertion. Abbreviations: dsDNA (double stranded DNA); ssDNA (single stranded DNA, dsRNA (double stranded RNA); RNA-ve (negative sense, single stranded RNA); RNA-ve (negative sense, single stranded RNA); RNA+ve (positive sense, single stranded RNA).</p>", "links"=>[], "tags"=>["replication", "endogenous", "viral", "genomic", "fossil"], "article_id"=>487273, "categories"=>["Evolutionary Biology", "Infectious Diseases"], "users"=>["Aris Katzourakis", "Robert J. Gifford"], "doi"=>["https://dx.doi.org/10.1371/journal.pgen.1001191.g001"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Viral_replication_strategies_endogenous_viral_elements_and_the_genomic_fossil_record_/487273", "title"=>"Viral replication strategies, endogenous viral elements, and the genomic fossil record.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2010-11-18 02:01:13"}
• {"files"=>["https://ndownloader.figshare.com/files/816990"], "description"=>"<p>(a) Summary genetic structures of Mononegavirus EVE sets (<i>Borna</i>-, <i>Rhabdo</i>- and <i>Filoviridae</i>) shown relative to genus type species. The most intact elements are shown for each host taxon. Vertical lines between EVEs in the same host species that are derived from distinct genes indicate that the EVEs are not contiguous in the host genome. Abbreviations for viral type species (bold), host species (italics), and host taxa (bold, italic, underline) are indicated to the left of each EVE. Taxonomic groups are shown for EVE insertions identified as orthologs. Poly-A tails are shown for EVEs that had these features. Intact ORFs (circles) and expressed sequences (crosses) are indicated. Phylogenetic relationships of (b) bornavirus, (c) rhabdovirus and (d) filovirus EVEs and representative exogenous viruses. Taxa that are shown as genetic structures in (a) are indicated by colored squares. Support for the ML phylogenetic trees was evaluated using 1,000 nonparametric bootstrap replicates, and all three trees are midpoint rooted for display purposes. Abbreviations: BDV = Borna disease virus; ZEBOV = Zaire ebola virus; VSV = vesicular stomatitis virus, L-pol = L-polymerase.</p>", "links"=>[], "tags"=>["structures", "phylogenetic", "relationships", "mononegavirus"], "article_id"=>487357, "categories"=>["Evolutionary Biology", "Infectious Diseases"], "users"=>["Aris Katzourakis", "Robert J. Gifford"], "doi"=>["https://dx.doi.org/10.1371/journal.pgen.1001191.g002"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Genetic_structures_and_phylogenetic_relationships_of_Mononegavirus_EVEs_/487357", "title"=>"Genetic structures and phylogenetic relationships of Mononegavirus EVEs.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2010-11-18 02:02:37"}
• {"files"=>["https://ndownloader.figshare.com/files/817069"], "description"=>"<p>Summary genetic structures of EVEs derived from segmented RNA viruses (a) <i>Reoviridae</i> (Seadornavirus genus), (b) <i>Orthomyxoviridae</i> (Quarjavirus genus), (c) <i>Bunyaviridae</i> (Nairovirus and Phlebovirus genera)) shown relative to the genus type species. The most intact elements are shown for each host taxon. Intact ORFs (circles) and expressed sequences (crosses) are indicated. Maximum likelihood phylogenies of EVEs and exogenous viruses are shown; (d) <i>Reoviridae</i> (segment 5) (e) <i>Orthomyxoviridae</i> (GP), (f) Nairovirus (NP) (g) Phlebovirus (NP) Colored boxes indicate taxa that are shown as genetic structures in panels a-c. Support for trees was evaluated using 1,000 nonparametric bootstrap replicates. Abbreviations: LNV = Liaoning virus; CCHF = Crimean-Congo hemorrhagic fever virus; UUKV = Uukuniemi virus; QRFV = Quaranfil virus.</p>", "links"=>[], "tags"=>["structures", "phylogenetic", "relationships", "eves", "segmented", "rna"], "article_id"=>487433, "categories"=>["Evolutionary Biology", "Infectious Diseases"], "users"=>["Aris Katzourakis", "Robert J. Gifford"], "doi"=>["https://dx.doi.org/10.1371/journal.pgen.1001191.g003"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Genetic_structures_and_phylogenetic_relationships_of_EVEs_related_to_segmented_RNA_viruses_/487433", "title"=>"Genetic structures and phylogenetic relationships of EVEs related to segmented RNA viruses.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2010-11-18 02:03:53"}
• {"files"=>["https://ndownloader.figshare.com/files/817138"], "description"=>"<p>(a) Genetic structures of non-overlapping flavivirus EVEs in the <i>Aedes aegyptii</i> genome. (b) Phylogenetic relationship of consensus flavivirus EVE sequences (spanning most of the region shown in (a) with exogenous and endogenous flaviruses. (c) Genetic structures of non-overlapping rtDNA (hepadnavirus) EVEs shown relative to the genus type species. Numbers to the left indicate the <i>T. guttata</i> chromosome on which the EVE is present. (d) Phylogenetic relationships of consensus zebrafinch EVEs and representative exogenous viruses. Avihepadnavirus genus is rooted on Woodchuck HBV (Orthohepadnavirus). All ML phylogenetic trees were inferred from amino acid alignments using the best-fitting model of evolution. Support for trees was evaluated using 1,000 nonparametric bootstrap replicates. Abbreviations: KRV = Kamiti River virus, HBV = hepatitis B virus, dHBV = duck hepatitis B virus.</p>", "links"=>[], "tags"=>["structures", "phylogenetic", "relationships", "eves", "flaviviruses"], "article_id"=>487506, "categories"=>["Evolutionary Biology", "Infectious Diseases"], "users"=>["Aris Katzourakis", "Robert J. Gifford"], "doi"=>["https://dx.doi.org/10.1371/journal.pgen.1001191.g004"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Genetic_structures_and_phylogenetic_relationships_of_EVEs_related_to_flaviviruses_and_hepadnaviruses_/487506", "title"=>"Genetic structures and phylogenetic relationships of EVEs related to flaviviruses and hepadnaviruses.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2010-11-18 02:05:06"}
• {"files"=>["https://ndownloader.figshare.com/files/817240"], "description"=>"<p>(a) Summary genetic structures of ssDNA EVE sets shown relative to the genus type species. The most intact elements are shown for each host taxon. EVE hosts (bold) and abbreviations for viral type species (bold, underline), and the total number of matches identified (italic) are indicated to the left of each EVE structure. Bars behind ORFs indicate non-coding viral DNA. Intact ORFs (circles) and expressed sequences (crosses) are indicated. ¹ The <i>M. lucifugus</i> element is a composite of two genomic contigs; ² Structures represent a composite of semi-overlapping fragments; ³ Element has undergone genomic rearrangements, with the arrow indicating the direction of the rearranged fragment. (b) Phylogenetic relationships of dependovirus EVEs and representative exogenous viruses, based on NS1 gene and rooted on snake parvovirus. A dolphin EVE (indicated by an asterisk) groups robustly with avian rather than mammalian isolates. (d) Phylogenetic relationships of parvovirus EVEs and representative exogenous viruses, based on NS1 gene and rooted on Aleutian mink disease virus. Support for both ML phylogenetic trees was evaluated using 1,000 nonparametric bootstrap replicates. EVEs potentially comprising a new genus are indicated. (d) Phylogenetic relationships of circovirus EVEs and representative exogenous viruses, based on the Rep gene and rooted on avian circoviruses, with support for the ML phylogenetic tree evaluated using 1,000 nonparametric bootstrap replicates. Taxa that are shown as genetic structures in (a) are indicated by colored squares (EVEs) and circles (exogenous viruses) (a). Abbreviations: AAV = adeno-associated virus; MMV = minute virus of mice, AMDV = Aleutian mink disease virus, PV = parvovirus, CV = circovirus, PCV = porcine circovirus; HSAV =  Human stool-associated circular virus.</p>", "links"=>[], "tags"=>["structures", "phylogenetic", "relationships", "eves", "ssdna"], "article_id"=>487610, "categories"=>["Evolutionary Biology", "Infectious Diseases"], "users"=>["Aris Katzourakis", "Robert J. Gifford"], "doi"=>["https://dx.doi.org/10.1371/journal.pgen.1001191.g005"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Genetic_structures_and_phylogenetic_relationships_of_EVEs_related_to_ssDNA_viruses_/487610", "title"=>"Genetic structures and phylogenetic relationships of EVEs related to ssDNA viruses.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2010-11-18 02:06:50"}
• {"files"=>["https://ndownloader.figshare.com/files/817345"], "description"=>"<p>Grey circles indicate nodes at which orthologous EVE insertions were identified. For all orthologous insertions identified here and elsewhere <a href=\"http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1001191#pgen.1001191-Horie1\" target=\"_blank\">[11]</a>, <a href=\"http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1001191#pgen.1001191-Taylor2\" target=\"_blank\">[22]</a>, the virus family and genomic region represented by the ortholog is shown. Abbreviation: TLS = Thirteen-lined ground squirrel.</p>", "links"=>[], "tags"=>["phylogenetic", "mammals", "screened", "bininda-emonds", "eves", "exogenous"], "article_id"=>487717, "categories"=>["Evolutionary Biology", "Infectious Diseases"], "users"=>["Aris Katzourakis", "Robert J. Gifford"], "doi"=>["https://dx.doi.org/10.1371/journal.pgen.1001191.g006"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Timescaled_phylogenetic_tree_of_mammals_screened_in_this_study_after_Bininda_Emonds_et_al_42_showing_the_known_distribution_of_EVEs_and_of_exogenous_Borna_Filo_Circo_and_Parvoviruses_/487717", "title"=>"Timescaled phylogenetic tree of mammals screened in this study (after Bininda-Emonds <i>et al</i>[<b>42</b>]) showing the known distribution of EVEs and of exogenous Borna-, Filo-, Circo-, and Parvoviruses.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2010-11-18 02:08:37"}
• {"files"=>["https://ndownloader.figshare.com/files/817440"], "description"=>"<p>(a) The primate clade marked by an asterisk in the phylogeny shown in <a href=\"http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1001191#pgen-1001191-g006\" target=\"_blank\">Figure 6</a> is shown in greater detail here, with the number of stop codons in the EBLN-1 locus indicated for seven species. Orthology across these species indicates that EBLN-1 predates the divergence of these species 54 million years ago <a href=\"http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1001191#pgen.1001191-BinindaEmonds1\" target=\"_blank\">[42]</a>. Monte Carlo simulations in which a consensus EBLN sequence was allowed to neutrally evolve at the primate neutral rate for this length of time showed that the average number of stop codons expected after this time is fifteen. (b) The distribution of the number of stop codons from 100,000 simulation replicates. Confidence intervals are indicated.</p>", "links"=>[], "tags"=>["ebln", "elements"], "article_id"=>487807, "categories"=>["Evolutionary Biology", "Infectious Diseases"], "users"=>["Aris Katzourakis", "Robert J. Gifford"], "doi"=>["https://dx.doi.org/10.1371/journal.pgen.1001191.g007"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Evolution_of_EBLN_elements_in_primates_/487807", "title"=>"Evolution of EBLN elements in primates.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2010-11-18 02:10:07"}
• {"files"=>["https://ndownloader.figshare.com/files/817513"], "description"=>"<p><b>Footnote:</b> Groups that have been reported as mediating their own integration are highlighted in bold. Asterisks denote families with representatives known to be capable of establishing persistent/latent infection. EVE insertions were considered to represent complete viral genomes or genes if more than 90% of the species-specific gene/genome was identified. Orthologous insertions in distinct species were not counted as distinct elements. Sequences that were identified by BLAST, but where the region used in phylogenetic trees did not match any viral sequences in reciprocal BLAST searches, were defined as unclassifiable. <i>^a</i> Numbers in parentheses indicate complete genomes.</p>", "links"=>[], "tags"=>["eves"], "article_id"=>487885, "categories"=>["Evolutionary Biology", "Infectious Diseases"], "users"=>["Aris Katzourakis", "Robert J. Gifford"], "doi"=>["https://dx.doi.org/10.1371/journal.pgen.1001191.t001"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Distribution_and_diversity_of_EVEs_identified_by_in_silico_screening_/487885", "title"=>"Distribution and diversity of EVEs identified by <i>in silico</i> screening.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2010-11-18 02:11:25"}

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F1000Prime