Unexpected Diversity and Expression of Avian Endogenous Retroviruses

ABSTRACT Endogenous retroviruses (ERVs) were identified and characterized in three avian genomes to gain insight into early retroviral evolution. Using the computer program RetroTector to detect relatively intact ERVs, we identified 500 ERVs in the chicken genome, 150 in the turkey genome, and 1,200...

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Autores principales:	Mohan Bolisetty, Jonas Blomberg, Farid Benachenhou, Göran Sperber, Karen Beemon
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Lenguaje:	EN
Publicado:	American Society for Microbiology 2012
Materias:	Microbiology QR1-502
Acceso en línea:	https://doaj.org/article/b5272b07cae244d6831d5f631919be75
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spelling	oai:doaj.org-article:b5272b07cae244d6831d5f631919be752021-11-15T15:39:12ZUnexpected Diversity and Expression of Avian Endogenous Retroviruses10.1128/mBio.00344-122150-7511https://doaj.org/article/b5272b07cae244d6831d5f631919be752012-11-01T00:00:00Zhttps://journals.asm.org/doi/10.1128/mBio.00344-12https://doaj.org/toc/2150-7511ABSTRACT Endogenous retroviruses (ERVs) were identified and characterized in three avian genomes to gain insight into early retroviral evolution. Using the computer program RetroTector to detect relatively intact ERVs, we identified 500 ERVs in the chicken genome, 150 in the turkey genome, and 1,200 in the zebra finch genome. Previous studies suggested that endogenous alpharetroviruses were present in chicken genomes. In this analysis, a small number of alpharetroviruses were seen in the chicken and turkey genomes; however, these were greatly outnumbered by beta-like, gamma-like, and alphabeta proviruses. While the avian ERVs belonged to the same major groups as mammalian ERVs, they were more heterogeneous. In particular, the beta-like viruses revealed an evolutionary continuum with the gradual acquisition and loss of betaretroviral markers and a transition from beta to alphabeta and then to alpharetroviruses. Thus, it appears that birds may resemble a melting pot for early ERV evolution. Many of the ERVs were integrated in clusters on chromosomes, often near centromeres. About 25% of the chicken ERVs were in or near cellular transcription units; this is nearly random. The majority of these integrations were in the sense orientation in introns. A higher-than-random number of integrations were >100 kb from the nearest gene. Deep-sequencing studies of chicken embryo fibroblasts revealed that about 20% of the 500 ERVs were transcribed and translated. A subset of these were also transcribed in vivo in chickens, showing tissue-specific patterns of expression. IMPORTANCE Studies of avian endogenous retroviruses (ERVs) have given us a glimpse of an earlier retroviral world. Three different classes of ERVs were observed with many features of mammalian retroviruses, as well as some important differences. Many avian ERVs were transcribed and translated.Mohan BolisettyJonas BlombergFarid BenachenhouGöran SperberKaren BeemonAmerican Society for MicrobiologyarticleMicrobiologyQR1-502ENmBio, Vol 3, Iss 5 (2012)
institution	DOAJ
collection	DOAJ
language	EN
topic	Microbiology QR1-502
spellingShingle	Microbiology QR1-502 Mohan Bolisetty Jonas Blomberg Farid Benachenhou Göran Sperber Karen Beemon Unexpected Diversity and Expression of Avian Endogenous Retroviruses
description	ABSTRACT Endogenous retroviruses (ERVs) were identified and characterized in three avian genomes to gain insight into early retroviral evolution. Using the computer program RetroTector to detect relatively intact ERVs, we identified 500 ERVs in the chicken genome, 150 in the turkey genome, and 1,200 in the zebra finch genome. Previous studies suggested that endogenous alpharetroviruses were present in chicken genomes. In this analysis, a small number of alpharetroviruses were seen in the chicken and turkey genomes; however, these were greatly outnumbered by beta-like, gamma-like, and alphabeta proviruses. While the avian ERVs belonged to the same major groups as mammalian ERVs, they were more heterogeneous. In particular, the beta-like viruses revealed an evolutionary continuum with the gradual acquisition and loss of betaretroviral markers and a transition from beta to alphabeta and then to alpharetroviruses. Thus, it appears that birds may resemble a melting pot for early ERV evolution. Many of the ERVs were integrated in clusters on chromosomes, often near centromeres. About 25% of the chicken ERVs were in or near cellular transcription units; this is nearly random. The majority of these integrations were in the sense orientation in introns. A higher-than-random number of integrations were >100 kb from the nearest gene. Deep-sequencing studies of chicken embryo fibroblasts revealed that about 20% of the 500 ERVs were transcribed and translated. A subset of these were also transcribed in vivo in chickens, showing tissue-specific patterns of expression. IMPORTANCE Studies of avian endogenous retroviruses (ERVs) have given us a glimpse of an earlier retroviral world. Three different classes of ERVs were observed with many features of mammalian retroviruses, as well as some important differences. Many avian ERVs were transcribed and translated.
format	article
author	Mohan Bolisetty Jonas Blomberg Farid Benachenhou Göran Sperber Karen Beemon
author_facet	Mohan Bolisetty Jonas Blomberg Farid Benachenhou Göran Sperber Karen Beemon
author_sort	Mohan Bolisetty
title	Unexpected Diversity and Expression of Avian Endogenous Retroviruses
title_short	Unexpected Diversity and Expression of Avian Endogenous Retroviruses
title_full	Unexpected Diversity and Expression of Avian Endogenous Retroviruses
title_fullStr	Unexpected Diversity and Expression of Avian Endogenous Retroviruses
title_full_unstemmed	Unexpected Diversity and Expression of Avian Endogenous Retroviruses
title_sort	unexpected diversity and expression of avian endogenous retroviruses
publisher	American Society for Microbiology
publishDate	2012
url	https://doaj.org/article/b5272b07cae244d6831d5f631919be75
work_keys_str_mv	AT mohanbolisetty unexpecteddiversityandexpressionofavianendogenousretroviruses AT jonasblomberg unexpecteddiversityandexpressionofavianendogenousretroviruses AT faridbenachenhou unexpecteddiversityandexpressionofavianendogenousretroviruses AT goransperber unexpecteddiversityandexpressionofavianendogenousretroviruses AT karenbeemon unexpecteddiversityandexpressionofavianendogenousretroviruses
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Unexpected Diversity and Expression of Avian Endogenous Retroviruses

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