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Origin and Deep Evolution of Human Endogenous Retroviruses in Pan-Primates

Human endogenous retroviruses (HERVs) are viral “fossils” in the human genome that originated from the ancient integration of exogenous retroviruses. Although HERVs have sporadically been reported in nonhuman primate genomes, their deep origination in pan-primates remains to be explored. Hence, base...

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Autores principales: Li, Yian, Zhang, Guojie, Cui, Jie
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9323773/
https://www.ncbi.nlm.nih.gov/pubmed/35891351
http://dx.doi.org/10.3390/v14071370
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author Li, Yian
Zhang, Guojie
Cui, Jie
author_facet Li, Yian
Zhang, Guojie
Cui, Jie
author_sort Li, Yian
collection PubMed
description Human endogenous retroviruses (HERVs) are viral “fossils” in the human genome that originated from the ancient integration of exogenous retroviruses. Although HERVs have sporadically been reported in nonhuman primate genomes, their deep origination in pan-primates remains to be explored. Hence, based on the in silico genomic mining of full-length HERVs in 49 primates, we performed the largest systematic survey to date of the distribution, phylogeny, and functional predictions of HERVs. Most importantly, we obtained conclusive evidence of nonhuman origin for most contemporary HERVs. We found that various supergroups, including HERVW9, HUERSP, HSERVIII, HERVIPADP, HERVK, and HERVHF, were widely distributed in Strepsirrhini, Platyrrhini (New World monkeys) and Catarrhini (Old World monkeys and apes). We found that numerous HERVHFs are spread by vertical transmission within Catarrhini and one HERVHF was traced in 17 species, indicating its ancient nature. We also discovered that 164 HERVs were likely involved in genomic rearrangement and 107 HERVs were potentially coopted in the form of noncoding RNAs (ncRNAs) in humans. In summary, we provided comprehensive data on the deep origination of modern HERVs in pan-primates.
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spelling pubmed-93237732022-07-27 Origin and Deep Evolution of Human Endogenous Retroviruses in Pan-Primates Li, Yian Zhang, Guojie Cui, Jie Viruses Article Human endogenous retroviruses (HERVs) are viral “fossils” in the human genome that originated from the ancient integration of exogenous retroviruses. Although HERVs have sporadically been reported in nonhuman primate genomes, their deep origination in pan-primates remains to be explored. Hence, based on the in silico genomic mining of full-length HERVs in 49 primates, we performed the largest systematic survey to date of the distribution, phylogeny, and functional predictions of HERVs. Most importantly, we obtained conclusive evidence of nonhuman origin for most contemporary HERVs. We found that various supergroups, including HERVW9, HUERSP, HSERVIII, HERVIPADP, HERVK, and HERVHF, were widely distributed in Strepsirrhini, Platyrrhini (New World monkeys) and Catarrhini (Old World monkeys and apes). We found that numerous HERVHFs are spread by vertical transmission within Catarrhini and one HERVHF was traced in 17 species, indicating its ancient nature. We also discovered that 164 HERVs were likely involved in genomic rearrangement and 107 HERVs were potentially coopted in the form of noncoding RNAs (ncRNAs) in humans. In summary, we provided comprehensive data on the deep origination of modern HERVs in pan-primates. MDPI 2022-06-23 /pmc/articles/PMC9323773/ /pubmed/35891351 http://dx.doi.org/10.3390/v14071370 Text en © 2022 by the authors. https://creativecommons.org/licenses/by/4.0/Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/).
spellingShingle Article
Li, Yian
Zhang, Guojie
Cui, Jie
Origin and Deep Evolution of Human Endogenous Retroviruses in Pan-Primates
title Origin and Deep Evolution of Human Endogenous Retroviruses in Pan-Primates
title_full Origin and Deep Evolution of Human Endogenous Retroviruses in Pan-Primates
title_fullStr Origin and Deep Evolution of Human Endogenous Retroviruses in Pan-Primates
title_full_unstemmed Origin and Deep Evolution of Human Endogenous Retroviruses in Pan-Primates
title_short Origin and Deep Evolution of Human Endogenous Retroviruses in Pan-Primates
title_sort origin and deep evolution of human endogenous retroviruses in pan-primates
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9323773/
https://www.ncbi.nlm.nih.gov/pubmed/35891351
http://dx.doi.org/10.3390/v14071370
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