2-AIN-506 a 2-AIN-252: Seminár z bioinformatiky (2) a (4)
Leto 2019

Alexander Hayward, Charlie K. Cornwallis, Patric Jern. Pan-vertebrate comparative genomics unmasks retrovirus macroevolution. Proceedings of the National Academy of Sciences of the United States of America, 112(2):464-469. 2015.

Download preprint: not available

Download from publisher: not available PubMed

Related web page: not available

Bibliography entry: BibTeX


Although extensive research has demonstrated host-retrovirus microevolutionary
dynamics, it has been difficult to gain a deeper understanding of the
macroevolutionary patterns of host-retrovirus interactions. Here we use recent
technological advances to infer broad patterns in retroviral diversity,
evolution, and host-virus relationships by using a large-scale phylogenomic
approach using endogenous retroviruses (ERVs). Retroviruses insert a proviral DNA
copy into the host cell genome to produce new viruses. ERVs are provirus
insertions in germline cells that are inherited down the host lineage and
consequently present a record of past host-viral associations. By mining ERVs
from 65 host genomes sampled across vertebrate diversity, we uncover a great
diversity of ERVs, indicating that retroviral sequences are much more prevalent
and widespread across vertebrates than previously appreciated. The majority of
ERV clades that we recover do not contain known retroviruses, implying either
that retroviral lineages are highly transient over evolutionary time or that a
considerable number of retroviruses remain to be identified. By characterizing
the distribution of ERVs, we show that no major vertebrate lineage has escaped
retroviral activity and that retroviruses are extreme host generalists, having an
unprecedented ability for rampant host switching among distantly related
vertebrates. In addition, we examine whether the distribution of ERVs can be
explained by host factors predicted to influence viral transmission and find that
internal fertilization has a pronounced effect on retroviral colonization of host
genomes. By capturing the mode and pattern of retroviral evolution and
contrasting ERV diversity with known retroviral diversity, our study provides a
cohesive framework to understand host-virus coevolution better.