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Genome-wide characterization of endogenous retroviruses in the bat Myotis lucifugus reveals recent and diverse infections.

ABSTRACT: Bats are increasingly recognized as reservoir species for a variety of zoonotic viruses that pose severe threats to human health. While many RNA viruses have been identified in bats, little is known about bat retroviruses. Endogenous retroviruses (ERVs) represent genomic fossils of past retroviral infections and, thus, can inform us on the diversity and history of retroviruses that have infected a species lineage. Here, we took advantage of the availability of a high-quality genome assembly for the little brown bat, Myotis lucifugus, to systematically identify and analyze ERVs in this species. We mined an initial set of 362 potentially complete proviruses from the three main classes of ERVs, which were further resolved into 13 major families and 86 subfamilies by phylogenetic analysis. Consensus or representative sequences for each of the 86 subfamilies were then merged to the Repbase collection of known ERV/long terminal repeat (LTR) elements to annotate the retroviral complement of the bat genome. The results show that nearly 5% of the genome assembly is occupied by ERV-derived sequences, a quantity comparable to findings for other eutherian mammals. About one-fourth of these sequences belong to subfamilies newly identified in this study. Using two independent methods, intraelement LTR divergence and analysis of orthologous loci in two other bat species, we found that the vast majority of the potentially complete proviruses identified in M. lucifugus were integrated in the last ~25 million years. All three major ERV classes include recently integrated proviruses, suggesting that a wide diversity of retroviruses is still circulating in Myotis bats.

SUBMITTER: Zhuo X

PROVIDER: S-EPMC3719839 | biostudies-literature | 2013 Aug

REPOSITORIES: biostudies-literature

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Genome-wide characterization of endogenous retroviruses in the bat Myotis lucifugus reveals recent and diverse infections.

Zhuo Xiaoyu X Rho Mina M Feschotte Cédric C

Journal of virology 20130529 15

Bats are increasingly recognized as reservoir species for a variety of zoonotic viruses that pose severe threats to human health. While many RNA viruses have been identified in bats, little is known about bat retroviruses. Endogenous retroviruses (ERVs) represent genomic fossils of past retroviral infections and, thus, can inform us on the diversity and history of retroviruses that have infected a species lineage. Here, we took advantage of the availability of a high-quality genome assembly for ...[more]

PMID: 23720713

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Project description:The little brown bat (Myotis lucifugus) is one of the most widespread bat species in North America and is experiencing severe population declines because of an emerging fungal disease, white-nose syndrome (WNS). To manage and conserve this species effectively it is important to understand patterns of gene flow and population connectivity to identify possible barriers to disease transmission. However, little is known about the population genetic structure of little brown bats, and to date, no studies have investigated population structure across their entire range. We examined mitochondrial DNA and nuclear microsatellites in 637 little brown bats (including all currently recognized subspecific lineages) from 29 locations across North America, to assess levels of genetic variation and population differentiation across the range of the species, including areas affected by WNS and those currently unaffected. We identified considerable spatial variation in patterns of female dispersal and significant genetic variation between populations in eastern versus western portions of the range. Overall levels of nuclear genetic differentiation were low, and there is no evidence for any major barriers to gene flow across their range. However, patterns of mtDNA differentiation are highly variable, with high ΦST values between most sample pairs (including between all western samples, between western and eastern samples, and between some eastern samples), while low mitochondrial differentiation was observed within two groups of samples found in central and eastern regions of North America. Furthermore, the Alaskan population was highly differentiated from all others, and western populations were characterized by isolation by distance while eastern populations were not. These data raise the possibility that the current patterns of spread of WNS observed in eastern North America may not apply to the entire range and that there may be broad-scale spatial variation in the risk of WNS transmission and occurrence if the disease continues to spread west.

Dataset Information

Genome-wide characterization of endogenous retroviruses in the bat Myotis lucifugus reveals recent and diverse infections.

Publications

Genome-wide characterization of endogenous retroviruses in the bat Myotis lucifugus reveals recent and diverse infections.

Similar Datasets

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