Analysis of Simian Endogenous Retrovirus (SERV) Full-Length Proviruses in Old World Monkey Genomes
Abstract
:1. Introduction
2. Materials and Methods
2.1. Identifying Simian Endogenous Retrovirus (SERV) Sequences in Cercopithecinae
2.2. Analysis of Proviral Sequences
3. Results
- Sequence and assembly quality may vary;
- Not all species have been sequenced;
- For most species, only a single genome assembly is available;
- Y chromosome sequences are not always present;
- Heterozygous EVEs are omitted from assemblies;
- Full-length proviruses may be younger than fragmented ones;
- It is not likely that all viral variation has been captured in the germ line.
3.1. Phylogenetic Analysis of Cercopithecinae SERV Proviruses
3.1.1. SERV Diversity in OWM
3.1.2. Cer-SERV Integrations in the T. gelada Genome
3.2. Mutation Patterns in SERV Proviruses
3.2.1. CpG Methylation-Associated Mutations
3.2.2. APOBEC3G and -Non-3G Signature Patterns
3.2.3. PBS Variation
3.3. Genomic Features of SERV Proviruses
3.3.1. Cer-SERV LTR Sequence Diversity and Dating
3.3.2. Cer-SERV Coding Region Diversity
3.4. Shared SERV Proviral Integrations in Macaques
3.5. Shared Cer-SERV Proviral Integrations in Baboon and Gelada
4. Discussion
5. Conclusions
- Shared, ancient proviral Cer-SERV integrations between species are rare;
- Most Cer-SERV proviral integrations are relatively young;
- Species-specific young, but not old, Cer-SERV clusters are seen in OWM genomes;
- Cer-SERV PBS sequences show evidence of tRF suppression, a mechanism only operational in the early embryo;
- Some young Cer-SERV-1 LTRs have acquired binding sites for embryo-specific transcription factors;
- Cer-SERV pol genes are more often uninterrupted than Cer-SERV env genes;
- Cer-SERV Env expression from integrated proviruses should be able to block the receptor to prevent Env-mediated reinfection of the cell. However, reinfections of the germ line are common.
Supplementary Materials
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Conflicts of Interest
References
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OWM Species | Specimen, Gender, Origin | No. of Full-Length, HOMOZYGOUS, Cer-SERV GENOMES 1 |
---|---|---|
Chlorocebus aethiops (vervet) | (a) #1994-021, male, Caribbean C. aethiops sabeus (b) WHO Vero cell line RCB 10–87, female sabaeus monkey 2 | (a) 6 (3 SERV-1, 3 SERV-2) (b) 6 (1 SERV-1, 5 SERV-2) |
Erythrocebus patas (red guenon) | #BS28, unknown sex, San Diego Zoo | 1 (SERV-2) |
Macaca fascicularis (crab-eating macaque) | #MacFas5, female, from Tinjil, Java, Indonesia | 2 (1 SERV-1, 1 SERV-2) |
Macaca fuscata (Japanese macaque) | #JAMA01, unknown sex, Japan | 7 (4 SERV-1, 3 SERV-2) |
Macaca mulatta (rhesus monkey) | #17573, female, Indian origin + separate Y chromosome | 9 (6 SERV-1, 3 SERV-2) |
Macaca nemestrina (pig-tailed macaque) | #M95218, female, Washington National Primate Research Center | 1 (SERV-1) 3 |
Mandrillus leucophaeus (drill) | Isolate #KB7577, female, San Diego Zoo | 1 (SERV-2) 3 |
Papio anubis (olive baboon) | (a) #X1155, female, Kenyan ancestry (b) #15944, male, Southwest National Primate Research Center | (a) 7 (5 SERV-1, 2 SERV-2) (b) 15 (12 SERV-1, 3 SERV-2) |
Theropithecus gelada (gelada) | #Dixy, female, Ethiopia | 26 (21 SERV-1, 5 SERV-2) |
Genotype/ No. of Sequences | Mean Group LTR nt Distance K 1 | LTR nt Distance K, Range | Calculated Integration Time (Fast Rate) 2 | Calculated Integration Time (Slow Rate) 2 |
---|---|---|---|---|
Cer-SERV-1 N = 55 | 0.023 ± 0.014 | 0.000–0.053 | 2.3 ± 1.4 mya (range <0.3–5.3) | 5.0 ± 3.0 mya (range <0.3–11.5) |
Cer-SERV-2 N = 26 | 0.039 ± 0.019 | 0.011–0.084 | 3.9 ± 1.9 mya (range 2.4–18.0) | 8.5 ± 4.0 mya (range 2.4–18.0) |
Chromosome 17 Cer-SERV-2 LTR | K (nt Distance) 1 | Estimated Age T of Integration 2 | Event, with Average Estimated Age |
---|---|---|---|
5′/3′ LTR gelada | 0.072 | ~7.2/~15.7 mya | Integration of chr. 17 Cer-SERV-2 provirus: ~7.7/~16.8 mya |
5′/3′ LTR baboon 1 5′/3′ LTR baboon 2 | 0.084 0.075 | ~8.4/~18.3 mya ~7.5/~16.3 mya | |
5′ LTR gelada/ 5′ LTR baboon 1 5′ LTR gelada/ 5′ LTR baboon 2 | 0.037 0.028 | ~3.7/~8.0 mya ~2.8/~6.1 mya | TMRCA 3 of gelada and baboon chr. 17 Cer-SERV-2: ~2.3/~5.6 mya |
3′ LTR gelada/ 3′ LTR baboon 1 3′ LTR gelada/ 3′ LTR baboon 2 | 0.013 0.013 | ~1.3/~2.8 mya | |
5′ LTR baboon 1/ 5′ LTR baboon 2 | 0.019 | ~1.9/~4.1 mya | TMRCA of two P. anubis chr. 17 Cer-SERV-2: <0.8/~2.2 mya |
3′ LTR baboon 1/ 3′ LTR baboon 2 | 0.000 | <0.3 mya | |
5′ LTR gelada/ 5′ LTR mangabey | 0.047 | ~4.7/~10.2 mya | TMRCA gelada/baboon/mangabey chr. 17 Cer-SERV-2: ~3.8/~8.3 mya |
5′ LTR baboon 1/ 5′ LTR mangabey | 0.035 | ~3.5/~7.6 mya | |
5′ LTR baboon 2/ 5′ LTR mangabey | 0.033 | ~3.3/~7.2 mya |
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van der Kuyl, A.C. Analysis of Simian Endogenous Retrovirus (SERV) Full-Length Proviruses in Old World Monkey Genomes. Genes 2022, 13, 119. https://doi.org/10.3390/genes13010119
van der Kuyl AC. Analysis of Simian Endogenous Retrovirus (SERV) Full-Length Proviruses in Old World Monkey Genomes. Genes. 2022; 13(1):119. https://doi.org/10.3390/genes13010119
Chicago/Turabian Stylevan der Kuyl, Antoinette C. 2022. "Analysis of Simian Endogenous Retrovirus (SERV) Full-Length Proviruses in Old World Monkey Genomes" Genes 13, no. 1: 119. https://doi.org/10.3390/genes13010119
APA Stylevan der Kuyl, A. C. (2022). Analysis of Simian Endogenous Retrovirus (SERV) Full-Length Proviruses in Old World Monkey Genomes. Genes, 13(1), 119. https://doi.org/10.3390/genes13010119