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Evolutionarily Young African Rhinoceros Gammaretroviruses.
Kyriakos Tsangaras1, Jens Mayer2, Omar Mirza3
1Department of Life and Health Sciences, University of Nicosia, Nicosia, Cyprus.
Journal of Virology
|April 6, 2023
Summary
African rhinoceros genomes contain novel endogenous gammaretroviruses (ERVs), named SimumERV and DicerosERV. These recently acquired ERVs, closely related to rodent retroviruses, suggest an African origin and challenge previous assumptions about perissodactyl genomes lacking such elements.
Area of Science:
- Virology and Genomics
- Retroviral Evolution
- Mammalian Genetics
Background:
- Previous studies indicated that perissodactyl genomes, including rhinoceros, lacked gammaretroviruses.
- High-throughput sequencing of Southern white rhinoceros revealed unexpected retroviral sequences.
- Endogenous retroviruses (ERVs) are remnants of ancient retroviral infections integrated into host genomes.
Purpose of the Study:
- To investigate the presence and characteristics of gammaretroviruses in African rhinoceros genomes.
- To identify and characterize novel endogenous retroviruses (ERVs) in white and black rhinoceros.
- To determine the evolutionary origin and age of these newly discovered rhinoceros ERVs.
Main Methods:
- High-throughput sequencing of DNA and cDNA from white rhinoceros.
- Bioinformatic screening of updated white and black rhinoceros draft genomes for retroviral sequences.
- Comparative genomic analysis including Asian rhinoceros, extinct rhinoceros, horse, and tapir genomes.
- Phylogenetic analysis to determine evolutionary relationships with known retroviruses.
Main Results:
- Identification of high-copy orthologous gammaretroviral ERVs, designated SimumERV (white rhinoceros) and DicerosERV (black rhinoceros).
- Discovery of two distinct long terminal repeat (LTR) variants (LTR-A and LTR-B) in black rhinoceros ERVs, with LTR-A also found in white rhinoceros.
- Divergence age estimation suggests African rhinoceros ERVs colonized genomes within the last 8 million years, with a close evolutionary relationship to rodent ERVs, indicating a possible African origin.
Conclusions:
- African white and black rhinoceros genomes harbor evolutionarily young, high-copy gammaretroviruses (SimumERV and DicerosERV).
- These ERVs likely expanded in multiple waves and their restriction to African rhinoceros suggests an African origin.
- The findings revise the understanding of retroviral presence in perissodactyl genomes, particularly challenging the notion of their absence in rhinoceros.
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