An endogenous adeno-associated virus element in elephants

Area of Science:

• Genomics
• Viral Evolution
• Mammalian Genetics

Background:

• Endogenous viral elements (EVEs) are remnants of ancient viral infections integrated into host genomes.
• Adeno-associated virus (AAV) derived elements, specifically enAAV-rep, have been identified in various mammals.
• Previous studies noted enAAV-rep expression in the liver of degu.

Purpose of the Study:

• To identify and characterize enAAV-rep in Asian elephants and rock hyraxes.
• To investigate the evolutionary origins and selection pressures on enAAV-rep in these species.
• To determine the tissue-specific expression patterns of enAAV-rep in Asian elephants.

Main Methods:

• Genomic DNA sequencing to identify enAAV-rep.
• Phylogenetic analysis to infer evolutionary relationships and integration events.
• Bioinformatic analysis of open reading frame (ORF) sequences to detect selection.
• RNA sequencing (or similar transcriptomic analysis) to assess tissue-specific gene expression.

Main Results:

• Newly identified enAAV-rep in Asian elephant and rock hyrax genomes.
• Elephantine enAAV-rep is orthologous, originating from a single AAV integration event >6 million years ago.
• Rock hyrax enAAV-rep appears to have an independent origin.
• Negative selection observed on the enAAV-rep ORF in elephants.
• enAAV-rep mRNA expression is specifically detected in the liver of Asian elephants, similar to degu.

Conclusions:

• The integration of enAAV-rep occurred independently in the evolutionary lineages of elephants and degu.
• The AAV Rep protein has been repeatedly co-opted for functions within the mammalian liver.
• This study expands the known diversity and evolutionary history of endogenous AAV elements in mammals.