A comprehensive analysis of gorilla-specific LINE-1 retrotransposons

Area of Science:

• Genomics
• Evolutionary Biology
• Molecular Biology

Background:

• Long interspersed element-1 (LINE-1 or L1) retrotransposons constitute approximately 17% of the primate genome.
• Full-length L1s possess the enzymatic machinery to mobilize to new genomic locations.
• The gorilla genome offers insights into primate evolution due to its close relation to humans.

Purpose of the Study:

• To identify gorilla-specific LINE-1 (L1) elements using an updated gorilla reference genome.
• To characterize the integrity and evolutionary significance of identified gorilla-specific L1s.

Main Methods:

• Computational analysis and manual inspection were employed to identify gorilla-specific L1 candidates.
• L1Xplorer software was utilized to assess the intactness of full-length L1 elements.
• Sequence conservation of intact L1s was evaluated by aligning their open reading frames (ORFs) with the L1PA2 consensus sequence.

Main Results:

• Over 2000 gorilla-specific L1 candidates were identified, with 1883 manually inspected.
• Twelve intact, full-length gorilla-specific L1s, primarily from the L1PA2 subfamily, were found.
• These 12 L1s exhibited 14 conserved nonsynonymous mutations, with two mutations in ORF1 being unique to gorillas compared to chimpanzees and humans.

Conclusions:

• Gorilla-specific LINE-1 (L1) elements may have significantly influenced the gorilla genome.
• These L1s contribute to the genomic distinctiveness of gorillas compared to other primates.
• The identified mutations highlight potential drivers of gorilla genome evolution.