More single-nucleotide mutations surround small insertions than small deletions in primates

Area of Science:

• Genomics
• Evolutionary Biology
• Molecular Biology

Background:

• Previous research indicates increased single-nucleotide mutation rates near insertions and deletions (indels).
• The precise role of natural selection in shaping genome-wide indel patterns and adjacent single-nucleotide mutations remains unclear.

Purpose of the Study:

• To investigate how natural selection shapes genome-wide patterns of indels and nearby single-nucleotide mutations in primates.
• To characterize the relationship between small insertions, small deletions, and surrounding single-nucleotide mutation rates.

Main Methods:

• Comparative genomic analysis across primate species.
• Examination of mutation patterns within 150 base pair (bp) sequences flanking indels.
• Assessment of patterns across diverse genomic contexts (e.g., exons, introns, GC content, recombination rates).

Main Results:

• A higher frequency of single-nucleotide mutations was observed surrounding small insertions compared to small deletions in primates.
• This pattern was consistent across various genomic properties, including sequence context, replication timing, and indel density.
• The observed pattern was confined to sequences within 150 bp of indels.

Conclusions:

• A distinct genome-wide evolutionary pattern exists for indels and adjacent single-nucleotide changes in primates.
• Natural selection likely drives this pattern, potentially through sequence context preferences for mutation formation or indel heterozygosity.
• This evolutionary bias may influence primate genome evolution and contribute to phenotypic variation.