Structural variants are enriched in deleterious visible phenotypes in Drosophila

Area of Science:

• Genomics
• Population Genetics
• Developmental Biology

Background:

• Genome structural variants (SVs) contribute significantly to genetic variation but are often missed by short-read sequencing.
• The role of SVs in organismal traits is not well understood, despite their potential importance.
• Long-read sequencing technologies offer improved detection of complex SVs.

Purpose of the Study:

• To investigate the molecular basis of classical phenotypes in Drosophila melanogaster using long-read sequencing.
• To identify novel structural variants underlying phenotypic variation.
• To assess the contribution of SVs to deleterious traits.

Main Methods:

• Generated highly contiguous de novo genome assemblies for 11 Drosophila melanogaster strains using Oxford Nanopore long reads.
• Constructed a pangenome graph to map nucleotide-resolution SVs, including complex rearrangements.
• Validated candidate causal mutations using CRISPR-Cas9.

Main Results:

• Identified new candidate causal mutations for 15 phenotypes and new molecular alleles for 2 mutations.
• Discovered various SVs, including transposable element insertions and duplications, underlying specific Drosophila phenotypes (e.g., Ablp^eyD, plexus, Curved).
• Uncovered previously uncharacterized SVs in known phenotype-associated genes, such as white and yellow.

Conclusions:

• Structural variants, particularly those over 100 bp, are disproportionately enriched in genes associated with phenotypic changes in Drosophila.
• SVs play a substantial role in causing deleterious visible phenotypes in Drosophila.
• Long-read sequencing and pangenome graphs are powerful tools for dissecting the genetic basis of complex traits.