Higher-order Architecture Shapes Concerted Evolution in a Y-linked repeat array.

Area of Science:

• Evolutionary genetics
• Molecular biology
• Genomics

Background:

• Tandem repeat arrays on nonrecombining sex chromosomes face evolutionary challenges due to inherent instability.
• The Y-linked Suppressor of Stellate (Su(Ste)) locus in Drosophila melanogaster produces piRNAs to silence the X-linked Stellate gene, but its maintenance mechanism is unknown.

Purpose of the Study:

• To investigate the maintenance mechanisms of the Su(Ste) tandem repeat array on the nonrecombining Y chromosome.
• To understand how sequence identity and copy number are preserved in functional repeat arrays.

Main Methods:

• Comparative analysis of repeat-resolved assemblies of the Su(Ste)/PCKR tandem array across three Drosophila strains.
• Examination of sequence similarity patterns and copy-number variation within the array.

Main Results:

• The Su(Ste) array is organized into discrete domains with elevated sequence identity, showing an alternating pattern of similarity.
• Copy-number variation is concentrated within specific domains, while the overall array architecture remains stable.
• Domain boundaries are associated with inverted repeat elements, suggesting structural constraints on gene conversion.

Conclusions:

• Concerted evolution in the Su(Ste) array operates within structurally defined domains, not uniformly.
• Higher-order array architecture, influenced by inverted repeats, structures gene conversion on nonrecombining chromosomes.
• This provides a framework for understanding the maintenance of functional repeat arrays, contrasting with Y-linked rDNA arrays.