Biology subjects

Samano, A.

Publications and source records attributed to Samano, A..

4 recordsLinked to original sources

bioRxiv2026

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

The maintenance of functional repeat arrays on nonrecombining sex chromosomes presents an evolutionary paradox: tandem repeats are intrinsically unstable yet must preserve sequence identity and copy number to remain functional. The Y-linked Suppressor of Stellate (Su(Ste)) locus in Drosophila melanogaster is a large tandem array that produces piRNAs to silence the X-linked meiotic driver Stellate, but how such arrays are maintained remains unclear. Here, we reconstruct and compare repeat-resolved assemblies of the Su(Ste)/PCKR tandem array across three strains and show that the array is partitioned into discrete domains of elevated sequence identity. These domains exhibit an alternating pattern of similarity, in which nonadjacent regions are more similar to each other than to neighboring regions, and this organization is conserved across strains. Copy-number variation occurs primarily within specific domains, while overall array architecture remains stable. These results indicate that concerted evolution in the Su(Ste) array operates within structurally defined domains rather than uniformly across the array. The association of domain boundaries with inverted repeat elements suggests that higher-order structure constrains gene conversion, shaping both sequence homogenization and copy-number dynamics. In contrast, Y-linked rDNA arrays show uniform sequence similarity across long genomic distances, indicating a distinct mode of homogenization. Together, our findings demonstrate that gene conversion on nonrecombining chromosomes is structured by higher-order array architecture, providing a general framework for the maintenance of functional repeat arrays.

genomics↗

bioRxiv2026

A conserved architectural domain shapes centromere evolution in Drosophila

Centromeres ensure faithful chromosome segregation despite being embedded within rapidly evolving repetitive DNA, a contradiction known as the centromere paradox. While centromere identity is defined by the histone variant CENP-A, how conserved function is maintained amid rapid DNA turnover remains unclear. Here, we generate highly contiguous genome assemblies from single Drosophila melanogaster individuals that, for the first time, resolve a chromosome through its centromere, linking the chromosome 3 arms within a continuous sequence. Comparative assemblies from wild-derived strains reveal extensive structural variation in pericentromeric satellites, including large-scale expansions, contractions, and sequence divergence. Despite this variation, the CENP-A-associated centromeric core exhibits conserved organization across strains. Integration of Hi-C interaction maps with sequence analyses shows that flanking dodeca satellite arrays form a spatially interacting domain that bridges both sides of the centromere, whereas adjacent Prodsat arrays are more variable and show weaker interactions. These results support a model in which rapidly evolving centromeric DNA is constrained by conserved higher-order architecture, providing a framework for reconciling the rapid evolution of centromere sequence with its conserved function.

genomics↗

bioRxiv2025

Structural variants are enriched in deleterious visible phenotypes in Drosophila

Genome structural variants (SVs) comprise a sizable portion of functionally important genetic variation in all organisms; yet, many SVs evade discovery using short reads. While long-read sequencing can find the hidden SVs, the role of SVs in variation in organismal traits remains largely unclear. To address this gap, we investigate the molecular basis of 50 classical phenotypes in 11 Drosophila melanogaster strains using highly contiguous de novo genome assemblies generated with Oxford Nanopore long reads. These assemblies enabled the creation of a pangenome graph containing comprehensive, nucleotide-resolution maps of SVs, including complex rearrangements such as the interchromosomal inverted duplication Dp(2;4)eyD and large tandem duplications at the Bar locus. We uncovered new candidate causal mutations for 15 phenotypes and new molecular alleles for 2 mutations comprising tandem duplications, transposable element (TE) insertions, and indels. For example, we mapped the tarsal joint defect AblpeyD to an 8 kb Roo retrotransposon insertion into an intergenic enhancer, a finding validated via CRISPR-Cas9. The wing vein phenotype plexus (px1) was linked to a 1.5 kb partial tandem gene duplication, and the century-old Curved (c1) wing phenotype was linked to a 7.5 kb DM412 retrotransposon inserted into the coding sequence of the muscle protein gene Strn-Mlck. We also unveiled 8 SV alleles of previously identified causal genes, including previously uncharacterized SVs underlying the extensively studied white and yellow phenotypes. Overall, 67.4% of the genes causing phenotypic changes harbored candidate SVs over 100 bp, whereas only 28% is expected based on euchromatic SVs. Our data, based on the 50 Drosophila phenotypes, 44 of which are strongly deleterious, suggests a disproportionately larger contribution of SVs to deleterious changes in visible phenotypes in Drosophila.

genomics↗

bioRxiv2024

Genome structural variants shape adaptive success of an invasive urban malaria vector Anopheles stephensi

Global changes are associated with the emergence of several invasive species. However, the genomic determinants of the adaptive success of an invasive species in a new environment remain poorly understood. Genomic structural variants (SVs), consisting of copy number variants, play an important role in adaptation. SVs often cause large adaptive shifts in ecologically important traits, which makes SVs compelling candidates for driving rapid adaptations to environmental changes, which is critical to invasive success. To address this problem, we investigated the role SVs play in the adaptive success of Anopheles stephensi, a primary vector of urban malaria in South Asia and an invasive malaria vector in several South Asian islands and Africa. We collected whole genome sequencing data from 115 mosquitoes from invasive island populations and four locations from mainland India, an ancestral range for the species. We identified 2,988 duplication copy number variants and 16,038 deletions in these strains, with [~]50% overlapping genes. SVs are enriched in genomic regions with signatures of selective sweeps in the mainland and invasive island populations, implying a putative adaptive role of SVs. Nearly all high-frequency SVs, including the candidate adaptive variants, in the invasive island populations are present on the mainland, suggesting a major contribution of existing variation to the success of the island populations. Among the candidate adaptive SVs, three duplications involving toxin-resistance genes evolved, likely due to the widespread application of insecticides in India since the 1950s. We also identify two SVs associated with the adaptation of An. stephensi larvae to brackish water in the island and two coastal mainland populations, where the mutations likely originated. Our results suggest that existing SVs play a vital role in the evolutionary success of An. stephensi in new environmental conditions.

evolutionary biology↗