Amanda M. Larracuente

Disruption of small RNAs and mechanistic variation in Segregation Distorter, a sperm-killing drive system in Drosophila melanogaster

The paper investigates the role of Rsp-derived small RNAs in the Segregation Distorter drive system in Drosophila melanogaster, showing haplotype-specific variations in their contribution to drive strength.

kmerRRR: A k-mer based tool for functional genomics in Repeat Rich Regions

kmerRRR improves analysis of repetitive genomic regions by using k-mer frequency analysis to enhance mappability and recover lost biological signals in chromatin and small RNA data.

Satellite DNA dynamics across phylogenetic scales in ground beetles and other insects

The paper examines satellite DNA dynamics across multiple insect orders and ground beetle species, revealing significant variation in satDNA abundance and turnover across evolutionary scales.

Pervasive suppressors halt the spread of selfish Segregation Distorter in a natural population

The paper identifies suppressors that limit the spread of the selfish Segregation Distorter in Drosophila melanogaster by analyzing genetic variation across 90 strains.

Targeted editing of pericentromeric satellite DNA alters sensitivity to meiotic drive

This study uses CRISPR/Cas9 to edit pericentromeric satellite DNA in Drosophila and shows that copy number affects sensitivity to a meiotic drive system.

600+ insect genomes reveal repetitive element dynamics and highlight biodiversity-scale repeat annotation challenges

The paper analyzes repetitive elements across 601 insect species, revealing challenges in repeat annotation and the benefits of long-read sequencing.

Centromere-associated retroelement evolution in Drosophila melanogaster reveals an underlying conflict

The paper studies the evolution of G2/Jockey-3, a retroelement associated with centromeres in Drosophila melanogaster, finding it is likely a selfish element that targets centromeres to evade host defenses.

The nanoCUT&RUN technique visualizes telomeric chromatin in Drosophila

The paper introduces nanoCUT&RUN, a modified CUT&RUN technique for mapping chromatin protein binding sites in Drosophila, showing its effectiveness for TRL, HipHop, and HOAP proteins.

Unique structure and positive selection promote the rapid divergence of Drosophila Y chromosomes

The paper studies Y chromosome evolution in Drosophila species, finding rapid divergence, new gene families under positive selection, and biased repair mechanisms.

Heterochromatin-dependent transcription of satellite DNAs in the Drosophila melanogaster female germline

The paper shows that satDNA transcription and piRNA production in Drosophila melanogaster germline depend on the Rhino-Deadlock-Cutoff complex and Moonshiner, establishing heterochromatin at satDNA loci.

Distinct spermiogenic phenotypes underlie sperm elimination in the Segregation Distorter meiotic drive system

The paper investigates spermiogenic defects in Drosophila melanogaster SD/SD+ males and links them to Rsp satellite DNA copy number, showing how high Rsp levels trigger sperm elimination.

Long-reads are revolutionizing 20 years of insect genome sequencing

The paper analyzes 601 insect genome assemblies, highlighting taxonomic bias, assembly quality, and the impact of long-read sequencing technologies on contiguity.

Evolution of genome structure in the Drosophila simulans species complex

The paper generates high-quality genomes for Drosophila simulans species complex to study repetitive DNA evolution and structural divergence between species.

RepeatProfiler: a pipeline for visualization and comparative analysis of repetitive DNA profiles

RepeatProfiler generates and compares repetitive DNA profiles from low-coverage data to study evolutionary history in diverse species.

Dynamic evolution of euchromatic satellites on the X chromosome in Drosophila melanogaster and the simulans clade

The paper studies the evolutionary dynamics of two satellite DNAs in Drosophila species, showing their dynamic changes in location, abundance, and composition across species.

Islands of retroelements are the major components of Drosophila centromeres

The paper identifies the sequence composition of Drosophila melanogaster centromeres, showing they are composed of retroelement islands flanked by satellite repeats, with G2/Jockey-3 being the most enriched retroelement.

Heterochromatin-enriched assemblies reveal the sequence and organization of the Drosophila melanogaster Y chromosome

The paper develops a method to assemble heterochromatic regions of the Drosophila melanogaster Y chromosome, revealing its sequence organization and evolutionary dynamics.

Firefly genomes illuminate parallel origins of bioluminescence in beetles

The paper generates genomes for three bioluminescent beetles to study the genetic basis of bioluminescence and finds at least two independent evolutionary origins of the trait.