Biology subjects

Kaether, K.-K.

Publications and source records attributed to Kaether, K.-K..

3 recordsLinked to original sources

bioRxiv2025

Anchors for Homology-Based Scaffolding

Homology-based scaffolding orders contigs based on conserved collinearity of homologous sequences across related species. Existing methods often rely on costly whole-genome alignments or show limited robustness when integrating multiple references. Here, we introduce an anchor-based scaffolding framework that adapts synteny anchors to efficiently infer contig order and orientation relative to one or more reference genomes. Our approach leverages precomputed, sufficiently unique anchors and their respective high-confidence homology matches in a greedy approach, combining single-reference to multi-reference scaffolds using a maximum matching. Across simulated and real datasets, anchor-based scaffolding achieves accuracy comparable to state-of-the-art methods. Notably, the approach shows particular strengths in multi-reference settings. These results demonstrate that synteny-anchor-based scaffolding provides an additional tool for homology-based scaffolding with robust accuracy and superior performance in multi-reference scenarios.

bioinformatics↗

bioRxiv2025

Recently evolved, stage-specific genes are enriched at life stage transitions in flies

Understanding how genomic information is selectively utilized across different life stages is essential for deciphering the developmental and evolutionary strategies of metazoans. In holometabolous insects, the dynamic expression of genes enables distinct functional adaptations at embryonic, larval, pupal and adult stages, likely contributing to their evolutionary success. While Drosophila melanogaster has been extensively studied, less is known about the evolutionary dynamics that could govern stage-specific gene expression. To address this question, we compared the distribution of stage-specific genes, i.e., genes expressed in temporally restricted developmental stages, across development of D.melanogaster and Aedes aegypti. Using tau-scoring, a computational method to determine gene expression specificity, we found that, on average, a large proportion of genes (20 to 30% of all protein-coding genes) in both species exhibit restricted expression to specific developmental stages. Phylostratigraphy analysis, a method to date the age of genes, further revealed that stage-specific genes fall into two major categories: highly conserved and recently evolved. Notably, many of the recently evolved and stage-specific genes identified in A.aegypti and D.melanogaster are restricted to Diptera order (20 to 35% of all stage-specific genes), highlighting ongoing evolutionary processes that continue to shape life-stage transitions. Overall, our findings underscore the complex interplay between gene evolutionary age, expression specificity, and morphological transformations in development. These results suggest that the attraction of genes to critical life stage transitions is an ongoing process that may not be constant across evolutionary time or uniform between different lineages, offering new insights into the adaptability and diversification of dipteran genomes. Research HighlightsMetazoan genomes contain instructions for a single cell to develop into a complete adult organism. We investigated stage-specific genes, i.e. genes that expressed only during certain developmental stages, in two dipteran species. We found that between 20 to 35% of stage-specific genes are active during transitions between major life stages and have emerged recently, suggesting an ongoing evolutionary process shaping life-stage transitions.

evolutionary biology↗

bioRxiv2025

Telomerase RNA gene duplications drive telomeric repeatdiversity and evolution in Andrena bees

Most organisms in the animal kingdom require a non-coding telomerease RNA (TR) in conjunction with the telomerase reverse transcriptase (TERT) to add telomere tandem repeats to chromosome ends to genomic instability. Recent studies reported an extensive diversity in the sequence of telomeric repeats in some insect species. Our investigation of TR genes in the Andrena genus provides convincing evidence for the presence of multiple TR gene copies with different template sequences for synthesis of distinct telomeric repeat sequences in several species. In this study we describe the structure, genomic coordinates and abundance of these TR genes, and correlate our findings with the levels of tandem repeats found in DNAseq data. Based on an analysis of the synthenic context of these newly predicted TR genes, we show evidence for the existence of multiple TR paralogs that diverged during the evolution of the genus Andrena. To our knowledge this is the first time such a phenomenon is observed in animals, although recently reported for plants. Interestingly, the comprehensive annotation of all TERT genes found in yet unannotated Andrena species shows no corresponding evolutionary changes in related TERT proteins encoded by a single copy gene. Our study suggests an evolutionary mechanism for diversification of telomeric repeat sequences in certain insect species through telomerase RNA gene duplication.

bioinformatics↗