Biology subjects

Saenko, S.

Publications and source records attributed to Saenko, S..

3 recordsLinked to original sources

bioRxiv2025

Annotation of 200 Insect Genomes with BRAKER for Consistent Comparisons across Species

The annotation of genomes lags behind their sequencing and assembly. For example, of 5,092 insect species in GenBank, as one of the most widely used databases, only 375 currently have annotated genomes within this database. Additionally, species that were previously annotated can benefit from reannotation using RNA-Seq and protein data that have been added since their last annotation, as well as from state-of-the-art annotation methods, whose accuracy has improved. Heterogeneous annotations performed with different tools and protein databases can introduce artifactual differences when comparing gene sets or gene structures between species. Recently, the BRAKER3 annotation pipeline was introduced that integrates evidence from RNA-Seq and from a protein database. It was benchmarked as one of the most accurate annotation methods. Here, we introduce an automated genome annotation workflow that allows to annotate a list of species with BRAKER3 and VARUS for RNA-Seq retrieval, or in the absence of transcriptome data, with BRAKER2, with minimal manual intervention. We selected a diverse set of 200 insect species from different families, including 85 species previously lacking annotations in GenBank. Using currently available RNA-Seq and protein sequence data, we applied our automated workflow to annotate these genomes and conducted downstream analyses typically performed in comparative genomics studies. We present the resulting gene structures, protein sequences, gene ontology terms, orthologous gene groups and a species tree.

genomics↗

bioRxiv2025

How drought and ploidy level shape gene expression and DNA methylation in Phragmites australis

Drought stress significantly affects plant physiology and growth, yet the molecular mechanisms underlying drought responses remain poorly understood. In this study, we investigate how tetraploid and octoploid Phragmites australis (common reed), a key species in wetland ecosystems and paludiculture, respond to drought at the transcriptional and epigenetic levels. Using RNA-seq, we identify changes in gene expression after 20 and 30 days of drought and assess methylation-sensitive amplification polymorphism (MSAP) over 50 days of drought. Transcriptomic analysis reveals that key drought-response genes are shared between ploidy levels, including those involved in the saccharopine pathway, water deprivation response, cell wall remodelling, and the mevalonate pathway. Drought supresses photosynthesis, with a pronounced down-regulation of the photosynthetic gene PsbP. Ploidy level influences gene expression under both drought and non-stress conditions, highlighting distinct adaptive strategies. In control samples, gene expression differed between ploidy levels, with octoploids up-regulating genes related to translation and metabolism, while tetraploids activate genes involved in cell wall modification and transmembrane transport. Prolonged drought increases DNA methylation variability, though no significant correlation is found between methylation levels and drought duration. Methylation differences are more pronounced between ploidy levels, with octoploids exhibiting lower overall methylation. These findings highlight the complex interactions between gene expression, epigenetic modifications, and polyploidy in drought response and provide a theoretical framework for future selection, hybridization, and conservation initiatives. Main ConclusionKey drought-response genes regulate saccharopine and mevalonate pathways, and cell wall remodelling. Ploidy level influences gene expression under drought and non-stress conditions. Octoploids overall exhibit lower methylation than tetraploids.

ecology↗

bioRxiv2017

Partial restoration of mutational robustness after addition of genetic polymorphism and in the presence of sexual selection

The interaction between mutational (i.e. genetic) robustness, cryptic genetic variation and epistasis is currently under much debate, as is the question whether mutational robustness evolved under direct selection or as a by-product of environmental robustness. Here we report that mutational robustness was restored in a mutant line of the butterfly Bicyclus anynana after the spontaneous mutation, comet, appeared in a genetically polymorphic wild type population. The comet mutation modified two phenotypic traits known to be under sexual selection in this butterfly: the dorsal forewing eyespot, which is normally round, but became comet-shaped, and the androconia, the structures producing the male sex pheromone, which were reduced in size. The comet mutant line remained phenotypically stable for [~]7 seven years, but when outcrossed to the genetically polymorphic wild type population, the outcrossed comet line surprisingly recovered the wild type phenotype within 8 generations. This suggests that mutational robustness against the comet mutation was recovered in the comet outcrossed line by epistatic interactions with the genetic polymorphism originating from wild types. The extent of wild type phenotype recovery in the comet outcrossed line was trait- and developmental temperature-dependent, such that mutational robustness was partially recovered at high, but not at low developmental temperatures. We hypothesized that sexual selection through mate choice, which is sex-reversed between developmental temperatures in this butterfly, could produce mutational robustness at a high (but not at a low) temperature. Females are the choosy sex and exert stabilizing or directional selection on male secondary sexual wing traits but only at higher temperatures. Male mating success experiments under semi-natural conditions then revealed that males with the typical comet mutant phenotype suffered from lower mating success compared to wild type males, while mating success of comet males resembling wild types was partially restored. Altogether, we document the roles of cryptic genetic variation and epistasis in restoration of mutational robustness against a spontaneous mutation with known fitness effects, and we provide experimental evidence, for the first time to our knowledge, that sexual selection can produce mutational robustness.

evolutionary biology↗