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Pisarenco, V. A.

Publications and source records attributed to Pisarenco, V. A..

4 recordsLinked to original sources

Genomic signatures of positive selection and relaxed selective constraints associated with convergent dietary specialisation

Island radiations provide ideal frameworks for studying the molecular basis of convergent evolution. The rapid diversification of Dysdera spiders in Canary Islands provides a striking example, with repeated dietary shifts towards specialisation on woodlice, accompanied by morphological, metabolic, and behavioural modifications that facilitate the exploitation of this heavy-metal-rich prey. Here, we investigate two independent events of dietary specialisation on different islands. By analysing six high-quality genome-assemblies, including three newly generated in this study, we investigate the genomic signals of positive selection and relaxed selection in protein-coding genes, upstream regulatory regions, and gene family turnover rates. We detected signatures of positive selection associated with the two specialists, accompanied by a twofold increase in gene loss rates relative to generalist ancestors. Notably, positive selection targeted a smaller, functionally coherent set of genes, potentially involved in detoxification likely through heavy metal excretion. In contrast, relaxation of selection affected a broader set of genes associated with functions that may have become dispensable under the new dietary regime. Furthermore, we found contractions in gene families associated with vesicular transport, potentially reflecting a reduced reliance on vesicle-mediated metal accumulation. Overall, our findings suggest that similar ecological pressures can drive parallel, yet non-identical, adaptive and non-adaptive responses, pointing to partially predictable evolutionary trajectories in an island radiation.

evolutionary biology↗

The first chromosome-scale Dugesia genomes shed light on structural rearrangements and genome size evolution in flatworms

AbstractHigh-quality, chromosome-scale genomes are crucial for understanding biological processes, yet many metazoan lineages, including most Lophotrochozoa, remain underrepresented in genome databases. Among these, planarians (Platyhelminthes, Tricladida), particularly Dugesia, are a globally distributed and phenotypically diverse group that has become an important model in evolutionary biology, notably for investigating the genetic effects of agametic asexuality. However, the lack of chromosome-scale assemblies has limited progress. Here, we present the first chromosome-scale genomes of four Western Mediterranean Dugesia species, displaying the first intra- and intergeneric comparisons. Comparison with the regeneration model organism Schmidtea mediterranea, rejects a whole-genome duplication as the cause of differences in chromosomal number and genome size between genera. Instead, Dugesia shows extensive lineage-specific and differential expansions of DNA transposable elements, likely contributing to genome size variation during diversification. Despite differences in the dynamics of structural genome rearrangements observed between genera, both groups lack the conservation of ancestral metazoan linkage groups, supporting the idea that genome structural instability is a key feature of flatworm genome evolution. Our newly generated genomic resources and findings offer vital insights into the genetic basis of diversification and establish Dugesia as a valuable model for studying metazoan genome dynamics, including the evolution of alternative reproductive systems.

genomics↗

How did evolution halve genome size during an oceanic island colonization?

Red devil spiders of the genus Dysdera colonised the Canary Islands and underwent an extraordinary diversification. Notably, their genomes are nearly half the size of their mainland counterparts ([~]1.7 vs. [~]3.3 Gb). This offers a unique model to solve long-standing debates regarding the roles of adaptive and non-adaptive forces on shaping genome size genome size evolution. To address these, we conducted comprehensive genomic analyses based on three high-quality chromosome-level assemblies, including two newly generated ones. We find that insular species experienced a reduction in genome size, affecting all genomic elements, including intronic and intergenic regions, with transposable element (TE) loss accounting for most of this contraction. Additionally, autosomes experienced a disproportionate reduction compared to the X chromosome. Paradoxically, island species exhibit higher levels of nucleotide diversity and recombination, lower TE activity in recent times, and evidence of intensified natural selection, collectively pointing to larger long-term effective population sizes in species from the Canary Islands. Overall, our findings align with the non-adaptive mutational hazard hypothesis, supporting purifying selection against slightly deleterious DNA and TE insertions as the primary mechanism driving genome size reduction.

genomics↗

GALEON: A Comprehensive Bioinformatic Tool to Analyse and Visualise Gene Clusters in Complete Genomes

MotivationGene clusters, defined as a set of genes encoding functionally-related proteins, are abundant in eukaryotic genomes. Despite the increasing availability of chromosome-level genomes, the comprehensive analysis of gene family evolution remains largely unexplored, particularly for large and highly dynamic gene families or those including very recent family members. These challenges stem from limitations in genome assembly contiguity, particularly in repetitive regions such as large gene clusters. Recent advancements in sequencing technology, such as long reads and chromatin contact mapping, hold promise in addressing these challenges. ResultsTo facilitate the identification, analysis, and visualisation of physically clustered gene family members within chromosome-level genomes, we introduce GALEON, a user-friendly bioinformatic tool. GALEON identifies gene clusters by studying the spatial distribution of pairwise physical distances among gene family members along with the genome-wide gene density. The pipeline also enables the simultaneous analysis and comparison of two gene families, and allows the exploration of the relationship between physical and evolutionary distances. This tool offers a novel approach for studying the origin and evolution of gene families. Availability and ImplementationGALEON is freely available from http://www.ub.edu/softevol/galeon, and from https://github.com/molevol-ub/galeon

genomics↗