Biology subjects

Sobczyk, M.

Publications and source records attributed to Sobczyk, M..

7 recordsLinked to original sources

bioRxiv2025

Sex-biased duplicates are rapidly generated during Drosophila tRNA repertoire evolution

Eukaryotic genomes encode hundreds of transfer RNA genes ostensibly to ensure efficient translation. How these seemingly redundant tRNA copies arise and are naturally selected in metazoan genomes and populations remains largely unexplored, owing to challenges in accurate sequencing of tRNA loci and their transcripts. We leveraged long-read genome assemblies of 24 Drosophilid species to infer the origination times of the entire Drosophila melanogaster tRNA gene repertoire and found that continuous gain and loss of tRNA duplicates throughout 60 million years of divergence has resulted in rapid taxonomic restriction of isodecoding and isoaccepting copies--even producing one isodecoder specific to D. melanogaster. Moreover, we identified patterns of global codon usage, especially in lineage-specific genes, incongruous with translational efficiency hypotheses. Through generation of tRNA sequencing in D. melanogaster we observed that recently duplicated, taxonomically restricted tRNA copies had sexually dimorphic patterns of expression, fragmentation, and nucleoside modification. Our work implicates the emergence of taxonomically restricted tRNA genes as sources of regulatory diversity and reveals that sexual and natural selection affect the evolutionary dynamics of the tRNA gene family in metazoan species.

evolutionary biology↗

bioRxiv2025

A high-resolution diel survey of surface ocean metagenomes, metatranscriptomes, and transfer RNA transcripts

The roles of marine microbes in ecosystem processes are inherently linked to their ability to sense, respond, and ultimately adapt to environmental change. Capturing the nuances of this perpetual dialogue and its long-term implications requires insight into the subtle drivers of microbial responses to environmental change that are most accessible at the shortest scales of time. Here, we present a multi-omics dataset comprising surface ocean metagenomes, metatranscriptomes, tRNA transcripts, and biogeochemical measurements, collected every 1.5 hours for 48 hours at two stations within coastal and adjacent offshore waters of the tropical Pacific Ocean. We expect that this integrated dataset of multiple sequence types and environmental parameters will facilitate novel insights into microbial ecology, microbial physiology, and ocean biogeochemistry and help investigate the different mechanisms of adaptation that drive microbial responses to environmental change.

microbiology↗

bioRxiv2025

RNA localization to nuclear speckles follows splicing logic

Nuclear speckles are membraneless organelles implicated in multiple RNA processing steps. In this work, we systematically characterize the sequence logic determining RNA localization to nuclear speckles. We find extensive similarities between the speckle localization code and the RNA splicing code, even for transcripts that do not undergo splicing. Specifically, speckle localization is enhanced by the presence of unspliced exon-like or intron-like sequence features. We demonstrate that interactions required for early splicesomal complex assembly contribute to speckle localization. We also show that speckle localization of isolated endogenous exons is reduced by disease-associated single nucleotide variants. Finally, we find that speckle localization strongly correlates with splicing kinetics of splicing-competent constructs and is tightly linked to the decision between exon inclusion and skipping. Together, these results suggest a model in which RNA speckle localization is associated with the formation of the early spliceosomal complex and enhances the efficiency of splicing reactions. HighlightsO_LISequences containing hallmarks of pre-mRNA dictate speckle localization C_LIO_LIRNA speckle localization is coupled to early spliceosome assembly C_LIO_LIDisease-associated single nucleotide variants reduce localization of isolated exons C_LIO_LIRNA speckle localization strongly correlates with splicing kinetics C_LI O_FIG O_LINKSMALLFIG WIDTH=191 HEIGHT=200 SRC="FIGDIR/small/656493v1_ufig1.gif" ALT="Figure 1"> View larger version (57K): org.highwire.dtl.DTLVardef@1efbb02org.highwire.dtl.DTLVardef@1deb7aaorg.highwire.dtl.DTLVardef@ec1ec2org.highwire.dtl.DTLVardef@1d78b72_HPS_FORMAT_FIGEXP M_FIG Graphical Abstract C_FIG

biochemistry↗

bioRxiv2021

Ancient genomes reveal long range influence of the site and culture of Tiwanaku

Tiwanaku was a civilization that flourished in the Lake Titicaca Basin (present-day Bolivia) between 500 and 1000 CE. At its apogee, Tiwanaku controlled the lakes southern shores and influenced certain areas of the Southern Andes. There is a considerable amount of archaeological and anthropological data concerning the Tiwanaku culture; however, our understanding of the population of the site of Tiwanaku is limited. To understand the population dynamics at different stages of the Tiwanaku cultural development, we analyzed 17 low-coverage genomes from individuals dated between 300 and 1500 CE. We found that the population from the Lake Titicaca Basin remained genetically unchanged throughout more than 1200 years, indicating that significant cultural and political changes were not associated with large scale population movements. In contrast, individuals excavated from Tiwanakus ritual core were highly heterogeneous, some with genetic ancestry from as far away as the Amazon, supporting the proposition of foreign presence at the site. However, mixed-ancestry individuals presence suggests they were local descendants of incomers from afar rather than captives or visiting pilgrims. A number of human offerings from the Akapana Platform dating to ca. 950 CE mark the end of active construction and maintenance of the monumental core and the wane of Tiwanaku culture. Significance StatementTiwanaku was an important pre-Inca polity in South America and an example of primary social complexity on par with civilizations in the Indus and Nile river valley. Flourishing between 500 and 1000 CE, Tiwanaku exercised control in the south Titicaca basin and influenced a vast area in southern Peru, Bolivia, and northern Chile. Comprehensive archeological studies provided information about the rise, expansion, and fall of the Tiwanaku culture, but little is known about the monumental sites population. To address this lacuna, we generated low coverage genomes for 17 individuals, revealing that while the Titicaca basins residential population was homogenous, the individuals excavated from the ritual core of Tiwanaku drew their ancestry from distant regions.

genomics↗

bioRxiv2020

Clonal thermal preferences affect the strength of the temperature-size rule

Genetically similar organisms act as a powerful study system for the subtle differences in various aspects of life histories. The issue of trade-offs among traits is of special interest. We used six parthenogenetic rotifer clones previously exposed to different thermal laboratory conditions. Interclonal differences in female body size were examined in common garden conditions. We estimated the population growth rate and strength of the size-to-temperature response across four thermal regimes. We tested hypotheses on the existence of the relationships between (i) thermal acclimation and species body size, (ii) thermal specialization and fitness and (iii) thermal specialization and strength of the temperature-size rule. Positive verification of (i) would make it justifiable to refer the other investigated traits to thermal preference and, further, to thermal specialization. Addressing the issues (ii) and (iii) is our pioneering contribution to the question on the strength of size-to-temperature response as differing across life strategies. We hypothesized that this plastic response may be affected by the level of thermal specialization and that this pattern may be traded off with the temperature-dependent potential for population growth rate. Additionally, we investigated the differences in reproductive strategy (number of eggs laid by a female and female lifetime duration) in one temperature assumed optimal, which acts as an important supplement to the general clonal life strategy. We confirmed that the thermal acclimation of a clone is related to body size, with clones acclimated to higher temperatures being smaller. We also found that warm-acclimated clones have a narrower thermal range (= are more specialized), and that the temperature-size rule is stronger in rotifers acclimated to intermediate thermal conditions than in specialists. Our results contribute into the issue of trade-offs between generalist and specialist strategies, in the context of plastic body size respone to different temperatures.

ecology↗

bioRxiv2020

Aerobic scope does matter in temperature-size rule, but only under optimal conditions

We united the theoretical predictions on the factors responsible for the occurrence and evolutionary significance of the temperature-size rule. We tested the causal connection among them assuming that (i) the temperature-size rule is the response to temperature-dependent oxygenic conditions, (ii) body size decrease is a consequence of cell shrinkage in response to exposure to hypoxia, (iii) this response enables to keep the wide scope for aerobic performance, and (iv) it prevents the decrease in fitness. We conducted our tests on three clones of the rotifer Lecane inermis with different thermal preferences. These clones were exposed to three experimental regimes: mild hypoxia, severe hypoxia driven by a too high temperature, and severe hypoxia driven by an inadequate oxygen concentration. The results showed that our causative reasoning was generally correct, but only under mildly hypoxic conditions. In more stressful environments, rotifers had clone- and condition-specific responses, which in fact were equally successful in terms of the levels of fitness. Our results join for the first time all factors connecting the cause and effect in the temperature-size rule. They indicate the importance of the conditions under which it should be tested. The most important messages from this study were that (i) a decrease in the body size was one of but not the only option for preventing fitness reduction under hypoxia, and (ii) such a response to higher temperature enabled the maintenance of wide aerobic scope in clone-specific, thermally optimal conditions.

ecology↗

bioRxiv2018

Identification of powdery mildew resistance QTL in Fragaria x ananassa

The obligate biotrophic fungus Podosphaera aphanis is the causative agent of powdery mildew on cultivated strawberry (Fragaria x ananassa). Genotypes from two bi-parental mapping populations Emily x Fenella and Redgauntlet x Hapil were phenotyped for powdery mildew disease severity in a series of field trials. Here we report multiple QTL associated with resistance to powdery mildew, identified in ten phenotyping events conducted across different years and locations. Seven QTL show a level of stable resistance across multiple phenotyping events however many other QTL were represented in a single phenotyping event and therefore must be considered transient. One of the identified QTL was closely linked to an associated resistance gene across the wider germplasm. Furthermore, a preliminary association analysis identified a novel conserved locus for further investigation. Our data suggests that resistance is highly complex and that multiple additive sources of quantitative resistance to powdery mildew exist across strawberry germplasm. Implementation of the reported markers in marker-assisted breeding or genomic selection would lead to improved powdery mildew resistant strawberry cultivars, particularly where the studied parents, progeny and close pedigree material are included in breeding germplasm.\n\nKey MessagePowdery mildew resistance in two strawberry mapping populations is controlled by both stable and transient novel QTL of moderate effect. Some transferability of QTL across wider germplasm was observed.

pathology↗