Would you like to confirm your cloning success with full plasmid sequencing?
NanoPlasmiQC allows automatic analysis of dozens of plasmids in a single ONT sequencing run. If you would like to test it with your own plasmids, read more in the preprint and feel free to reach out:
https://doi.org/10.64898/2026.04.01.715842
#Genomics #Bioinformatics #OpenScience #Biotechnology #SynBio #iGEM
@PuckerLab
New #ISEPpapers! Nucleomorph phylogenomics suggests a deep and ancient origin of cryptophyte plastids within Rhodophyta https://nph.onlinelibrary.wiley.com/doi/10.1111/nph.71116 by @animalculum et al.
#Protist #Algae #Microbes #Evolution #Nucleomorph #Genomics #Rhodophyta #Plastids
🧬 Can AI truly decode gene expression, or is it being misled by too much data?
🔗 Artificial Intelligence in Bulk RNA-Seq: Challenges and Potential Solutions. Computational and Structural Biotechnology Journal (CSBJ). DOI: https://doi.org/10.34133/csbj.0039
📚 CSBJ - A Science Partner Journal: https://spj.science.org/journal/csbj
#ArtificialIntelligence #MachineLearning #Bioinformatics #Genomics #RNAseq #ComputationalBiology #SystemsBiology #AI #PrecisionMedicine #BigData #AIinHealthcare
🧬 Next @deNBI training course: Nanopore Sequencing 101: 🧬
Join us for a deep dive into ONT technology! 🚀
📅 30 June - 2 July 2026
📍 Bielefeld, Germany
💻 Focus: Linux basics, Library Prep, de.NBI Cloud, Genome Assembly & Metagenomics.
🛠️ Tools: Dorado, Flye, CheckM, Bakta & more!
Perfect for PhDs & Postdocs. No prior bioinformatics knowledge required 🐧
Register here: https://www.denbi.de/training-courses-2026/2071-nanopore-sequencing-101-from-library-prep-to-genomics-and-metagenomic-analysis
#Genomics #Bioinformatics #Nanopore #ONT #Bielefeld #deNBI #ScienceTraining #Metagenomics #Linux
Genetic evidence for fluctuating selection has begun to accumulate for different species over the past few decades, especially for the Drosophila genus where studies have reported hundreds of loci undergoing putatively adaptive oscillations across successive seasons. However, most theoretical and simulation studies of fluctuating selection have relied on abstract or weakly parameterized models, making it difficult to assess their relevance for natural populations. In this study, we simulate multilocus seasonally fluctuating selection under a recently developed model and examine its effect on the variance effective population size (Ne) at a genome-wide scale. By recapitulating genomic, demographic, and evolutionary parameters from natural Drosophila populations in our simulations, we were able to reproduce allele frequency oscillations reported in recent studies and show that these lead to ~50% genome-wide reductions in Ne. We also demonstrate that Ne reductions are well predicted by the maximum frequency amplitude among all adaptively fluctuating loci, and that the frequency amplitudes are largely determined by the number of adaptively fluctuating loci and the strength of their epistatic interactions. Our results demonstrate that fluctuating selection can substantially reduce effective population size and underscore the importance of temporally variable selection in shaping genome-wide patterns of variation beyond classical models.
Background: Although strict maternal transmission of mitochondria is a general feature of animals and humans for ensuring homogeneity in mitochondrial DNA (mtDNA) across generations, exceptions were reported in the recent past. For example, some extremely rare but spectacular cases of heteroplasmy and paternal transmission in humans have questioned the universal evolutionary principle. Hence, as an alternative, the Mega-NUMT concept was coined to explain this discovery and was thereafter partly proven to exist. This concept expands on the quite common transfer of mtDNA fragments to the nucleus (NUMTs) by considering the existence of multicopy mitochondrial nuclear insertions. Mega-NUMT reports are currently restricted to a few cases in animals, including humans. However, even in humans, their detailed genomic organization, natural prevalence, and potential biological functions remain unclear. Methodology/Principal Findings: Here, we discovered that up to 60 full-sized mitochondrial genomes are integrated into the nuclear genome of the neotropical fruit fly Drosophila paulistorum using long-read sequencing and confirmed their presence by in situ hybridization. The copies are organized in one cluster on chromosome 3, which we, due to its similarity with the Mega-NUMT concept, designated the Dpau Mega-NUMT. Contrary to the rarity in humans, this Mega-NUMT is found at high prevalence (40%) in both long-term laboratory lines and natural D. paulistorum populations of different semispecies. Additionally, the mitochondrial copies in the Mega-NUMT cluster are phylogenetically separated from the current mitotypes of D. paulistorum. Together, these observations suggest long-term maintenance of the Mega-NUMT in nature. Hence, we propose that the Dpau Mega-NUMT may have been transferred to the nuclear genome before D. paulistorum semispecies radiation and maintained at relatively high prevalence in nature by balancing selection due to yet undetermined functions. Conclusions/Significance: To our knowledge, this is the first verified existence and detailed dissection of a Mega-NUMT outside cats and humans. We show that Mega-NUMTs can be persistent in nature, even at high prevalence, potentially due to balancing selection. Our findings strengthen the importance of high-quality long-read sequencing technologies for deciphering complex repeat-rich genomic regions to deepen our understanding of the dynamics of genome evolution within genomic dark matter. ### Competing Interest Statement The authors have declared no competing interest. FWF Austrian Science Fund, P28255B22, FW613A0501, FW613A0502 Swedish Research Council, 20144353
Sexual signals are thought to reflect metabolic capacity, allowing females to assess male genetic quality. In insects, cuticular hydrocarbons (CHCs) are central to mate recognition and sexual signalling, and their biosynthesis is directly tied to mitochondrial metabolism. Because mitochondrial performance requires coordination between the mitochondrial and nuclear genomes, non-compatible genomes may disrupt CHC production and reduce male attractiveness. We tested this prediction using a global Drosophila melanogaster mitonuclear panel comprising 80 cybrid genotypes. Multivariate analyses of male CHC profiles revealed strong nuclear effects, smaller but significant mitochondrial effects, and substantial non-additive mitonuclear interactions that accounted for ~10% of the variance after controlling for body mass. These interactions reorganised CHC blends in genotype-specific ways, with certain hydrocarbons contributing disproportionately to differentiation. In behavioural assays, females preferentially mated with males whose mitonuclear genomes were coadapted. Conversely, coadapted males had higher copulation success than males presenting disrupted combinations to the female. Our results demonstrate that mitonuclear compatibility influences the production of sexual signals and shapes reproductive outcomes, linking genomic interactions to mate choice. ### Competing Interest Statement The authors have declared no competing interest. Leverhulme Trust, RPG-2023-198 UK Research and Innovation, NE/V014307/1
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