2025 Hyper Recent •CC0 1.0 Universal

This work is dedicated to the public domain. No rights reserved.

Access Preprint From Server
January 22nd, 2025
Version: 1
Department of Plant Biology, University of Georgia, 2502 Miller Plant Sciences, Athens GA 30602, U.S.A
genomics
biorxiv

Low level contamination confounds population genomic analysis

Ward, A.Open in Google Scholar•Scopel, E. F. C.Open in Google Scholar•Shuman, B.Open in Google Scholar•Momany, M.Open in Google Scholar•Bensasson, D.Open in Google Scholar

Genome sequence contamination has a variety of causes and can originate from within or between species. Previous research focused primarily on cross-species contamination or on prokaryotes. This paper visualizes B-allele frequency to test for intra-species contamination, and measures its effects on phylogenetic and admixture analysis in two fungal species. Using a standard base calling pipeline, we found that contaminated genomes superficially appeared to produce good quality genome data. Yet as little as 5-10% genome contamination was enough to change phylogenetic tree topologies and make contaminated strains appear as hybrids between lineages (genetically admixed). We recommend the use of B-allele frequency plots to screen genome resequencing data for intra-species contamination.

Similar Papers

biorxiv
Tue Apr 01 2025
BioToken and BioFM - Biologically-Informed Tokenization Enables Accurate and Efficient Genomic Foundation Models
Genomic variation underlies human phenotypic diversity, disease susceptibility, and evolutionary adaptation. Although large-scale genomic sequencing has transformed our ability to map genetic variation, accurately modeling and interpreting this data remains challenging due to fundamental limitations in existing genomic foundation models (GFMs). Current genomic models typically treat DNA simplistic...
Medvedev, A.
•
Viswanathan, K.
•
Kanithi, P.
•
Vishniakov, K.
...•
Khan, S.
biorxiv
Tue Apr 01 2025
Exonic enhancers are a widespread class of dual-function regulatory elements
Exonic enhancers (EEs) occupy an under-appreciated niche in gene regulation. By integrating transcription factor binding, chromatin accessibility, and high-throughput enhancer-reporter assays, we demonstrate that many protein-coding exons possess enhancer activity across species. These EEs exhibit characteristic epigenomic signatures, form long-range interactions with gene promoters, and can be al...
Mouren, J.-C.
•
Torres, M.
•
van Ouwerkerk, A.
•
Manosalva, I.
...•
Ballester, B.
biorxiv
Tue Apr 01 2025
Multimodal epigenetic and enhancer network remodeling shape the transcriptional landscape of beige adipocytes
Epigenetic regulation is a key determinant of adipocyte fate and function, conferring phenotypic plasticity to adipose tissue in response to metabolic and thermal challenges. To understand the spatiotemporal regulation of chromatin during the establishment of a beige thermogenic adipocyte phenotype, we analyzed the transcriptomic, epigenetic, and enhancer connectome dynamics during white and beige...
Hazell Pickering, S.
•
Galigniana, N. M.
•
Abdelhalim, M.
•
Sorensen, A. L.
...•
BRIAND, N.
biorxiv
Tue Apr 01 2025
Trypanosoma cruzi Has 32 Chromosomes: A Telomere-to-Telomere Assembly Defines Its Karyotype.
Trypanosoma cruzi, the causative agent of Chagas disease, exhibits remarkable genomic plasticity and possesses an expanded genome rich in multigene families. However, its precise chromosomal composition has remained elusive due to challenges in resolving repetitive regions. Using PacBio HiFi long-read sequencing, we assembled the complete nuclear genome of the Dm28c strain into 32 telomere-to-telo...
Greif, G.
•
Diaz-Viraque, F.
•
Chiribao, M. L.
•
Sanz-Rodriguez, C.
•
Robello, C.
biorxiv
Tue Apr 01 2025
Illuminating the mystery of thylacine extinction: a role for relaxed selection and gene loss
Gene loss shapes lineage-specific traits but is often overlooked in species survival. In this study, we investigate the role of ancestral gene loss using the extinction icon-thylacine (Thylacinus cynocephalus). While studies of neutral genetic variation indicate a population decline before extinction, the impact of thylacine-specific ancestral gene losses remains unexplored. The availability of a ...
Salve, B. G.
•
Vijay, N.
biorxiv
Mon Mar 31 2025
Sex chromosome dosage compensation in a sex reversing skink is not influenced by sexual phenotype
Background Lizards have sex determination systems that can differ between even closely related species. These include XY and ZW systems, and thermolabile systems where genes and temperature interact to determine sex. The eastern three-lined skink (Bassiana duperreyi) has a differentiated XY sex determination system, in which low temperature incubation during development can cause female to male se...
Hanrahan, B. J.
•
Chang, J. K.
•
Milton, A. M.
•
Lister, N. C.
...•
Waters, P. D.
biorxiv
Sun Mar 30 2025
A Single-Cell Atlas of RNA Alternative Splicing in the Glioma-Immune Ecosystem
Single-cell analysis has refined our understanding of cellular heterogeneity in glioma, yet RNA alternative splicing (AS) - a critical layer of transcriptome regulation - remains underexplored at single-cell resolution. Here, we present a pan-glioma single-cell AS analysis in both tumor and immune cells through integrating seven SMART-seq2 datasets of human gliomas. Our analysis reveals lineage-sp...
Song, X.
•
Tiek, D.
•
Lu, M.
•
Yu, X.
...•
Cheng, S.-Y.
biorxiv
Sun Mar 30 2025
Antagonistic Regulation of LINE-1/Alu Elements and Their Repressor APOBEC3B in Cellular Senescence
Long Interspersed Nuclear Elements-1 (LINE-1 or L1) make up approximately 21% of the human genome, with some L1 loci containing intact open reading frames (ORFs) that facilitate retrotransposition. Because retrotransposition can have deleterious effects leading to mutations and genomic instability, L1 activity is typically suppressed in somatic cells through transcriptional and post-transcriptiona...
Munot, D. N.
•
Najjar, G.
•
Singh, M.
•
guenes, C.
...•
Arora, A.
biorxiv
Sun Mar 30 2025
Genomic erosion through the lens of comparative genomics
Loss of genetic diversity threatens species survival, yet the dynamics of such loss and species\' responses thereof can vary widely depending on their evolutionary histories, life-history traits and demographic trajectories. Comparative genomics offers a powerful framework to explore the dynamics of genomic erosion across species. Here, we analysed the genomes of three species -- the Mauritius par...
Wang, X.
•
Fontsere, C.
•
Caballero, X. A.
•
Nielsen, S. D.
...•
Morales, H. E.
biorxiv
Sun Mar 30 2025
Exploring the mycovirome: novel and diverse mycoviruses in Botrytis cinerea
Botrytis cinerea is a necrotrophic fungal pathogen that causes significant economic losses to many crops.The management of B. cinerea is difficult due to a rise in fungicide resistance. Harnessing mycoviruses that cause hypovirulence in B. cinerea is a promising alternative.This research explored, for the first time in Canada, the mycovirome of B. cinerea. Isolates of B. cinerea were collected fro...
Drury, S. C.
•
Poursalavati, A.
•
Lemoyne, P.
•
Xu, D.
...•
Fall, M. L.