bioRxiv Science⌕ Search
Home/Archive/bioRxiv

bioRxiv · 10.64898/2026.10.08.757646

Organelle intergenic DNA is preferentially distributed between opposite-polarity gene pairs.

Sanita Lima, M.·Dupin, B.·Smith, D. R.
View original source ↗Export metadata ↓

Abstract

Across eukaryotes, mitochondrial and plastid genomes vary enormously in size and noncoding content. This variation is often attributed to diverging mutation rates, DNA repair mechanisms, and the power of genetic drift. Although these processes can help explain how much noncoding DNA an organelle genome may retain, they do not explain how this noncoding DNA is distributed throughout the genome. We analyzed over 2.6 million intergenic regions (IGRs) from ~37,000 mitochondrial and plastid genomes to test whether gene-pair polarity marks local differences in the distribution of organelle intergenic DNA. Taxonomy-structured mixed models, controlling for flanking-gene length and type, showed that IGRs between opposite-polarity gene pairs were 1.1-3.2-fold longer than those between same-polarity genes. IGRs between convergent (+-) and divergent (-+) gene pairs showed distinct residual-dispersion patterns, indicating that they are not homogeneous in their length distribution. The prevalence of opposite-polarity gene pairs showed no consistent relationship with organelle genome size or intergenic DNA fraction. Ultimately then, gene-pair polarity consistently marks where organelle intergenic DNA is preferentially located.

Explore related subjects

evolutionary biologyPreprint

Keep this discovery

Explore connections, maps & timelines

BibTeXRIS

Sanita Lima, M., Dupin, B., Smith, D. R.. 2026-10-10. Organelle intergenic DNA is preferentially distributed between opposite-polarity gene pairs.. https://doi.org/10.64898/2026.10.08.757646

Cite the original work for its findings. Save a collection to share your selection of sources.

KEEP EXPLORING

Related preprints

bioRxiv2026

An unconstrained Euclidean parametrisation of phylogenetic tree space

Phylogenetic trees combine a discrete topology with continuous branch lengths, which makes them difficult to work with. We introduce a recursive contour-grafting construction that encodes both components using unconstrained real-valued coordinates. After fixing an order of the leaves, each new leaf is attached at a point selected by a contour traversal of the tree constructed so far. Moving a graft coordinate continuously along the contour enables changes of topology when internal branches contract to zero. For trees with n labelled leaves, we apply the construction to rooted ultrametric trees, rooted trees with unrestricted branch lengths, and unrooted trees, obtaining parametrisations of dimensions n-1, 2n-2, and 2n-3, respectively. We show that the resulting construction functions are surjective and continuous onto the corresponding spaces of phylogenetic trees. We also determine the number of representations of a generic tree and calculate the Jacobian of each parametrisation. These results provide explicit change-of-variables formulae between Euclidean coordinates and the phylogenetic tree spaces, and we show how probability distributions on tree space can be sampled using generic algorithms that target unconstrained Euclidean coordinates. This approach paves the way for the development and application of new methodology in Bayesian phylogenetic inference.

evolutionary biology↗
bioRxiv2026

Triangulating evidence to detect signatures of stabilizing selection acting on protein levels in humans

Stabilizing selection is thought to maintain quantitative traits near evolutionary optima, yet the extent to which it constrains human molecular phenotypes remains largely unknown. Here, we investigate signatures of stabilizing selection on the circulating levels of 2'923 plasma proteins in up to 50'000 UK Biobank participants by integrating complementary evidence across evolutionary timescales. We combine genetic signatures of selection accumulated over generations with associations between protein abundance and contemporary fitness-related outcomes. Genetic evidence was assessed using the frequency-dependent architecture of common variants with LDpred2 and a newly developed likelihood-based framework leveraging rare loss-of-function variant burdens. Contemporary evidence was obtained through quadratic associations between protein abundance and three fitness proxies: reproductive success, somatic health, and parental longevity. Across all approaches, negative selection coefficients predominated. Among significant estimates, 100% of common-variant and 92.4% of rare-variant estimates were consistent with stabilizing selection, compared with 99.8% for somatic health, 97.7% for parental longevity, and 89.3% for reproductive success. Despite capturing distinct aspects of selection, the approaches showed partial convergence. Rare-variant-based estimates correlated with health-score-derived coefficients (rho = 0.36, p = 5.2 x 10^-6) and independent measures of evolutionary constraint, including protein heritability, loss-of-function intolerance, and cross-species transcript evolutionary rates. Together, our findings suggest that stabilizing selection is widespread across the human plasma proteome and highlight the value of integrating genetic architecture with fitness-related phenotypes to understand evolutionary constraints on molecular variation.

evolutionary biology↗
bioRxiv2026

Strain-specific higher-order interactions break phylogenetic conservatism in microbial communities

Whether strains of the same species sharing the same ecological role are truly interchangeable has not been directly tested experimentally in communities, where higher-order interactions govern outcomes. Using 79 co-occurring Bacillaceae isolates from the Cuatrocienegas Basin, we combined whole-genome analyses with systematic strain substitutions in BARS, a three-species community in which a resistant strain protects a sensitive strain from an antagonist. Trait conservatism strongly predicted pairwise antagonistic outcomes. Yet across 34 assembled triads, 13 showed rescue beyond pairwise expectations and five showed suppression; single-strain substitutions rarely restored protection, although protection was recovered in one fully reconfigured triad. These outcomes could not be inferred from taxonomic relatedness, pangenomic content or pairwise assays; phylogenetic conservatism thus reaches its limit at the transition from pairwise to higher-order interactions. To explain this limit, we propose that strains behave as non-equivalent biological tiles whose interaction edges must align, a dynamic biological tessellation.

evolutionary biology↗