Biology subjects

Apuli, R.-P.

Publications and source records attributed to Apuli, R.-P..

3 recordsLinked to original sources

bioRxiv2026

Whole-genome duplication drives biosynthetic gene cluster fragmentation and regulatory rewiring of monoterpene indole alkaloid metabolism in Strychnos

Whole-genome duplications (WGDs) reshape plant genomes by generating redundancy, after which lineage-specific architectures emerge through fractionation, gene loss and rearrangement. How specialized metabolic pathways remain functionally integrated after such large-scale restructuring remains poorly understood. This problem is especially relevant for biosynthetic gene clusters (BGCs), which physically organize specialized-metabolism genes yet can be disrupted by post-duplication rearrangement. Here, we present the first chromosome-level genomes for Loganiaceae, including near telomere-to-telomere assemblies of Strychnos ignatii and S. pubescens, together with a draft genome of the extinct species S. ridleyi. Following a lineage-specific WGD, the two extant Strychnos species evolved contrasting genome-evolutionary trajectories and metabolite profiles: S. ignatii shows expansion of monoterpenoid- and monoterpene indole alkaloid (MIA)-associated gene families and strychnine-type MIA dominance, whereas S. pubescens exhibits elevated transposable element activity associated with DNA-binding with one finger (DOF)-linked regulatory rewiring and broader sesquiterpenoid- and triterpenoid-rich chemistry. Crucially, both species retain active strychnine biosynthesis despite fragmentation of a deeply conserved alkaloid BGC in MIA-producing Gentianales, revealing how pathway function can persist after disruption of ancestral BGC architecture. Comparative metabolomic and transcriptomic pathway analyses indicate norfluorocurarine oxidase (NO) as a major divergence point associated with strychnine accumulation. Promoter analyses, yeast one-hybrid assays, and electrophoretic mobility shift assays support a model in which S. ignatii retains the canonical jasmonate-responsive MYB, MYC2/bHLH, and AP2/ERF cis-regulatory module at NO, whereas the orthologous S. pubescens promoter shows reduced capacity to recruit these activators and instead exhibits a DOF-associated architecture. Together, our results show that WGD can decouple physical cluster architecture from pathway function, allowing specialized metabolic pathways to remain active while divergent chemical phenotypes evolve through lineage-specific combinations of coding-space expansion and transposable-element-associated cis-regulatory rewiring.

evolutionary biology↗

bioRxiv2020

The genetic basis of adaptation in phenology in an introduced population of Black Cottonwood (Populus trichocarpa, Torr. & Gray)

O_LIEntering and exiting winter dormancy presents important trade-offs between growth and survival at northern latitudes and many forest trees display local adaptation across latitude. Transfers of a species outside its native range introduce the species to novel combinations of environmental conditions potentially requiring different combinations of alleles to optimize growth. C_LIO_LIWe performed genome wide association analyses and a selection scan in a P. trichocarpa mapping population derived from crossings between clones collected across the native range and introduced into Sweden. GWAS analyses were performed using phenotypic data collected across two field seasons and in a controlled phytotron experiment. C_LIO_LIWe uncovered 629 putative candidate genes associated with spring and autumn phenology traits as well as with growth. Many regions harboring variation significantly associated with the initiation of leaf shed and leaf autumn coloring appeared to have been evolving under positive selection in the native environments of P. trichocarpa. C_LIO_LIA comparison between the candidate genes identified with results from earlier GWAS analyses performed in the native environment found a smaller overlap for spring phenology traits than for autumn phenology traits, aligning well with earlier observations that spring phenology transitions have a more complex genetic basis that autumn phenology transitions. C_LI

evolutionary biology↗

bioRxiv2019

Constructing a high-density linkage map to infer the genomic landscape of recombination rate variation in European Aspen (Populus tremula)

The rate of meiotic recombination is one of the central factors determining levels of linkage disequilibrium and the efficiency of natural selection, and many organisms show a positive correlation between local rates of recombination and levels of nucleotide diversity indicating that linked selection is an important factor determining genome-wide levels of nucleotide diversity. Several methods for estimating recombination rates from segregating polymorphisms in natural populations have recently been developed. These methods have been extensively used in part because they are relatively simple to implement even in many non-model organisms, but also because they potentially offer higher resolution than traditional map-based methods. However, thorough comparisons of LD and map-based estimates of recombination are not readily available in plants. Here we present a new, high-resolution linkage map for Populus tremula and use this to estimate variation in recombination rates across the P. tremula genome. We compare these results to recombination rates estimated based on linkage disequilibrium in a large number of unrelated individuals. We also assess how variation in recombination rates is associated with genomic features, such as gene density, repeat density and methylation levels. We find that recombination rates obtained from the two methods largely agree, although the LD-based method identify a number of genomic regions with very high recombination rates that the map-based method fail to detect. Linkage map and LD-based estimates of recombination rates are positively correlated and show similar correlations with other genomic features, showing that both methods can accurately infer recombination rate variation across the genome.

evolutionary biology↗