Biology subjects

Salojarvi, J.

Publications and source records attributed to Salojarvi, J..

14 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↗

bioRxiv2025

BBX transcription factor evolution in the green plant lineage

BBX transcription factors play versatile roles in integrating environment cues and regulating plant development. The model plant Arabidopsis continues to be a primary tool for the molecular investigation of protein function, but comprehensive evolutionary studies across different plant species can support translational research. Here, we constructed robust maximum likelihood phylogenies of full-length BBX proteins, the B-box domain, and the CCT domains by using diverse plant species ranging from algae to eudicots and monocots. Our analysis resolved five major structural groups (I-V) with BBXs from algae at the root of major clades. Our results suggest that Group II emerged after the split between Chlorophytes and Streptophytes. Our results also highlight subgroupings in the different BBXs clades. The evolution of the B-box domains showed a dynamic domain losses and acquisitions overall correlating with the BBX phylogeny. While the CCT domain was overall highly conserved across all groups, we identified secondary loss of the CCT domain in select lineages. We also detected significant expansions and contractions among angiosperm BBX orthogroups. Overall, the BBX family demonstrates ancient origins, structural plasticity via domain gain, loss and duplication, and lineage-specific innovations that underpin their diverse roles in light signaling, development and stress responses.

plant biology↗

bioRxiv2025

Maximum likelihood point estimates for improved population genetics statistics

Likelihood-based approaches that incorporate the uncertainty in basecalling have become a standard approach in genotyping. Likewise, the accuracy of population genetic estimators could be improved if these uncertainties could be taken into account. Moreover, the classic asymptotically unbiased estimators for population genetic parameters may yield impossible values with finite data, and introduce a median bias driven by sample size, which complicates the comparison of populations of different sizes. Here we develop an approach (https://github.com/anulin/PiThetic) that more accurately estimates the population genetic parameters and addresses the question of comparison (median) bias. Our approach improves by directly estimating population genetic parameters from basecall accuracies in terms of Phred scores, instead of using allele frequencies. We provide three improvements to classic statistical estimates: (i) we apply Phred scores to improve the accuracy of the estimates, (ii) we show how the pursuit for an unbiased estimator can lead to impossible and/or less accurate values, and provide a corrected estimator, and (iii) we provide a new estimator that minimizes the median bias for nucleotide diversity and another estimator that reduces error for D, because the standard Watterson {theta} and Tajimas D estimators have high error. Overall, this work facilitates the more accurate estimation of population genetics statistics from sequencing data.

genomics↗

bioRxiv2025

Contrasting centromere structures in carnivorous sundews uncover a dynamic evolutionary trajectory shaped by polyploidy and chromosomal remodeling

Centromeres are essential for chromosome function, yet their role in shaping genome evolution in polyploid plants remains poorly understood. Allopolyploidy, where post-hybridization genome doubling merges parental genomes that may differ markedly in chromosomal architecture, has the potential to increase centromeric complexity and influence genomic plasticity. We explore this possibility in carnivorous Caryophyllales, a morphologically and chromosomally diverse plant lineage encompassing sundews, Venus flytraps, and Nepenthes pitcher plants. Focusing on sundews (Drosera), we generated chromosome-scale assemblies of holocentric D. regia and monocentric D. capensis, which share an allohexaploid origin but have diverged dramatically in genome structure. D. regia retains ancestral chromosomal fusions, dispersed centromeric repeats, and conserved synteny, whereas D. capensis exhibits extensive chromosomal reorganization and regionally localized centromeres after a lineage-specific genome duplication. Phylogenomic evidence traces D. regia to an ancient hybridization between sundew- and Venus flytrap-like ancestors, setting it apart within its infrageneric context. Genus-wide satellite DNA repeat profiling reveals rapid turnover and species-level variation in centromere organization. Together, these results establish sundews as a natural system for investigating how centromere dynamics interact with recurrent polyploidization and episodes of ecological innovation to shape genomic resilience.

genomics↗

bioRxiv2025

Single-cell and spatial transcriptomics uncover the role of B chromosomes in driving plant invasiveness

Invasive plants pose a major threat to global biodiversity, yet the molecular and genomic mechanisms underlying their success remain poorly understood. Here, we investigate the common reed (Phragmites australis), a grass species that became invasive in North America after introduction from Europe, to unravel the molecular mechanisms of its invasiveness. By integrating single-cell RNA sequencing, spatial transcriptomics, and comparative genomics, we constructed a single-cell atlas of P. australis and identified 19 transcriptionally distinct cell types, including shoot apical meristem, epidermal, and vascular tissues. Comparative analysis of common garden-grown native (European) and invasive (North American) populations revealed a significant proportion of differentially expressed genes (DEGs) located on B chromosomes, which underwent copy number expansion in invasive genomes. The proportion of B chromosome genes in DEGs varies across cell types, with the highest proportions observed in the epidermis and mesophyll, and lower proportions in the vascular tissues. Gene IMPA-3, a B chromosome gene likely derived from transposable element activity, exhibited an elevated mutation rate compared to its ancestral counterparts, potentially enhancing adaptive evolution in invasive populations. Invasive individuals also displayed molecular regulatory networks related to photosynthetic efficiency, stress tolerance, and growth-defense trade-offs. Together, our findings provide a cell-type-resolved molecular atlas of a non-model invasive plant and offer key insights into the cellular and genomic architecture of plant invasiveness, with implications for ecological management.

evolutionary biology↗

bioRxiv2024

Late Quaternary climatic impact on the woodland strawberry genome: a perennial herb's tale

Exploring a species paleohistory is crucial for understanding its responsiveness to climatic events, identifying drivers of adaptation, and developing effective biodiversity conservation strategies in the face of ongoing climate change. We analyzed 200 genomes of the perennial herb woodland strawberry (Fragaria vesca L.) from across Europe and investigated the population structure and demographic history of the species during past geoclimatic events. We found a clear division of populations into western and eastern genetic clusters, indicative of distinct glacial refugia and adaptations to variation in temperature seasonality. The eastern core populations were several times larger (defined as effective population size, NE) than populations in other regions, showed no evidence of inbreeding, and were resilient to several glacial maxima. However, we observed decreasing NE and higher inbreeding in populations toward range edges, particularly in the north, where these individuals went through bottlenecks during glaciations. Population divergence suggested that western and eastern Europe were colonized from separate refugia in multiple waves during the Holocene, while the largest current populations from the northern Mediterranean to southern regions of the Nordic countries formed a connected population chain with gene flow between eastern core populations and western Europe, primarily occurring through Central Europe. Similar patterns of colonization and hybridization may have occurred during past interglacial periods, contributing to the present-day population structure of woodland strawberry. We suggest that the unprecedented resolution of the species climatic history across six glacial-interglacial cycles presented here holds the promise of transforming the general understanding of species paleohistory through geoclimatically tracing ancestral haplotypes.

plant biology↗

bioRxiv2023

The genome and population genomics of allopolyploid Coffea arabica reveal the diversification history of modern coffee cultivars

Coffea arabica, an allotetraploid hybrid of C. eugenioides and C. canephora, is the source of approximately 60% of coffee products worldwide, and its cultivated accessions have undergone several population bottlenecks. We present chromosome-level assemblies of a di-haploid C. arabica accession and modern representatives of its diploid progenitors, C. eugenioides and C. canephora. The three species exhibit largely conserved genome structures between diploid parents and descendant subgenomes, with no obvious global subgenome dominance. We find evidence for a founding polyploidy event 350,000-610,000 years ago, followed by several pre-domestication bottlenecks, resulting in narrow genetic variation. A split between wild accessions and cultivar progenitors occurred [~]30.5 kya, followed by a period of migration between the two populations. Analysis of modern varieties, including lines historically introgressed with C. canephora, highlights their breeding histories and loci that may contribute to pathogen resistance, laying the groundwork for future genomics-based breeding of C. arabica.

genomics↗

bioRxiv2023

Complex Polyploids: Origins, Genomic Composition, and Role of Introgressed Alleles

AbstractIntrogression allows polyploid species to acquire new genomic content from diploid progenitors or from other unrelated diploid or polyploid lineages, contributing to genetic diversity and facilitating adaptive allele discovery. In some cases, high levels of introgression elicit the replacement of large numbers of alleles inherited from the polyploids ancestral species, profoundly reshaping the polyploids genomic composition. In such complex polyploids it is often difficult to determine which taxa were the progenitor species and which taxa provided additional introgressive blocks through subsequent hybridization. Here, we use population-level genomic data to reconstruct the phylogenetic history of Betula pubescens (downy birch), a tetraploid species often assumed to be of allopolyploid origin and which is known to hybridize with at least four other birch species. This was achieved by modeling of polyploidization and introgression events under the multispecies coalescent and then using an approximate Bayesian computation (ABC) rejection algorithm to evaluate and compare competing polyploidization models. We provide evidence that B. pubescens is the outcome of an autoploid genome doubling event in the common ancestor of B. pendula and its extant sister species, B. platyphylla, that took place approximately 178,000-188,000 generations ago. Extensive hybridization with B. pendula, B. nana, and B. humilis followed in the aftermath of autopolyploidization, with the relative contribution of each of these species to the B. pubescens genome varying markedly across the species range. Functional analysis of B. pubescens loci containing alleles introgressed from B. nana identified multiple genes involved in climate adaptation, while loci containing alleles derived from B. humilis revealed several genes involved in the regulation of meiotic stability and pollen viability in plant species.

genomics↗

bioRxiv2021

Insights into bear evolution from a Pleistocene polar bear genome

The polar bear (Ursus maritimus) has become a symbol of the threat to biodiversity from climate change. Understanding polar bear evolutionary history may provide insights into apex carnivore responses and prospects during periods of extreme environmental perturbations. In recent years, genomic studies have examined bear speciation and population history, including evidence for ancient admixture between polar bears and brown bears (Ursus arctos). Here, we extend our earlier studies of a 130,000-115,000-year-old polar bear from the Svalbard Archipelago using a 10X coverage genome sequence and ten new genomes of polar and brown bears from contemporary zones of overlap in northern Alaska. We demonstrate a dramatic decline in effective population size for this ancient polar bears lineage, followed by a modest increase just before its demise. A slightly higher genetic diversity in the ancient polar bear suggests a severe genetic erosion over a prolonged bottleneck in modern polar bears. Statistical fitting of data to alternative admixture graph scenarios favors at least one ancient introgression event from brown bears into the ancestor of polar bears, possibly dating back over 150,000 years. Gene flow was likely bidirectional, but allelic transfer from brown into polar bear is the strongest detected signal, which contrasts with other published works. These findings may have implications for our understanding of climate change impacts: polar bears, a specialist Arctic lineage, may not only have undergone severe genetic bottlenecks, but also been the recipient of generalist, boreal genetic variants from brown bear during critical phases of Northern Hemisphere glacial oscillations. SignificanceInterspecific hybridization is a widespread phenomenon, but measuring its extent, directionality, and adaptive importance remains challenging. Ancient genomes, however, can help illuminate the history of modern organisms. Here, we present a genome retrieved from a 130,000-115,000-year-old polar bear and perform genome analyses of modern polar and brown bears throughout their geographic range. We find that the principal direction of ancient allele sharing was from brown bear into polar bear, although gene flow between them has likely been bidirectional. This inverts the current paradigm of unidirectional gene flow from polar into brown bear, and it suggests that polar bears were recipients of external genetic variation prior to their extensive population decline.

evolutionary biology↗

bioRxiv2021

Convergent evolution of mevalonate pathway in Inonotus obliquus and Betula pendula.

Inonotus obliquus, Chaga mushroom, is a fungal species from Hymenochaetaceae family (Basidiomycota) which has been widely used for traditional medicine in Europe and Asia. Here, chaga genome was sequenced using Pacbio sequencing into a 50.7Mbp assembly consisting of 301 primary contigs with an N50 value of 375 kbp. Genome evolution analyses revealed a lineage-specific whole genome duplication event and an expansion of Cytochrome P450 superfamily. Fungal biosynthetic clusters were enriched for tandemly duplicated genes, suggesting that biosynthetic pathway evolution has proceeded through small-scale duplications. Metabolomic fingerprinting confirmed a highly complex terpene biosynthesis chemistry when compared against related fungal species lacking the genome duplication event.

evolutionary biology↗

bioRxiv2021

Genome-wide analysis illustrates the effect of polyploidization in Phragmites australis

Polyploidization is a common event in plant evolution, and it plays an important role in plant speciation and adaptation. To address the role of polyploidization in grass diversification, we studied Phragmites australis, a species with intraspecific variation of chromosome numbers ranging from 2n=36 to 144. A combined analysis of genome structure, phylogeny and population genetics were used to study the evolution of P. australis. Whole-genome sequencing of three representative lineages revealed the allopolyploid origin of the species, with subgenome divergence dating back to approximately 29 million years ago, and the genomes showed hallmarks of relaxed selection associated with asexual propagation. Genome-wide analysis of 88 individuals from different populations around the world using restriction site associated DNA sequencing (RAD-seq) identified seven main intraspecific lineages with extensive genetic admixture. Each lineage was characterized by a distinct ploidy level, mostly tetraploid or octoploid, suggesting several polyploid events. Furthermore, we observed octoploid and hexaploid lineages at contact zones in Romania, Hungary and South Africa, suggestively due to genomic conflicts in allotetraploid parental lineages. Polyploidy may have evolved as a strategy to escape from the evolutionary dead-end of asexual propagation and the resulting decrease in genomic plasticity.

evolutionary biology↗

bioRxiv2020

The photoreceptor UVR8 mediates the perception of both UV-B and UV-A wavelengths up to 350 nm of sunlight with responsivity moderated by cryptochromes

The photoreceptors UV RESISTANCE LOCUS 8 (UVR8) and CRYPTOCHROMES 1 and 2 (CRYs) play major roles in the perception of UV-B (280-315 nm) and UV-A/blue radiation (315-500 nm), respectively. However, it is poorly understood how they function in sunlight. The roles of UVR8 and CRYs were assessed in a factorial experiment with Arabidopsis thaliana wild-type and photoreceptor mutants exposed to sunlight for 6 h or 12 h under five types of filters with cut-offs in UV and blue-light regions. Transcriptome-wide responses triggered by UV-B and UV-A wavelengths shorter than 350 nm (UV-Asw) required UVR8 whereas those induced by blue and UV-A wavelengths longer than 350 nm (UV-Alw) required CRYs. UVR8 modulated gene expression in response to blue light while lack of CRYs drastically enhanced gene expression in response to UV-B and UV-Asw. These results agree with our estimates of photons absorbed by these photoreceptors in sunlight and with in vitro monomerization of UVR8 by wavelengths up to 335 nm. Motif enrichment analysis predicted complex signaling downstream of UVR8 and CRYs. Our results highlight that it is important to use UV waveband definitions specific to plants photomorphogenesis as is routinely done in the visible region.

plant biology↗

bioRxiv2019

The Avocado Genome Informs Deep Angiosperm Phylogeny, Highlights Introgressive Hybridization, and Reveals Pathogen Influenced Gene Space Adaptation

The avocado, Persea americana, is a fruit crop of immense importance to Mexican agriculture with an increasing demand worldwide. Avocado lies in the anciently-diverged magnoliid clade of angiosperms, which has a controversial phylogenetic position relative to eudicots and monocots. We sequenced the nuclear genomes of the Mexican avocado race, P. americana var. drymifolia, and the most commercially popular hybrid cultivar, Hass, and anchored the latter to chromosomes using a genetic map. Resequencing of Guatemalan and West Indian varieties revealed that [~]39% of the Hass genome represents Guatemalan source regions introgressed into a Mexican race background. Some introgressed blocks are extremely large, consistent with the recent origin of the cultivar. The avocado lineage experienced two lineage-specific polyploidy events during its evolutionary history. Although gene-tree/species-tree phylogenomic results are inconclusive, syntenic ortholog distances to other species place avocado as sister to the enormous monocot and eudicot lineages combined. Duplicate genes descending from polyploidy augmented the transcription factor diversity of avocado, while tandem duplicates enhanced the secondary metabolism of the species. Phenylpropanoid biosynthesis, known to be elicited by Colletotrichum (anthracnose) pathogen infection in avocado, is one enriched function among tandems. Furthermore, transcriptome data show that tandem duplicates are significantly up- and down-regulated in response to anthracnose infection, whereas polyploid duplicates are not, supporting the general view that collections of tandem duplicates contribute evolutionarily recent \"tuning knobs\" in the genome adaptive landscapes of given species.\n\nSIGNIFICANCE STATEMENTAvocado is a nutritious, economically important fruit species that occupies an unresolved position near the earliest evolutionary branchings of flowering plants. Our nuclear genome sequences of Mexican and Hass variety avocados inform ancient evolutionary relationships and genome doublings, the admixed nature of Hass, and provide a look at how pathogen interactions have shaped avocados more recent genomic evolutionary history.

genomics↗

bioRxiv2019

ELIMAKI locus is required for mechanosensing and proprioception in birch trees

The remarkable vertical and radial growth observed in tree species, encompasses a major physical challenge for wood forming tissues. To compensate with increasing size and weight, cambium-derived radial growth increases the stem width, thereby supporting the aerial body of trees. This feedback appears to be part of a so-called \"proprioception\" (1, 2) mechanism that controls plant size and biomass allocation. Yet, how trees experience or respond to mechanical stress derived from their own vertical loading, remains unknown. Here, we combined two strategies to dissect the proprioceptive response in birch. First, we show that in response to physical loading, trees promote radial growth with different magnitudes along the stem. Next, we identified a mutant cultivar (B. pubescens cv. Elimaki) in which the main stem shows normal vertical development, but collapses after three months. By inducing precocious flowering, we generated a backcrossed population (BC1) by producing two generations in 4 years. In his scheme, we uncovered a recessive trait (eki) that segregates and genetically maps with a Mendelian monogenic pattern. Unlike WT, eki is resistant to vertical mechanical stimulation. However, eki responds normally to the gravitropic stimulus by making tension wood. Before the collapse, cell size in eki is compromised resulting in radial growth defects, depending on stem height. Cell walls of developing xylem and phloem tissues have delayed differentiation in eki, and its tissues are softer compared to WT as indicated by atomic force microscopy (AFM). The transcriptomic profile of eki highlighted the overlap with that of the Arabidopsis response to touch. Taken together, our results suggest that the mechanical environment and cell wall properties of developing woody tissues, can significantly affect the growth responses to vertical loading thereby compromising their proprioceptive capacity. Additionally, we introduce a fast forward genetics strategy to dissect complex phenotypes in trees.

plant biology↗