Biology subjects

Paajanen, P.

Publications and source records attributed to Paajanen, P..

14 recordsLinked to original sources

bioRxiv2026

A wheat immune receptor pair executes cell death through a helper MLKL

To promote disease resistance, plant nucleotide-binding, leucine-rich repeat (NLR) immune receptors often require paired co-receptors. In many cases, paired NLRs comprise one NLR to perceive effectors (the sensor) and another NLR to execute cell death (the helper). However, NLRs can also pair with sensor kinase fusion protein (KFP) receptors, but whether non-NLR components within such pairs can execute cell death, remains unclear. Here, we investigate the mechanism of an immune receptor pair comprising the wheat NLR Rwt3.6.8 NLR (R3NLR) and an MLKL protein, Rwt3.6.8 associated kinase (R3AK). Using Nicotiana benthamiana transient expression assays we confirmed that both R3NLR and R3AK are required for cell death in response to blast pathogen effectors PWT3, PWT6 or PWT8. Through mutational analysis we show the 4-helical bundle (4HB) domain of R3AK is required to execute cell death and R3AK can be made auto-active by perturbing the kinase catalytic active site. Activation of R3AK is also associated with a shift to a higher oligomeric state. Furthermore, as the NLR R3NLR is not actively involved in the execution of cell death we hypothesise that R3AK acts as a helper. A phylogenetic analysis indicates widespread distribution of this paired configuration in Poales. Together, this study establishes a novel resistance mechanism involving a non-canonical NLR/MLKL system. Significance StatementHere we investigate the mechanism of a novel plant immune receptor pair from wheat, R3NLR/R3AK. A nucleotide-binding, leucine-rich repeat (NLR) receptor and a mixed lineage kinase like (MLKL) protein are both required to mediate resistance to blast pathogen effector proteins PWT3, PWT6 and PWT8. Adopting a mutagenesis approach, we show that the MLKL protein executes cell death through its N-terminal 4-helical bundle domain, and this is associated with a shift to a higher oligomeric state. Mutations of conserved sequence motifs in the NLR support its role as a sensor, although effector interactions have not yet been observed. This study reveals a plant immune receptor pair that functions via a putative NLR sensor paired to a cell death executing MLKL protein.

plant biology↗

bioRxiv2026

Vernalisation-induced changes to the Arabidopsis circadian clock require Polycomb Repressive Complex 2 and are FLC-independent

In many plants, prolonged winter cold and seasonal day-length changes align the transition to flowering with spring. This occurs through the vernalisation and photoperiod pathways, respectively. Despite roles for the circadian clock in regulating both pathways, their mechanisms have mainly been studied in isolation and their interactions are not fully understood. We found that vernalisation elicits changes in the circadian clock and this is linked to alterations in several clock-controlled outputs, including photoperiodic flowering. Importantly, vernalisation-induced changes in specific clock genes are stable and persist upon return to warmth, providing the circadian clock with a memory of prior long-term cold exposure. The changes are not systematic and affect specific circadian oscillator genes. This change requires the epigenetic regulator Polycomb Repressive Complex 2 (PRC2), but not the major genetic determinants of vernalisation FRIGIDA (FRI) and FLOWERING LOCUS C (FLC). In contrast to their role in FLC silencing, core PRC2 components but not accessory proteins are required for these changes in the clock post-vernalisation. Our work raises the possibility that long-term cold feeds epigenetic information into the clock as a seasonal response mechanism, potentially preparing plants for the coming season.

plant biology↗

bioRxiv2026

Circadian entrainment to environmental cues in a natural plant population

Circadian clocks coordinate physiology, development and behaviour with cycles of day and night, which contributes to organismal fitness. For this to occur, the circadian clock must be aligned with the natural daily fluctuations in the environmental conditions. Here, we investigated under natural conditions the role of environmental cues in adjusting the circadian clock, and how this affects clock outputs. By combining novel field-based experimentation in a natural plant population with genome-wide analysis and machine-learning strategies for data interpretation, we inferred that temperature cues change circadian timing under natural conditions. We inferred that low temperature cues can shift circadian phase under naturally fluctuating conditions, and that there are seasonal changes in the effects of temperature upon circadian entrainment. We also identified extensive circadian modulation of temperature responses under field conditions. Therefore, plasticity of circadian timing under natural conditions allows flexible responses of both the clock and its outputs to environmental stimuli.

plant biology↗

bioRxiv2025

Pollinator-relevant floral traits underlie bidirectional hybridisation in the orchid genus Gymnadenia

Reproductive isolation is mediated by ecological, phenotypic, and genetic barriers. Where such barriers are not upheld, hybridisation can occur, revealing insight about the formation of species. Here, we provide an integrative investigation of hybrid formation between the orchids Gymnadenia conopsea and G. rhellicani and potential isolating barriers in zones of overlap in the European Alps. We examine opportunities for hybridisation by quantifying hybrid frequency and pollinator assemblages of parent species. Next, we characterise floral phenotypes and genetic parentage of hybrids to examine how genetic inheritance of traits shapes ecological interactions, and thus fitness, of hybrids. We find that pollinator assemblages of parents overlap partially, consistent with observed rare hybrids (<1% of the population). Phenotypically, hybrids were intermediate across floral traits, consistent with all hybrids being identified as F1s, resulting from a primary hybridisation event between G. conopsea and G. rhellicani. No evidence of backcrossing or introgression was found, but direction of pollen transfer varied across sites. Additionally, hybrids were heterozygous for parental alleles at two loci impacting anthocyanin production, suggesting hybrids intermediate floral colour reflects inheritance of these alleles. Finally, we find little support that ploidy variation or hybrid seed infertility explains the absence of advanced generations of hybrids. Thus, we suggest that floral isolation represents an important isolating mechanism between G. conopsea and G. rhellicani in limiting the formation of uncommon, unfit hybrids and shaping species boundaries.

plant biology↗

bioRxiv2024

Re-analysis of mobile mRNA datasets highlights challenges in the detection of mobile transcripts from short-read RNA-Seq data

Short-read RNA-Seq analyses of grafted plants have led to the proposal that large numbers of mRNAs move over long distances between plant tissues, acting as potential signals. The detection of transported transcripts by RNA-Seq is both experimentally and computationally challenging, requiring successful grafting, delicate harvesting, rigorous contamination controls and data processing approaches that can identify rare events in inherently noisy data. Here, we perform a meta-analysis of existing datasets and examine the associated bioinformatic pipelines. Our analysis reveals that technological noise, biological variation and incomplete genome assemblies give rise to features in the data that can distort the interpretation. Taking these considerations into account, we find that a substantial number of transcripts that are currently annotated as mobile are left without support from the available RNA-Seq data. Whilst several annotated mobile mRNAs have been validated, we cannot exclude that others may be false positives. The identified issues may also impact other RNA-Seq studies, in particular those using single nucleotide polymorphisms (SNPs) to detect variants.

plant biology↗

bioRxiv2024

The plant specific cohesin subunit SYN4 contributes to 3D genome organization and activity

O_LIChromatin architecture in the cells of animals and fungi influences gene expression. The molecular factors that influence higher genome architecture in plants and their effects on gene expression remain unknown. Cohesin complexes, conserved in eukaryotes, are essential factors in genome structuring. Here, we investigated the relevance of the plant-specific somatic cohesin subunit SYN4 for chromatin organisation in Arabidopsis thaliana. C_LIO_LIPlants mutated in SYN4 were studied using HRM, Hi-C, RNA sequencing, untargeted and targeted metabolomics and physiological assays to understand the role of this plant-specific cohesin. C_LIO_LIWe show that syn4 mutants exhibit altered intra- and interchromosomal interactions, expressed as sharply reduced contacts between telomeres and chromosome arms but not between centromeres, and differences in the placement and number of topologically associated domains (TADs)-like structures. By transcriptome sequencing, we also show that syn4 mutants have altered gene expression, including numerous genes that control abiotic stress responses. C_LIO_LIThe response to drought stress in Arabidopsis is strongly influenced by the genome structure in syn4 mutants, potentially due to altered expression of CYP707A3, an ABA 8-hydroxylase. C_LI In briefThe 3D architecture of the genome extensively influences gene expression in animals and fungi. We show that the plant-specific cohesin subunit SYN4 affects intra- and interchromosomal interactions including telomere clustering, with consequences for the expression of genes of transient and induced biological pathways and the biosynthesis of bioactive compounds. Highly condensed genome structures at the CYP707A3 locus positively affects the stress response to water deprivation regulated by abscisic acid.

genetics↗

bioRxiv2023

afila, the origin and nature of a major innovation in the history of pea breeding

The afila (af) mutation of Pisum sativum L. (pea) is characterised by leaves that are composed of a basal pair of stipules, a petiole and a branched mass of tendrils. These are bipinnate leaves in which the leaflet primordia are replaced by midrib-like, or terminal tendril, primordia. The phenotype was first reported as a spontaneous mutation in 1953, and several reports of spontaneously occurring af mutants and induced mutations have been published since then. Despite its wide-scale introgression to improve standing ability in combine-harvested dry pea crops, the molecular basis of af has remained unknown. Here, we show that the deletion of two tandemly-arrayed Q-type Cys(2)His(2)-zinc finger transcription factors, viz. PsPALM1a and PsPALM1b, is responsible for the af phenotype. Based on molecular evidence for the presence/absence of seven consecutive pea genes, we identified eight haplotypes in the genomic region of chromosome 2 that harbours af. These haplotypes differ in the presence or absence of PsPALM1a-b and close genes and in the size of the deletion. Representative cultivars and spontaneous or induced mutants were assigned to the different haplotypes. The hitherto unrecognised diversity at the af locus reveals highly rich, unexplored, potential for pea improvement and sheds light on the breeding history of pea. This knowledge can also be used to breed innovative cultivars in related crops.

genetics↗

bioRxiv2023

Integrated Phenomics and Genomics reveals genetic loci associated with inflorescence growth in Brassica napus

A fundamental challenge to the production of climate-resilient crops is how to measure dynamic yield-relevant responses to the environment, such as growth rate, at a scale which informs mechanistic understanding and accelerates breeding. The timing, duration and architectural characteristics of inflorescence growth are crucial for optimising crop productivity and have been targets of selection during domestication. We report a robust and versatile procedure for computationally assessing environmentally-responsive flowering dynamics. In the oilseed crop, Brassica napus, there is wide variation in flowering response to winter cold (vernalization). We subjected a diverse set of B. napus accessions to different vernalization temperatures and monitored shoot responses using automated image acquisition. We developed methods to computationally infer multiple aspects of flowering from this dynamic data, enabling characterisation of speed, duration and peaks of inflorescence development across different crop types. We input these multiple traits to genome- and transcriptome-wide association studies, and identified potentially causative variation in a priori phenology genes (including EARLY FLOWERING3) for known traits and in uncharacterised genes for computed traits. These results could be used in marker assisted breeding to design new ideotypes for improved yield and better adaptation to changing climatic conditions.

plant biology↗

bioRxiv2022

Genome-wide circadian gating of a cold temperature response in bread wheat

Circadian rhythms coordinate the responses of organisms to their daily fluctuating environments, by establishing a temporal program of gene expression. This schedules aspects of metabolism, physiology, development and behaviour according to the time of day. Circadian regulation in plants is extremely pervasive, and is important because it underpins both productivity and seasonal reproduction. Circadian regulation extends to the control of environmental responses through a regulatory process known as circadian gating. Circadian gating is the process whereby the circadian clock regulates the response to an environmental cue, such that the magnitude of response to an identical cue varies according to the time of day of the cue. Here, we show that there is genome-wide circadian gating of responses to cold temperatures in plants. By using bread wheat as an experimental model, we establish that circadian gating is crucial to the programs of gene expression that underlie the environmental responses of a crop of major socioeconomic importance. Furthermore, we identify that circadian gating of cold temperature responses are distributed unevenly across the three wheat subgenomes, which might reflect the geographical origins of the ancestors of modern wheat. One-sentence summaryThere is genome-wide circadian gating of a response to low temperatures in a crop of major socioeconomic importance.

plant biology↗

bioRxiv2020

Convergence and novelty in adaptation to whole genome duplication in three independent polyploids

Convergent evolution is observed broadly across the web of life, but the degree of evolutionary constraint during adaptation of core intracellular processes is not known. High constraint has been assumed for conserved processes, such as cell division and DNA repair, but reports of nimble evolutionary shifts in these processes have confounded this expectation. Whole genome duplication (WGD) necessitates the concerted adjustment of a wide range of fundamental intracellular functions but nevertheless has been repeatedly survived in all kingdoms. Given this repeated adaptation to WGD despite obvious intracellular challenges to core processes such as meiosis, we asked: how do lineages not only survive WGD, but sometimes ultimately thrive? Are the solutions employed constrained or diverse? Here we detect genes and processes under selection following WGD in the Cochlearia species complex by performing a scan for selective sweeps following WGD in a large-scale survey of 73 resequenced individuals from 23 populations across Europe. We then contrast our results from two independent WGDs in Arabidopsis arenosa and Cardamine amara. We find that while WGD does require the adaptation of particular functional processes in all three cases, the specific genes recruited to respond are highly flexible. We also observe evidence of varying degrees of convergence between different cases. Our results point to a polygenic basis for the distributed adaptive systems that control meiotic crossover number, ionomic rewiring, cell cycle control, and nuclear regulation. Given the sheer number of loci under selection post-WGD, we surmise that this polygenicity may explain the general lack of convergence between these species that are ~30 million years diverged. Based on our results, we speculate that adaptive processes themselves - such as the rate of generation of structural genomic variants--may be altered by WGD in nascent autopolyploids, contributing to the occasionally spectacular adaptability of autopolyploids observed across kingdoms.

evolutionary biology↗

bioRxiv2020

Genomic novelty versus convergence in the basis of adaptation to whole genome duplication

Whole genome duplication (WGD) occurs across kingdoms and can promote adaptation. However, a sudden increase in chromosome number, as well as changes in physiology, are traumatic to conserved processes. Previous work in Arabidopsis arenosa revealed a coordinated genomic response to WGD, involving physically interacting meiosis proteins, as well as changes related to cell cycle and ion homeostasis. Here we ask: is this coordinated shift in the same processes repeated in another species following WGD? To answer this, we resequenced and cytologically assessed replicated populations from a diploid/autotetraploid system, Cardamine amara, and test the hypothesis that gene and process-level convergence will be prevalent between these two WGDs adaptation events. Interestingly, we find that gene-level convergence is negligible, with no more in common than would be expected by chance. This was most clear at meiosis-related genes, consistent with our cytological assessment of somewhat lower meiotic stability in C. amara, despite establishment and broad occurrence of the autotetraploid in nature. In contrast, obvious convergence at the level of functional processes, including meiotic cell cycle, chromosome organisation and stress signalling was evident. This indicates that the two autotetraploids survived challenges attendant to WGD via contrasting solutions, modifying different players from similar processes. Overall, this work gives the first insight into the salient adaptations required to cope with a genome-doubled state and brings the first genomic evidence that autopolyploids can utilize multiple trajectories to achieve adaptation to WGD. We speculate that this flexibility increases the likelihood a nascent polyploid overcomes early stringent challenges to later access the spectrum of evolutionary opportunities of polyploidy. Significance statementWhole genome duplication (WGD) is a tremendous mutation and an important evolutionary force. It also presents immediate changes to meiosis and cell physiology that nascent polyploids must overcome to survive. Given the dual facts that WGD adaptation is difficult, but many lineages nevertheless survive WGD, we ask: how constrained are the evolutionary responses to a genome-doubled state? We previously identified candidate genes for WGD adaptation in Arabidopsis arenosa, which has natural diploid and tetraploid variants. Here we test for evolutionary convergence in adaptation to WGD in a species 17 million years distant, Cardamine amara. This work gives the first genomic insight into of how autopolyploids utilize multiple adaptive trajectories to manage a genome-doubled state.

evolutionary biology↗

bioRxiv2019

Interspecific introgression mediates adaptation to whole genome duplication

Adaptive gene flow is a consequential evolutionary phenomenon across all kingdoms of life. While recognition of widespread gene flow is growing, examples lack of bidirectional gene flow mediating adaptations at specific loci that cooperatively manage core cellular processes. We previously described concerted molecular changes among physically interacting members of the meiotic machinery controlling crossover number and distribution upon adaptation to whole genome duplication (WGD) in Arabidopsis arenosa. Here we conduct a population genomic study to test the hypothesis that escape from extinction following the trauma of WGD was mediated by adaptive gene flow between A. arenosa and its congener Arabidopsis lyrata. We show that A. lyrata underwent WGD more recently than A. arenosa, indicating that specific pre-adapted alleles donated by A. arenosa underwent selection and rescued the nascent A. lyrata tetraploids from early extinction. At the same time, we detect specific signals of gene flow in the opposite direction at other functionally interacting gene coding loci that display dramatic signatures of selective sweep in both tetraploid species. Cytological analysis shows that A. lyrata tetraploids exhibit similar levels of meiotic stability as A. arenosa tetraploids. Taken together, these data indicate that bidirectional gene flow allowed for an escape from extinction of the young autopolyploids, especially the rare tetraploid A. lyrata, and suggest that the merger of these species is greater than the sum of their parts.

evolutionary biology↗

bioRxiv2018

Pervasive population genomic consequences of genome duplication in Arabidopsis arenosa

Ploidy-variable species allow direct inference of the effects of chromosome copy number on fundamental evolutionary processes. While an abundance of theoretical work suggests polyploidy should leave distinct population genomic signatures, empirical data remains sparse. We sequenced [~]300 individuals from 39 populations of Arabidopsis arenosa, a naturally diploid-autotetraploid species. We find the impacts of polyploidy on population genomic processes are subtle yet pervasive, including reduced efficiency on linked and purifying selection as well as rampant gene flow from diploids. Initial masking of deleterious mutations, faster rates of nucleotide substitution, and interploidy introgression all conspire to shape the evolutionary potential of polyploids.

evolutionary biology↗

bioRxiv2017

A critical comparison of technologies for a plant genome sequencing project

A high quality genome sequence of your model organism is an essential starting point for many studies. Old clone based methods are slow and expensive, whereas faster, cheaper short read only assemblies can be incomplete and highly fragmented, which minimises their usefulness. The last few years have seen the introduction of many new technologies for genome assembly. These new technologies and new algorithms are typically benchmarked on microbial genomes or, if they scale appropriately, human. However, plant genomes can be much more repetitive and larger than human, and plant biology makes obtaining high quality DNA free from contaminants difficult. Reflecting their challenging nature we observe that plant genome assembly statistics are typically poorer than for vertebrates. Here we compare Illumina short read, PacBio long read, 10x Genomics linked reads, Dovetail Hi-C and BioNano Genomics optical maps, singly and combined, in producing high quality long range genome assemblies of the potato species S. verrucosum. We benchmark the assemblies for completeness and accuracy, as well as DNA, compute requirements and sequencing costs. We expect our results will be helpful to other genome projects, and that these datasets will be used in benchmarking by assembly algorithm developers.

genomics↗