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Gynandropsis gynandra (Cleomaceae) is a cosmopolitan leafy vegetable and medicinal plant, which has also been used as a model to study C4 photosynthesis due to its evolutionary proximity to C3 Arabidopsis (Arabidopsis thaliana). Here, we present the genome sequence of G. gynandra, anchored onto 17 main pseudo-molecules with a total length of 740 Mb, an N50 of 42 Mb and 30,933 well-supported gene models. The G. gynandra genome and previously released genomes of C3 relatives in the Cleomaceae and Brassicaceae make an excellent model for studying the role of genome evolution in the transition from C3 to C4 photosynthesis. Our analyses revealed that G. gynandra and its C3 relative Tarenaya hassleriana shared a whole-genome duplication event (Gg-alpha), then an addition of a third genome (Th-alpha, +1x) took place in T. hassleriana but not in G. gynandra. Analysis of syntenic copy number of C4 photosynthesis-related gene families indicates that G. gynandra generally retained more duplicated copies of these genes than C3T. hassleriana, and also that the G. gynandra C4 genes might have been under positive selection pressure. Both whole-genome and single-gene duplication were found to contribute to the expansion of the aforementioned gene families in G. gynandra. Collectively, this study enhances our understanding of the polyploidy history, gene duplication and retention, as well as their impact on the evolution of C4 photosynthesis in Cleomaceae. © The Author(s) 2023. Published by Oxford University Press on behalf of American Society of Plant Biologists.

Blastosporella zonata is one of the few basidiomycete fungi that produce asexual spores (conidia) on the mushroom. The role of these conidia in the fungal lifecycle is not known. We tested whether conidia are being utilized in local dispersal by looking for signatures of clonality in 21 samples from three localities separated by about three kilometres in Murillo, Colombia. To identify clonally related individuals, we sequenced three polymorphic markers at two unlinked loci (nuclear rRNA: ITS and LSU, and TEF1α) for all collections plus three herbarium samples. We identified two sets of clonally related individuals growing closely together in one of the three localities, and only one pair shared between localities. In all three localities we observed multiple non-clonally related dikaryons showing that sexual reproduction is also important. Our results indicate that the conidia on the mushroom are primarily important for local dispersal. Unexpectedly, our results also indicate two reproductively isolated populations, possibly representing cryptic biological species.

Bacteria primarily live in structured environments, such as colonies and biofilms, attached to surfaces or growing within soft tissues. They are engaged in local competitive and cooperative interactions impacting our health and well-being, for example, by affecting population-level drug resistance. Our knowledge of bacterial competition and cooperation within soft matrices is incomplete, partly because we lack high-throughput tools to quantitatively study their interactions. Here, we introduce a method to generate a large amount of agarose microbeads that mimic the natural culture conditions experienced by bacteria to co-encapsulate two strains of fluorescence-labeled Escherichia coli. Focusing specifically on low bacterial inoculum (1–100 cells/capsule), we demonstrate a study on the formation of colonies of both strains within these 3D scaffolds and follow their growth kinetics and interaction using fluorescence microscopy in highly replicated experiments. We confirmed that the average final colony size is inversely proportional to the inoculum size in this semi-solid environment as a result of limited available resources. Furthermore, the colony shape and fluorescence intensity per colony are distinctly different in monoculture and co-culture. The experimental observations in mono- and co-culture are compared with predictions from a simple growth model. We suggest that our high throughput and small footprint microbead system is an excellent platform for future investigation of competitive and cooperative interactions in bacterial communities under diverse conditions, including antibiotics stress.

In nature, light is never constant, while in the controlled environments used for vertical farming, in vitro propagation, or plant production for scientific research, light intensity is often kept constant during the photoperiod. To investigate the effects on plant growth of varying irradiance during the photoperiod, we grew Arabidopsis thaliana under three irradiance profiles: a square-wave profile, a parabolic profile with gradually increasing and subsequently decreasing irradiance, and a regime comprised of rapid fluctuations in irradiance. The daily integral of irradiance was the same for all three treatments. Leaf area, plant growth rate, and biomass at time of harvest were compared. Plants grown under the parabolic profile had the highest growth rate and biomass. This could be explained by a higher average light-use efficiency for carbon dioxide fixation. Furthermore, we compared the growth of wild type plants with that of the PsbS-deficient mutant npq4. PsbS triggers the fast non-photochemical quenching process (qE) that protects PSII from photodamage during sudden increases in irradiance. Based mainly on field and greenhouse experiments, the current consensus is that npq4 mutants grow more slowly in fluctuating light. However, our data show that this is not the case for several forms of fluctuating light conditions under otherwise identical controlled-climate room conditions.

A new species of Termitomyces symbiotic with the termite Macrotermes natalensis is described from Africa. As there are no records of field collected basidiocarps within this lineage, traditional basidiocarp-based morphological taxonomy is not practical. While basidiocarps may be obtained rarely from incubation of fungal comb fragments, their practical use for taxonomical purposes is limited. Therefore, the species is described based on an ITS nucleotide sequence, with comparisons to an asexual culture. Based on samples with similar ITS sequences, this species is likely associated with multiple termite hosts across a large part of Africa.

Mutations with large fitness benefits and mutations occurring at high rates may both cause parallel evolution, but their contribution is predicted to depend on population size. Moreover, high-rate and large-benefit mutations may have different long-term adaptive consequences. We show that small and 100-fold larger bacterial populations evolve resistance to a β-lactam antibiotic by using similar numbers, but different types of mutations. Small populations frequently substitute similar high-rate structural variants and loss-of-function point mutations, including the deletion of a low-activity β-lactamase, and evolve modest resistance levels. Large populations more often use low-rate, large-benefit point mutations affecting the same targets, including mutations activating the β-lactamase and other gain-of-function mutations, leading to much higher resistance levels. Our results demonstrate the separation by clonal interference of mutation classes with divergent adaptive consequences, causing a shift from high-rate to large-benefit mutations with increases in population size.

Background The termite-fungus symbiosis is an ancient stable mutualism of two partners that reproduce and disperse independently. With the founding of each termite colony the symbiotic association must be re-established with a new fungus partner. Complementarity in the ability to break down plant substrate may help to stabilize this symbiosis despite horizontal symbiont transmission. An alternative, non-exclusive, hypothesis is that a reduced rate of evolution may contribute to stabilize the symbiosis, the so-called Red King Effect. Methods To explore this concept, we produced the first linkage map of a species of Termitomyces, using genotyping by sequencing (GBS) of 88 homokaryotic offspring. We constructed a highly contiguous genome assembly using PacBio data and a de-novo evidence-based annotation. This improved genome assembly and linkage map allowed for examination of the recombination landscape and its potential effect on the mutualistic lifestyle. Results Our linkage map resulted in a genome-wide recombination rate of 22 cM/Mb, lower than that of other related fungi. However, the total map length of 1370 cM was similar to that of other related fungi. Conclusions The apparently decreased rate of recombination is primarily due to genome expansion of islands of gene-poor repetitive sequences. This study highlights the importance of inclusion of genomic context in cross-species comparisons of recombination rate.

Fermented maize starch, called ogi in Benin, is used for preparing akpan, a traditional yoghurt-like food that contributes to the food and nutrition security of its consumers. Current ogi processing technologies used by two socio-cultural groups of Benin, namely the Fon and the Goun, and aspects of the quality of the fermented starches were studied to assess the current state-of-the-art, explore changes in key product characteristics over time and identify priorities for follow-up research to increase product quality and shelf life. A survey on processing technologies was conducted in five municipalities in south Benin and samples of maize starch were collected, which were analysed after the fermentation required to obtain ogi. Four processing technologies were identified, two from the Goun (G1, G2) and two from the Fon (F1, F2). The main difference between the four processing technologies was the steeping procedure used for the maize grains. The pH of the ogi samples ranged between 3.1 and 4.2, with the highest values for G1 samples, which also contained relatively higher concentrations of sucrose (0.05–0.3 g/L) than F1 samples (0.02–0.08 g/L), and lower citrate and lactate concentrations (0.2–0.3 and 5.6–16.9 g/L, respectively) than F2 samples (0.4–0.5 and 14–27.7 g/L, respectively). Fon samples collected in Abomey were particularly rich in volatile organic compounds and free essential amino acids. Members of the genera Lactobacillus (8.6–69.3%), Limosilactobacillus (5.4–79.1%), Streptococcus (0.6–59.3%) and Weissella (2.6–51.2%) dominated the bacterial microbiota of ogi with a significant abundance of Lactobacillus spp. in Goun samples. Sordariomycetes (10.6–81.9%) and Saccharomycetes (6.2–81.4%) dominated the fungal microbiota. The yeast community of ogi samples mainly consisted of the genera Diutina, Pichia, Kluyveromyces, Lachancea and unclassified members of the Dipodascaceae family. Hierarchical clustering of metabolic data showed similarities between samples from different technologies at a default threshold of 0.05. No obvious trend in the composition of the samples’ microbial communities reflected the clusters observed for the metabolic characteristics. The results indicate that beyond the general impact of the use of Fon or Goun technologies on fermented maize starch, the individual contribution of processing practices warrants study, under controlled conditions, to determine the drivers of difference or similarity between maize ogi samples to further contribute to improving product quality and shelf life.

Fungal and plant mitochondria are known to exchange DNA with retroviral plasmids. Transfer of plasmid DNA to the organellar genome is best known and occurs through wholesale insertion of the plasmid. Less well known is the transfer of organellar DNA to plasmids, in particular tRNA genes. Presently, it is unknown whether fungal plasmids can adopt mitochondrial functions such as tRNA production through horizontal gene transfer. In this paper, we studied the exchange of DNA between fungal linear plasmids and fungal mtDNA, mainly focusing on the basidiomycete family Lyophyllaceae. We report at least six independent transfers of complete tRNA genes to fungal plasmids. Furthermore, we discovered two independent cases of loss of a tRNA gene from a fungal mitochondrial genome following transfer of such a gene to a linear mitochondrial plasmid. We propose that loss of a tRNA gene from mtDNA following its transfer to a plasmid creates a mutualistic dependency of the host mtDNA on the plasmid. We also find that tRNA genes transferred to plasmids encode codons that occur at the lowest frequency in the host mitochondrial genomes, possibly due to a higher number of unused transcripts. We discuss the potential consequences of mtDNA transfer to plasmids for both the host mtDNA and the plasmid.

Endosymbionts are maternally transmitted, and therefore benefit from maximizing female offspring numbers. Parthenogenesis-induction (PI) is the most effective type of manipulation for transmission, but has solely been detected in haplodiploid species, whereas cytoplasmic incompatibility (CI) is detected frequently across the arthropod phylum, including haplodiploids. This puzzling observation led us to hypothesize that the molecular sex-determination mechanism of the haplodiploid host may be a constraining factor in the ability of endosymbionts to induce parthenogenesis. Recent insights indicate that PI-endosymbionts may be able to directly manipulate sex-determination genes to induce the necessary steps required for PI in haplodiploids. However, sex- determination cascades vary extensively, so PI-induction would require a specialized and host-dependent tool set. Contrastingly, CI-related genes target conserved cell-cycle mechanisms, are located on mobile elements, and spread easily. Finally, endosymbiont-manipulations may have a strong impact on the effectiveness of haplodiploid biocontrol agents, but can also be used to enhance their efficacy.

Analysis of numerous air samples has indicated that dormant, viable fungal spores are highly present, which suggests that aerial dispersion is important for fungi. Whereas the majority of the spores may travel only very short distances, there is indication that a notable number of them cover much longer distances. Harmomegathy is a terminology coined by Wodehouse (1935) describing the natural folding of pollen to accommodate controlled and reversible water loss. Here, we discuss evidence that this concept may also apply to airborne fungal spores that face similar challenges and have to survive periods of drought and low temperatures while retaining viability to germinate after deposition upon a suitable moist substrate. In fact, (air)dried conidia, appear collapsed, survive for much longer times compared to spores in liquid, that deteriorate in time. This indicates that for some types of fungal spores, true dormancy is reached in the desiccated state. For these airborne spores this might be regarded as a pre-adaptation that supports long-distance transport of viable cells through air. We state that spores are naturally folded during transport in air if the humidity is low enough. We hypothesize that this is a pre-adaptation supporting release, dispersal and survival of airborne spores. Moreover, the smaller size of dry naturally-folded spores may also be relevant, e.g. for the opportunistic pathogenic fungus Aspergillus fumigatus reduced spore size supports deposition within the alveoli in the lung.

Background Arbuscular mycorrhizal (AM) fungi are arguably the most important symbionts of plants, offering a range of benefits to their hosts. However, the provisioning of these benefits does not appear to be uniform among AM fungal individuals, with genetic variation between fungal symbionts having a substantial impact on plant performance. Interestingly, genetic variation has also been reported within fungal individuals, which contain millions of haploid nuclei sharing a common cytoplasm. In the model AM fungus, Rhizophagus irregularis, several isolates have been reported to be dikaryotes, containing two genetically distinct types of nuclei recognized based on their mating-type (MAT) locus identity. However, their extremely coenocytic nature and lack of a known single nucleus stage has raised questions on the origin, distribution and dynamics of this genetic variation. Results Here we performed DNA and RNA sequencing at the mycelial individual, single spore and single nucleus levels to gain insight into the dynamic genetic make-up of the dikaryote-like R. irregularis C3 isolate and the effect of different host plants on its genetic variation. Our analyses reveal that parallel spore and root culture batches can have widely variable ratios of two main genotypes in C3. Additionally, numerous polymorphisms were found with frequencies that deviated significantly from the general genotype ratio, indicating a diverse population of slightly different nucleotypes. Changing host plants did not show consistent host effects on nucleotype ratio’s after multiple rounds of subculturing. Instead, we found a major effect of host plant-identity on allele-specific expression in C3. Conclusion Our analyses indicate a highly dynamic/variable genetic organization in different isolates of R. irregularis. Seemingly random fluctuations in nucleotype ratio’s upon spore formation, recombination events, high variability of non-tandemly repeated rDNA sequences and host-dependent allele expression all add levels of variation that may contribute to the evolutionary success of these widespread symbionts.

Hyperaccumulator plants exhibit extreme ecophysiological characteristics, which make them suited for phytoremediation. Understanding their ecological strategies might help identify the species and functions to be favored in phytoremediation, restoration, and conservation projects for metalliferous sites.

Agroecological food systems and socioeconomic characteristics are known to influence household food security and food consumption patterns and consequently have an impact on child nutritional status. The present study examined food consumption patterns among children aged 6–23 months in two geographic regions of Zambia, with special focus on consumption of fermented products, and its association with illnesses and nutritional status. The cross-sectional survey enrolled a total of 213 children from Namwala and Mkushi districts of Zambia. A 24 h recall and food frequency questionnaire (FFQ) were used to determine the number of food groups consumed and consequently dietary diversity scores and food consumption patterns, respectively. Determinants of child’s linear growth as measured by Height-for-Age Z-scores (HAZ) were assessed via multiple linear regression analysis. In total, 54% of the children met the minimum dietary diversity by consuming food from at least 5+ food groups. Maize meal porridge, Mabisi (fermented milk), Chibwantu and Munkoyo (fermented beverages based on cereals) and groundnuts were among the frequently consumed foods. A higher consumption of fermented beverages was observed in Namwala compared to Mkushi district. A significant association was observed between HAZ score (rho = 0.198, p = 0.004), Weight-for-Age Z-score (WAZ) (rho = 0.142, p = 0.039) and consumption of mabisi. Dietary intake had a positive association with child nutritional status. The frequent consumption of traditional non-alcoholic cereal and milk-based fermented foods underpinned their contribution to the children’s dietary intake. Moreover, the trend would be viewed as an indicator to nutrition and policy actors on possible unoptimized potential of indigenous fermented foods’ influence in nutritional and health status among children at regional and national levels. Although Zambia has a wide range of traditional non-alcoholic fermented food products, their prospects in provision of macro- and micronutrients along with microbiota benefits remain scanty despite global efforts increasingly advocating for the inclusion of such traditional foods in food-based recommendations.

Evolution has traditionally been a historical and descriptive science and predicting future evolutionary processes has long been considered impossible. However, evolutionary predictions are increasingly being developed and used in medicine, agriculture, biotechnology and conservation biology. Evolutionary predictions may be used for different purposes, such as to prepare for the future, to try and change the course of evolution or to determine how well we understand evolutionary processes. Similarly, the exact aspect of the evolved population that we want to predict may also differ, for example we could try to predict which genotype will dominate, the fitness of the population, or the extinction probability of a population. In addition, there are many uses of evolutionary predictions that may not always be recognized as such. The main goal of this review is to increase awareness of methods and data that are used to make these predictions in different research fields by showing the breadth of situations in which evolutionary predictions are made. We describe how diverse evolutionary predictions share a common structure described by the predictive scope, time scale and precision. Then, by using examples ranging from SARS-CoV2 and influenza to CRISPR-based gene drives and sustainable product formation in biotechnology, we discuss the methods for predicting evolution, the factors that affect predictability, and how predictions can be used to prevent evolution in undesirable directions or to promote beneficial evolution (i.e. evolutionary control). We hope that this review will stimulate collaboration between fields by creating a common language for evolutionary predictions.

Rare earth elements (REEs) are critical for numerous modern technologies, and demand is increasing globally; however,production steps are resource-intensive and environmentally damaging.Some plant species are able to hyper accumulate REEs, and understanding the biology behind this phenomenon could play a pivotal role in developing more environmentally friendly REE recovery technologies. Here, we identified a REE transporter NRAMP REE Transporter 1 (NREET1)from the REE hyper accumulator fern Dicranopteris linearis. AlthoughNREET1 belongs to the natural resistance-associated macrophage protein(NRAMP) family, it shares a low similarity with other NRAMP members.When expressed in yeast, NREET1 exhibited REE transport capacity, but itcould not transport divalent metals, such as zinc, nickel, manganese, or iron.NREET1 is mainly expressed in D. linearis roots and predominantly localized in the plasma membrane. Expression studies in Arabidopsis thaliana revealed that NREET1 functions as a transporter mediating REE uptake and transfer from root cell walls into the cytoplasm. Moreover, NREET1 has a higher affinity for transporting light REEs compared to heavy REEs, which is consistent to the preferential enrichment of light REEs in field-grown D. linearis. We therefore conclude that NREET1 may play an important role in the uptake and consequently hyper accumulation of REEs in D.linearis. These findings lay the foundation for the use of synthetic biology techniques to design and produce sustainable, plant-based REE recovery systems.

X-ray Fluorescence Spectroscopy (XRF) is a non-destructive analytical technique that has recently been developed as a tool for high throughput screening for the discovery of trace element hyperaccumulator species in herbarium collections. Herbarium XRF analysis was undertaken of representatives of the Brassicaceae family in the two herbaria in Belgrade (Serbia). This was coupled to field collection and chemical analysis of new samples of Cardamine waldsteinii. The data revealed a potentially new zinc hyperaccumulator species, C. waldsteinii, with 3050 mg kg−1 Zn in its leaves. This compares to 2210 mg kg−1 in the leaves of this species collected from the field. These values are below the notional hyperaccumulation threshold for zinc but are nevertheless unusual. The remarkably high accumulation factor for zinc are suggestive of the exceptional potential of C. waldsteinii for zinc uptake, even in non-metalliferous, zinc-deficient soils. We recommend following up this study with experimental investigations on C. waldsteinii to elucidate its ecophysiology and its zinc tolerance and accumulation characteristics.

Context: Root foraging by hyperaccumulator plants in response to patchily distributed metals has been observed in several obligate hyperaccumulators, but it is not known whether facultative hyperaccumulators respond similarly.Aims: This study investigated the root-growth behaviour in the leguminous zinc (Zn) hyperaccumulator Crotalaria novae-hollandiae compared with the non-accumulating Crotalaria cunninghamii in response to localised soil Zn enrichment in the soil to observe foraging versus avoidance responses.Methods: We conducted rhizotron experiments in which we exposed the Crotalaria species pair to juxtaposed treatments, which were either homogenous (each half of the treatments containing same Zn concentrations) or heterogenous (different Zn concentrations in each half of the treatments). The Zn concentrations were 0 μg Zn g−1 (control), 2000 μg Zn g−1 and 5000 μg Zn g−1 in the form of zinc carbonate).Key results: We found that none of the treatments had significantly different rooting density and root biomass, regardless of the Crotalaria species. This finding contrasts with increased root proliferation in Zn-rich patches found for other obligate hyperaccumulator species.Conclusions and implications: The no-preference root response towards Zn in Crotalaria may partly explain the facultative hyperaccumulation mechanism displayed by these species. This root response towards Zn may ultimately affect Zn phytoextraction efficacy when utilising Crotalaria species in a heterogenous Zn soil substrate. These findings highlight the need for rhizosphere investigations prior to field phytoextraction applications.

What causes evolution to be repeatable is a fundamental question in evolutionary biology. Pleiotropy, i.e. the effect of an allele on multiple traits, is thought to enhance repeatability by constraining the number of available beneficial mutations. Additionally, pleiotropy may promote repeatability by allowing large fitness benefits of single mutations via adaptive combinations of phenotypic effects. Yet, this latter evolutionary potential may be reaped solely by specific types of mutations able to realize optimal combinations of phenotypic effects while avoiding the costs of pleiotropy. Here, we address the interaction of gene pleiotropy and mutation type on evolutionary repeatability in a meta-analysis of experimental evolution studies with Escherichia coli. We hypothesize that single-nucleotide polymorphisms (SNPs) are principally able to yield large fitness benefits by targeting highly pleiotropic genes, whereas indels and structural variants (SVs) provide smaller benefits and are restricted to genes with lower pleiotropy. By using gene connectivity as proxy for pleiotropy, we show that non-disruptive SNPs in highly pleiotropic genes yield the largest fitness benefits, since they contribute more to parallel evolution, especially in large populations, than inactivating SNPs, indels and SVs. Our findings underscore the importance of considering genetic architecture together with mutation type for understanding evolutionary repeatability.This article is part of the theme issue ‘Predicting evolution’.

Insects have a wide variety of mating systems. For parasitic wasps, mating sites are often confined to where their hosts occur and this mutual interaction therefore greatly affects the evolution of alternative mating strategies. Parasitoids of the genus Nasonia (Hymenoptera: Pteromalidae) – comprising the species Nasonia vitripennis (Walker), Nasonia longicornis Darling, Nasonia giraulti Darling, and Nasonia oneida Raychouhury & Desjardins – parasitize blowfly pupae and typically mate immediately after emergence of the females from the host puparium. However, in one Nasonia species, N. giraulti, mating predominantly occurs within the host. Here, we re-assess within-host mating (WHM) rates within the Nasonia genus, using laboratory lines and field collected hosts, and including N. oneida for which no data were available yet. We confirm that WHM rates are low in N. vitripennis and N. longicornis, but high in N. giraulti. WHM is rare in N. oneida, despite its sympatry and close phylogenetic relationship with N. giraulti. Multiparasitization experiments with N. vitripennis and N. giraulti resulted in lower WHM proportions of N. giraulti. To evaluate whether this was due to an exit hole in the host pupa created by N. vitripennis males – where an exit hole may result in emergence of N. giraulti females and possibly males prior to mating – we artificially created exit holes in the host parasitized by N. giraulti only. This also yielded a lower WHM proportion. Progeny analysis of interspecific crosses of N. longicornis and N. oneida with N. giraulti, generating hybrid female but non-hybrid male offspring, revealed that WHM is largely determined by the maternal species and, hence, by the species to which the male offspring belong. We conclude that WHM is predominantly a male-mediated trait in N. giraulti, resulting from males refraining from making exit holes and mating with females inside the host. We discuss how these findings can be used to evaluate whether WHM contributes to preventing species hybridization.

Despite research efforts toward improving crop photosynthetic energy conver-sion efficiencies over the past 40 years, photosynthetic efficiencies remain far from their theoretical maxima. A major challenge has been that plant photosyn-thesis is a complex process, controlled by many underlying genetic factors and highly dynamic in response to short- term environmental changes. Recent ap-proaches to improving photosynthesis involved model- based identification of the bottlenecks in photosynthesis followed by their genetic modification (GM). While these approaches were successful and inspirational, their dependency on the use of GM techniques may restrict their implementation in some jurisdictions. We therefore suggest greater research focus on a different, yet complementary, ap-proach to improving photosynthetic efficiency: the exploration and exploitation of natural genetic variation in photosynthesis. A substantial improvement in phe-notyping and genotyping technology over the past decade has highlighted natu-ral variation in photosynthetic sub- traits for crop and model species. However, a comprehensive understanding of all the factors responsible for photosynthetic limitations is still lacking. We therefore propose the use of high photosynthetic capacity species as models for the exploration of the physiological and genetic basis of high photosynthetic efficiency. While most high photosynthetic capacity species are not suitable as models due to complex genetics and evolutionary dis-tance from crops, we have identified Brassicaceae species Hirschfeldia incana (L.) Lagr.- Foss as a promising candidate. In this perspective paper, we describe and advocate the use of H. incana as a model for the exploration of high maximum CO2 assimilation rates (Pmax) found in some C3 species. We describe the basic biology and evolutionary history of the species and report preliminary data on its photosynthetic characteristics. Our findings suggest H. incana is an excellent model species for studies aiming at understanding natural genetic variation in photosynthetic efficiency.

Background Broilers are among the most common and dense poultry production systems, where antimicrobials have been used extensively to promote animal health and performance. The continuous usage of antimicrobials has contributed to the appearance of resistant bacteria, such as extended-spectrum β-lactamase-producing Escherichia coli (ESBL-Ec). Here, we studied the ESBL-Ec prevalence and successional dynamics of the caecal microbiota of developing broilers in a commercial flock during their production life cycle (0–35 days). Broilers were categorised as ESBL-Ec colonised (ESBL-Ec+) or ESBL-Ec non-colonised (ESBL-Ec−) by selective culturing. Using 16S rRNA gene sequencing, we i. compared the richness, evenness and composition of the caecal microbiota of both broilers’ groups and ii. assessed the combined role of age and ESBL-Ec status on the broilers’ caecal microbiota. Results From day two, we observed an increasing linear trend in the proportions of ESBL-Ec throughout the broilers' production life cycle, X2 (1, N = 12) = 28.4, p − broilers, but significant differences between both broilers’ groups were found exclusively on day three (Wilcoxon rank-sum test, p = 0.016). Bray–Curtis distance-based RDA (BC-dbRDA) showed no explanatory power of ESBL-Ec status, while age explained 14% of the compositional variation of the caecal microbiota, F (2, 66) = 6.47, p = 0.001. Conclusions This study assessed the role of ESBL-Ec in the successional dynamics of the caecal microbiota in developing broilers and showed that the presence of ESBL-Ec is associated with mild but consistent reductions in alpha diversity and with transient bacterial compositional differences. We also reported the clonal spread of ESBL-Ec and pointed to the farm environment as a likely source for ESBLs.

Social insects are very successful invasive species, and the continued increase of global trade and transportation has exacerbated this problem. The yellow-legged hornet, Vespa velutina nigrithorax (henceforth Asian hornet), is drastically expanding its range in Western Europe. As an apex insect predator, this hornet poses a serious threat to the honey bee industry and endemic pollinators. Current suppression methods have proven too inefficient and expensive to limit its spread. Gene drives might be an effective tool to control this species, but their use has not yet been thoroughly investigated in social insects. Here, we built a model that matches the hornet’s life history and modelled the effect of different gene drive scenarios on an established invasive population. To test the broader applicability and sensitivity of the model, we also incorporated the invasive European paper wasp Polistes dominula. We find that, due to the haplodiploidy of social hymenopterans, only a gene drive targeting female fertility is promising for population control. Our results show that although a gene drive can suppress a social wasp population, it can only do so under fairly stringent gene drive-specific conditions. This is due to a combination of two factors: first, the large number of surviving offspring that social wasp colonies produce make it possible that, even with very limited formation of resistance alleles, such alleles can quickly spread and rescue the population. Second, due to social wasp life history, infertile individuals do not compete with fertile ones, allowing fertile individuals to maintain a large population size even when drive alleles are widespread. Nevertheless, continued improvements in gene drive technology may make it a promising method for the control of invasive social insects in the future.

During the transition from sexual to asexual reproduction, a suite of reproduction‐related sexual traits become superfluous, and may be selected against if costly. Female functional virginity refers to asexual females resisting to mate or not fertilizing eggs after mating. These traits appear to be among the first that evolve during transitions from sexual to asexual reproduction. The genetic basis of female functional virginity remains elusive. Previously, we reported that female functional virginity segregates as expected for a single recessive locus in the asexual parasitoid wasp Asobara japonica. Here, we investigate the genetic basis of this trait by quantitative trait loci (QTL) mapping and candidate gene analyses. Consistent with the segregation of phenotypes, we found a single QTL of large effect, spanning over 4.23 Mb and comprising at least 131 protein‐coding genes, of which 15 featured sex‐biased expression in the related sexual species Asobara tabida. Two of the 15 sex‐biased genes were previously identified to differ between related sexual and asexual population/species: CD151 antigen and nuclear pore complex protein Nup50. A third gene, hormone receptor 4, is involved in steroid hormone mediated mating behaviour. Overall, our results are consistent with a single locus, or a cluster of closely linked loci, underlying rapid evolution of female functional virginity in the transition to asexuality. Once this variant, causing rejection to mate, has swept through a population, the flanking region does not get smaller owing to lack of recombination in asexuals.

Nesidiocoris tenuis (Reuter) is an efficient predatory biological control agent used throughout the Mediterranean Basin in tomato crops but regarded as a pest in northern European countries. From the family Miridae, it is an economically important insect yet very little is known in terms of genetic information and no genomic or transcriptomic studies have been published. Here, we use a linked‐read sequencing strategy on a single female N. tenuis. From this, we assembled the 355 Mbp genome and delivered an ab initio, homology‐based and evidence‐based annotation. Along the way, the bacterial “contamination” was removed from the assembly. In addition, bacterial lateral gene transfer (LGT) candidates were detected in the N. tenuis genome. The complete gene set is composed of 24 688 genes; the associated proteins were compared to other hemipterans (Cimex lectularis, Halyomorpha halys and Acyrthosiphon pisum). We visualized the genome using various cytogenetic techniques, such as karyotyping, CGH and GISH, indicating a karyotype of 2n = 32. Additional analyses include the localization of 18S rDNA and unique satellite probes as well as pooled sequencing to assess nucleotide diversity and neutrality of the commercial population. This is one of the first mirid genomes to be released and the first of a mirid biological control agent., The annotated genome of predatory mirid Nesidiocoris tenuis presented here was generated from a single female insect using a linked‐read sequencing and assembly strategy.Potential contaminants and/or endosymbionts were identified during assembly decontamination along with putative lateral gene transfer candidates.Additional cytogenetic analysis includes karyotyping and investigations into the ancestral insect telomeric motif, sex chromosomes, rDNA and a very abundant DNA repeat scattered throughout the genome.

Azole resistance is a concern for the management of diseases caused by Aspergillus fumigatus in humans. Azole fungicide use in the environment has been identified as a possible cause for development of resistance, which increases the complexity and number of stakeholders involved in this emerging problem. A workshop was held in Amsterdam early 2019 in which stakeholders, including medical and agricultural researchers, representatives from the government, public health, fungicide producers and end-users, reviewed the current evidence supporting environmental selection for resistance and to discuss which research and measures are needed to retain the effectiveness of the azole class for environmental and medical applications. This paper provides an overview of the latest insights and understanding of azole resistance development in the clinical setting and the wider environment. A One Health problem approach was undertaken to list and prioritize which research will be needed to provide missing evidence and to enable preventive interventions.

Biological control is widely successful at controlling pests, but effective biocontrol agents are now more difficult to import from countries of origin due to more restrictive international trade laws (the Nagoya Protocol). Coupled with increasing demand, the efficacy of existing and new biocontrol agents needs to be improved with genetic and genomic approaches. Although they have been underutilised in the past, application of genetic and genomic techniques is becoming more feasible from both technological and economic perspectives. We review current methods and provide a framework for using them. First, it is necessary to identify which biocontrol trait to select and in what direction. Next, the genes or markers linked to these traits need be determined, including how to implement this information into a selective breeding program. Choosing a trait can be assisted by modelling to account for the proper agro-ecological context, and by knowing which traits have sufficiently high heritability values. We provide guidelines for designing genomic strategies in biocontrol programs, which depend on the organism, budget, and desired objective. Genomic approaches start with genome sequencing and assembly. We provide a guide for deciding the most successful sequencing strategy for biocontrol agents. Gene discovery involves quantitative trait loci analyses, transcriptomic and proteomic studies, and gene editing. Improving biocontrol practices includes marker-assisted selection, genomic selection and microbiome manipulation of biocontrol agents, and monitoring for genetic variation during rearing and post-release. We conclude by identifying the most promising applications of genetic and genomic methods to improve biological control efficacy

The filamentous fungus Podospora anserina has been used as a model organism for more than 100 years and has proved to be an invaluable resource in numerous areas of research. Throughout this period, P. anserina has been embroiled in a number of taxonomic controversies regarding the proper name under which it should be called. The most recent taxonomic treatment proposed to change the name of this important species to Triangularia anserina. The results of past name changes of this species indicate that the broader research community is unlikely to accept this change, which will lead to nomenclatural instability and confusion in literature. Here, we review the phylogeny of the species closely related to P. anserina and provide evidence that currently available marker information is insufficient to resolve the relationships amongst many of the lineages. We argue that it is not only premature to propose a new name for P. anserina based on current data, but also that every effort should be made to retain P. anserina as the current name to ensure stability and to minimise confusion in scientific literature. Therefore, we synonymise Triangularia with Podospora and suggest that either the type species of Podospora be moved to P. anserina from P. fimiseda or that all species within the Podosporaceae be placed in the genus Podospora.

Trichogramma brassicae (Bezdenko) are egg parasitoids that are used throughout the world as biological control agents and in laboratories as model species. Despite this ubiquity, few genetic resources exist beyond COI, ITS2, and RAPD markers. Aided by a Wolbachia infection, a wild-caught strain from Germany was reared for low heterozygosity and sequenced in a hybrid de novo strategy, after which several assembling strategies were evaluated. The best assembly, derived from a DBG2OLC-based pipeline, yielded a genome of 235 Mbp made up of 1,572 contigs with an N50 of 556,663 bp. Following a rigorous ab initio-, homology-, and evidence-based annotation, 16,905 genes were annotated and functionally described. As an example of the utility of the genome, a simple ortholog cluster analysis was performed with sister species T. pretiosum, revealing over 6000 shared clusters and under 400 clusters unique to each species. The genome and transcriptome presented here provides an essential resource for comparative genomics of the commercially relevant genus Trichogramma, but also for research into molecular evolution, ecology, and breeding of T. brassicae.

Aspergillus fumigatusis a saprobic fungus that causes a range of pulmonary diseases, some of which are characterised by fungal persistence such as is observed in cystic fibrosis (CF) patients. Creation of genetic variation is critical forA. fumigatusto adapt to the lung environment, but biofilm formation, especially in CF patients, may preclude mutational supply inA. fumigatusdue to its confinement to the hyphal morphotype. We tested our hypothesis that genetic variation is created through parasexual recombination in chronic biofilms by phenotypic and genetic analysis ofA. fumigatusisolates cultured from different origins.As diploids are the hallmark of parasex, we screened 799A. fumigatusisolates obtained from patients with CF, chronic pulmonary lung disease and acute invasive aspergillosis, and from the environment for spore size. Benomyl sensitivity, nuclear content measurements through fluorescence-activated cell sorting and scanning electron microscopy were used to confirm the diploid state of large size spores. Whole genome sequencing was used to characterise diploid-associated genetic variation.We identified 11 diploids in isolates recovered from six of 11 (55%) CF patients and from one of 24 (4%) chronic aspergillosis patients, but not in 368 isolates from patients with acuteAspergillusinfection and the environment. Diploid formation was associated with accumulation of mutations and variable haploid offspring including a voriconazole-resistant isolate.Parasexual recombination allowsA. fumigatusto adapt and persist in CF patients, and plays a role in azole resistance development. Our findings are highly significant for understanding the genetics and biology ofA. fumigatusin the human lung.

Seasonal polyphenism in Drosophila suzukii manifests itself in two discrete adult morphotypes, the “winter morph” (WM) and the “summer morph” (SM). These morphotypes are known to differ in thermal stress tolerance, and they co‐occur during parts of the year. In this study, we aimed to estimate morph‐specific survival and fecundity in laboratory settings simulating field conditions. We specifically analyzed how WM and SM D. suzukii differed in mortality and reproduction during and after a period of cold exposure resembling winter and spring conditions in temperate climates. The median lifespan of D. suzukii varied around 5 months for the WM flies and around 7 months for the SM flies. WM flies showed higher survival during the cold‐exposure period compared with SM flies, and especially SM males suffered high mortality under these conditions. In contrast, SM flies had lower mortality rates than WM flies under spring‐like conditions. Intriguingly, reproductive status (virgin or mated) did not impact the fly survival, either during the cold exposure or during spring‐like conditions. Even though the reproductive potential of WM flies was greatly reduced compared with SM flies, both WM and SM females that had mated before the cold exposure were able to continuously produce viable offspring for 5 months under spring‐like conditions. Finally, the fertility of the overwintered WM males was almost zero, while the surviving SM males did not suffer reduced fertility. Combined with other studies on D. suzukii monitoring and overwintering behavior, these results suggest that overwintered flies of both morphotypes could live long enough to infest the first commercial crops of the season. The high mortality of SM males and the low fertility of WM males after prolonged cold exposure also highlight the necessity for females to store sperm over winter to be able to start reproducing early in the following spring.

Potato (Solanum tuberosum) is an important food crop consumed all over the world, but it is generally sensitive to drought conditions. One of the major physiological processes affected by drought stress is carbon partitioning: the plant's choice of where to allocate its photoassimilates. Our aim was to investigate the molecular factors and possible bottlenecks affecting carbon partitioning during drought. We studied potato cultivars with contrasting drought responses in the greenhouse in the years 2013–2015, and further investigated the expression of genes involved in carbon partitioning and metabolite levels. Our results indicate that one of the most severe effects of drought stress on potato is the arrest of stolon differentiation and formation of tubers. We also identified some physiological traits like stomatal conductance and chlorophyll content as affecting carbon assimilation, partitioning and eventual tuber yield. The gene expressions and biochemical analyses highlight the various tissues prioritized by the plant for assimilate transport during drought stress, and give indications of what distinguishes drought tolerance and sensitivity of cultivated potato. Some of the key genes studied (like Sucrose synthase and Sucrose transporters) may be inclusive breeding targets for drought tolerance in potato.

The filamentous fungus Podospora anserina has been used as a model organism for more than 100 years and has proved to be an invaluable resource in numerous areas of research. Throughout this period, P. anserina has been embroiled in a number of taxonomic controversies regarding the proper name under which it should be called. The most recent taxonomic treatment proposed to change the name of this important species to Triangularia anserina. The results of past name changes of this species indicate that the broader research community is unlikely to accept this change, which will lead to nomenclatural instability and confusion in literature. Here, we review the phylogeny of the species closely related to P. anserina and provide evidence that currently available marker information is insufficient to resolve the relationships amongst many of the lineages. We argue that it is not only premature to propose a new name for P. anserina based on current data, but also that every effort should be made to retain P. anserina as the current name to ensure stability and to minimise confusion in scientific literature. Therefore, we synonymise Triangularia with Podospora and suggest that either the type species of Podospora be moved to P. anserina from P. fimiseda or that all species within the Podosporaceae be placed in the genus Podospora.

Information processing is an essential part of biology, enabling coordination of intra-organismal processes such as development, environmental adaptation and inter-organismal communication. Whilst in animals with specialised brain tissue a substantial amount of information processing occurs in a centralised manner, most biological computing is distributed across multiple entities, such as cells in a tissue, roots in a root system or ants in a colony. Physical context, called embodiment, also affects the nature of biological computing. While plants and ant colonies both perform distributed computing, in plants the units occupy fixed positions while individual ants move around. This distinction, solid versus liquid brain computing, shapes the nature of computations. Here we compare information processing in plants and ant colonies, highlighting how similarities and differences originate in, as well as make use of, the differences in embodiment. We end with a discussion on how this embodiment perspective may inform the debate on plant cognition.

Background Broilers are among the most common and dense poultry production systems, where antimicrobials have been used extensively to promote animal health and performance. The continuous usage of antimicrobials has contributed to the appearance of resistant bacteria, such as extended-spectrum β-lactamase-producing Escherichia coli (ESBL-Ec). Here, we studied the ESBL-Ec prevalence and successional dynamics of the caecal microbiota of developing broilers in a commercial flock during their production life cycle (0–35 days). Broilers were categorised as ESBL-Ec colonised (ESBL-Ec+) or ESBL-Ec non-colonised (ESBL-Ec−) by selective culturing. Using 16S rRNA gene sequencing, we i. compared the richness, evenness and composition of the caecal microbiota of both broilers’ groups and ii. assessed the combined role of age and ESBL-Ec status on the broilers’ caecal microbiota. Results From day two, we observed an increasing linear trend in the proportions of ESBL-Ec throughout the broilers' production life cycle, X2 (1, N = 12) = 28.4, p < 0.001. Over time, the caecal microbiota richness was consistently higher in ESBL-Ec− broilers, but significant differences between both broilers’ groups were found exclusively on day three (Wilcoxon rank-sum test, p = 0.016). Bray–Curtis distance-based RDA (BC-dbRDA) showed no explanatory power of ESBL-Ec status, while age explained 14% of the compositional variation of the caecal microbiota, F (2, 66) = 6.47, p = 0.001. Conclusions This study assessed the role of ESBL-Ec in the successional dynamics of the caecal microbiota in developing broilers and showed that the presence of ESBL-Ec is associated with mild but consistent reductions in alpha diversity and with transient bacterial compositional differences. We also reported the clonal spread of ESBL-Ec and pointed to the farm environment as a likely source for ESBLs.

Plasmids are important vectors for the spread of genes among diverse populations of bacteria. However, there is no standard method to determine the rate at which they spread horizontally via conjugation. Here, we compare commonly used methods on simulated and experimental data, and show that the resulting conjugation rate estimates often depend strongly on the time of measurement, the initial population densities, or the initial ratio of donor to recipient populations. Differences in growth rate, e.g. induced by sub-lethal antibiotic concentrations or temperature, can also significantly bias conjugation rate estimates. We derive a new ‘end-point’ measure to estimate conjugation rates, which extends the well-known Simonsen method to include the effects of differences in population growth and conjugation rates from donors and transconjugants. We further derive analytical expressions for the parameter range in which these approximations remain valid. We present an easy to use R package and web interface which implement both new and previously existing methods to estimate conjugation rates. The result is a set of tools and guidelines for accurate and comparable measurement of plasmid conjugation rates., Plasmid, 121

Allorecognition, the capacity to discriminate self from conspecific non-self, is a ubiquitous organismal feature typically governed by genes evolving under balancing selection. Here, we show that in the fungus Podospora anserina, allorecognition loci controlling vegetative incompatibility (het genes), define two reproductively isolated groups through pleiotropic effects on sexual compatibility. These two groups emerge from the antagonistic interactions of the unlinked loci het-r (encoding a NOD-like receptor) and het-v (encoding a methyltransferase and an MLKL/HeLo domain protein). Using a combination of genetic and ecological data, supported by simulations, we provide a concrete and molecularly defined example whereby the origin and coexistence of reproductively isolated groups in sympatry is driven by pleiotropic genes under balancing selection.

Background Cabbage white butterflies (Pieris spp.) can be severe pests of Brassica crops such as Chinese cabbage, Pak choi (Brassica rapa) or cabbages (B. oleracea). Eggs of Pieris spp. can induce a hypersensitive response-like (HR-like) cell death which reduces egg survival in the wild black mustard (B. nigra). Unravelling the genetic basis of this egg-killing trait in Brassica crops could improve crop resistance to herbivory, reducing major crop losses and pesticides use. Here we investigated the genetic architecture of a HR-like cell death induced by P. brassicae eggs in B. rapa. Results A germplasm screening of 56 B. rapa accessions, representing the genetic and geographical diversity of a B. rapa core collection, showed phenotypic variation for cell death. An image-based phenotyping protocol was developed to accurately measure size of HR-like cell death and was then used to identify two accessions that consistently showed weak (R-o-18) or strong cell death response (L58). Screening of 160 RILs derived from these two accessions resulted in three novel QTLs for Pieris brassicae-induced cell death on chromosomes A02 (Pbc1), A03 (Pbc2), and A06 (Pbc3). The three QTLs Pbc1–3 contain cell surface receptors, intracellular receptors and other genes involved in plant immunity processes, such as ROS accumulation and cell death formation. Synteny analysis with A. thaliana suggested that Pbc1 and Pbc2 are novel QTLs associated with this trait, while Pbc3 also contains an ortholog of LecRK-I.1, a gene of A. thaliana previously associated with cell death induced by a P. brassicae egg extract. Conclusions This study provides the first genomic regions associated with the Pieris egg-induced HR-like cell death in a Brassica crop species. It is a step closer towards unravelling the genetic basis of an egg-killing crop resistance trait, paving the way for breeders to further fine-map and validate candidate genes.

Understanding under which conditions conjugative plasmids encoding antibiotic resistance can invade bacterial communities in the gut is of particular interest to combat the spread of antibiotic resistance within and between animals and humans. We extended a one-compartment model of conjugation to a two-compartment model, to analyse how differences in plasmid dynamics in the gut lumen and at the gut wall affect the invasion of plasmids. We compared scenarios with one and two compartments, different migration rates between the lumen and wall compartments, and different population dynamics. We focused on the effect of attachment and detachment rates on plasmid dynamics, explicitly describing pair formation followed by plasmid transfer in the pairs. The parameter space allowing plasmid invasion in the one-compartment model is affected by plasmid costs and intrinsic conjugation rates of the transconjugant, but not by these characteristics of the donor. The parameter space allowing plasmid invasion in the two-compartment model is affected by attachment and detachment rates in the lumen and wall compartment, and by the bacterial density at the wall. The one- and two-compartment models predict the same parameter space for plasmid invasion if the conditions in both compartments are equal to the conditions in the one-compartment model. In contrast, the addition of the wall compartment widens the parameter space allowing invasion compared with the one-compartment model, if the density at the wall is higher than in the lumen, or if the attachment rate at the wall is high and the detachment rate at the wall is low. We also compared the pair-formation models with bulk-conjugation models that describe conjugation by instantaneous transfer of the plasmid at contact between cells, without explicitly describing pair formation. Our results show that pair-formation and bulk-conjugation models predict the same parameter space for plasmid invasion. From our simulations, we conclude that conditions at the gut wall should be taken into account to describe plasmid dynamics in the gut and that transconjugant characteristics rather than donor characteristics should be used to parameterize the models.

Allele frequencies change due to drift and selection. We investigated those changes for different selection methods. We simulated a livestock population with 50 generations of selection for an additive trait controlled by 2,000 segregating loci at the start of selection. Our results show that the average absolute change in allele frequency with genomic selection was slightly higher than with pedigree selection, and considerably higher than with mass selection. Genomic and pedigree selection both resulted in fixation of roughly three times more loci than mass selection, and roughly five times more loci became fixed for the unfavourable allele. While this was mainly a result of increased genetic drift, genomic selection also lost additional favourable alleles due to hitchhiking. This suggests that genomic selection can limit long-term genetic gain.

For centuries, perishable raw materials such as raw milk have been processed through traditional fermentation. For many, microbiological safety has not been assessed systematically. Here, we study the microbiological safety of an archetypical traditional fermented raw milk product with high cultural importance: Mabisi from Zambia. We focus on traditional processing without the use of defined starter culture – a method that is employed by local small-scale processors at home or at farmer cooperatives. In a field survey, we found that food associated pathogenic bacteria such as Salmonella sp. and Staphylococcus aureus were present in raw milk used for processing. In processed Mabisi these pathogens were found to be present albeit at levels that fall below common limits of microbiological safety for dairy products. In standardized laboratory experiments, we investigated the microbiological safety of traditionally processed Mabisi using challenge tests with important pathogens related to raw milk and Mabisi. Strains of S. aureus, Salmonella and Listeria monocytogenes could survive fermentation and were present in the end-product after 48 or 72 h of fermentation, yet below legally set thresholds of acceptability. Our work shows that use of traditional processing methods for fermentation of raw milk can result in products that are microbiologically safe.

Africa has a rich cultural heritage that is accompanied by rich traditional foods. Some of these foods are preserved by traditional fermentation processes, which are transferred from one generation to another. Fermentation is a low-cost technology, which converts raw materials into final products with improved nutritional value, organoleptic properties and extended shelf life. These traditional fermented foods are widely consumed in both rural and urban areas. This review uses mabisi, a traditional fermented milk product from Zambia to demonstrate the importance of indigenous knowledge of mabisi processing in the valorisation process with a view towards upscaling of not only mabisi but also other similar traditional food products. It highlights the different types, product characteristics and microbial communities of mabisi.