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Earth was impacted by global glaciations during the Cryogenian (720 to 635 million years ago; Ma), events invoked to explain both the origins of multicellularity in Archaeplastida and radiation of the first land plants. However, the temporal relationship between these environmental and biological events is poorly established, due to a paucity of molecular and fossil data, precluding resolution of the phylogeny and timescale of archaeplastid evolution. We infer a time-calibrated phylogeny of early archaeplastid evolution based on a revised molecular dataset and reappraisal of the fossil record. Phylogenetic topology testing resolves deep archaeplastid relationships, identifying two clades of Viridiplantae and placing Bryopsidales as sister to the Chlorophyceae. Our molecular clock analysis infers an origin of Archaeplastida in the late-Paleoproterozoic to early-Mesoproterozoic (1712 to 1387 Ma). Ancestral state reconstruction of cytomorphological traits on this time-calibrated tree reveals many of the independent origins of multicellularity span the Cryogenian, consistent with the Cryogenian multicellularity hypothesis. Multicellular rhodophytes emerged 902 to 655 Ma while crown-Anydrophyta (Zygnematophyceae and Embryophyta) originated 796 to 671 Ma, broadly compatible with the Cryogenian plant terrestrialization hypothesis. Our analyses resolve the timetree of Archaeplastida with age estimates for ancestral multicellular archaeplastids coinciding with the Cryogenian, compatible with hypotheses that propose a role of Snowball Earth in plant evolution. [ABSTRACT FROM AUTHOR]

The mitochondria contain their own genome derived from an alphaproteobacterial endosymbiont. From thousands of protein-coding genes originally encoded by their ancestor, only between 1 and about 70 are encoded on extant mitochondrial genomes (mitogenomes). Thanks to a dramatically increasing number of sequenced and annotated mitogenomes a coherent picture of why some genes were lost, or relocated to the nucleus, is emerging. In this review, we describe the characteristics of mitochondria-to-nucleus gene transfer and the resulting varied content of mitogenomes across eukaryotes. We introduce a 'burst-upon-drift' model to best explain nuclear-mitochondrial population genetics with flares of transfer due to genetic drift. [ABSTRACT FROM AUTHOR]

Over the past decade, molecular phylogenies have placed endoparasites of the genus Euduboscquella in a distinct subclade within clade 4 of the Marine Alveolate (MALV) Group I. Recently, however, rRNA gene sequences have become available for four novel Euduboscquella-like species that infect dinoflagellates, with phylogenies including these sequences indicating that the genus Euduboscquella is paraphyletic. Here, we provide a morphological characterization of the intracellular and extracellular life-cycle stages of a novel species that infects Cucumeridinium coeruleum, a warm water pelagic species sometimes found in coastal environments. We formally describe the novel parasite, Hobagella saltata n. gen, n. sp., and identify a constellation of morphological and developmental characters that distinguish it, as well as Euduboscquella melo and E. nucleocola, both parasites of dinoflagellates, from Euduboscquella species that infect ciliates. We recommend the reassignment of E. melo and E. nucleocola as Hobagella melo n. comb. and H. nucleocola n. comb., respectively. We also propose the family Hobagellidae for these three congeners. We anticipate that the character set developed for distinguishing species of Euduboscquella and Hobagella will be valuable for sorting other Euduboscquella-Hobagella-like taxa scattered across the Group I phylogeny and will provide insight into morphological evolutionary patterns within Group I. Lastly, we consider the potential influence of summer-fall typhoons on the occurrence of H. saltata and its host C. coeruleum in near-shore waters along the southeastern coast of Korea and propose a hypothesis regarding the northward transport and onshore advection of host and parasite populations. If future research supports the hypothesized mechanisms, it could help us better understand parasite distribution and potential changes in biogeography associated with ongoing global changes in surface seawater temperature. [ABSTRACT FROM AUTHOR]

Oxygen oases were the ecological niches where the evolutionary processes that led to the emergence of the first multicellular animals probably took place. These oases likely appeared in zones of maximum photosynthesis at depths of 10–30 meters in the pelagic zone and on the sea bottom, due to the delay in the release of oxygen from seawater into the atmosphere. The likelihood of the emergence of multicellularity among choanoflagellates, ancestral to Metazoa, is supported by their wide range of life forms, which through various morphogenetic pathways developed the main archetypes postulated by the hypotheses of Phagocytella, Gastraea, Synzoospores and their modifications. [ABSTRACT FROM AUTHOR]

Staphylococcus aureus modulates the host immune response directly by interacting with the immune cells or indirectly by secreting molecules (secretome). Relevant differences in virulence mechanisms have been reported for the secretome produced by different S. aureus strains. The present study investigated the S. aureus secretome impact on peripheral bovine mononuclear cells (PBMCs) by comparing two S. aureus strains with opposite epidemiological behavior, the genotype B (GTB)/sequence type (ST) 8, associated with a high within-herd prevalence, and GTS/ST398, associated with a low within-herd prevalence. PBMCs were incubated with different concentrations (0%, 0.5%, 1%, and 2.5%) of GTB/ST8 and GTS/ST398 secretome for 18 and 48 h, and the viability was assessed. The mRNA levels of pro- (IL1-β and STAT1) and anti-inflammatory (IL-10, STAT6, and TGF-β) genes, and the amount of pro- (miR-155-5p and miR-125b-5p) and anti-inflammatory (miR-146a and miR-145) miRNAs were quantified by RT-qPCR. Results showed that incubation with 2.5% of GTB/ST8 secretome increased the viability of cells. In contrast, incubation with the GTS/ST398 secretome strongly decreased cell viability, preventing any further assays. The GTB/ST8 secretome promoted PBMC polarization towards the pro-inflammatory phenotype inducing the overexpression of IL1-β, STAT1 and miR-155-5p, while the expression of genes involved in the anti-inflammatory response was not affected. In conclusion, the challenge of PBMC to the GTS/ST398 secretome strongly impaired cell viability, while exposure to the GTB/ST8 secretome increased cell viability and enhanced a pro-inflammatory response, further highlighting the different effects exerted on host cells by S. aureus strains with epidemiologically divergent behaviors. [ABSTRACT FROM AUTHOR]

Since the discovery of the first "giant virus," particular attention has been paid toward isolating and culturing these large DNA viruses through Acanthamoeba spp. bait systems. While this method has allowed for the discovery of plenty novel viruses in the Nucleocytoviricota, environmental -omics-based analyses have shown that there is a wealth of diversity among this phylum, particularly in marine datasets. The prevalence of these viruses in metatranscriptomes points toward their ecological importance in nutrient turnover in our oceans and as such, in depth study into non-amoebal Nucleocytoviricota should be considered a focal point in viral ecology. In this review, we report on Kratosvirus quantuckense (née Aureococcus anophagefferens Virus), an algae-infecting virus of the Imitervirales. Current systems for study in the Nucleocytoviricota differ significantly from this virus and its relatives, and a litany of trade-offs within physiology, coding potential, and ecology compared to these other viruses reveal the importance of K. quantuckense. Herein, we review the research that has been performed on this virus as well as its potential as a model system for algal-virus interactions. [ABSTRACT FROM AUTHOR]

Appendicularians play an important role in marine food webs, but the alimentary canal of hermaphroditic oikopleurids, which prevalent among urochordates, is little studied ultrastructurally. Serial microtomy revealed that the alimentary canal of Oikopleura gracilis consists of a wide pharynx and a U-shaped gut with typical for oikopleurids anatomy: oesophagus, a bilobed stomach, the vertical, short mid- and voluminous distal or rectal intestines, ending the anal papilla. The mid-intestine leaves under the right gastric lobe. TEM analysis diagnosed the following features in the alimentary canal of Oikopleura gracilis. First, the pharynx is lined with a single layer of highly flattened non-ciliated epithelium. Above the anterior part of the endostyle the pharyngeal epithelium forms a thickening – ciliated ring. It is formed by cells of two types: prismatic, ciliated microvillar cells arranged in several parallel rows, and two rows of narrow parietal cells covering the first cell type. Ciliated ring serves as a kind of first valve, prevents food reflux. Second, in the pharynx of one of the specimens three flagellate protozoans with ultrastructurally similarities of free-living kinetoplastids were found. Third, an additional row of gastric band cells was revealed in the upper part of the right gastric lobe compared to that of the gastric floor. Giant electron-lucent vesicles with homogenous content associated with rough endoplasmic reticulum found in the cytoplasm of the gastric band cell, indicating probable storage the protein digestive secrets in these cells. Large multivesicular bodies diagnosed in gastric band cells ultrastructurally corresponded to autophagosomes. Forth, a new cellular type was found, the osmiophilic enterocytes, scattered throughout the digestive epithelium, that shared ultrastructural signs with apoptotic cells. Fifth, TEM data revealed the peritrophic membrane structure and proposed its formation. The absence of its own microflora in the peritrophic membrane, i.e., the absence of an immunity barrier, may be connected with the short ontogeny of appendicularians. The ultrastructural features revealed in the alimentary canal of O. gracilis expand our knowledge of the functioning of the appendicularians and serve as the basis for further research. [ABSTRACT FROM AUTHOR]

Contemporary climate change in the Arctic is causing the reduction of the ice habitat. This process induces rearrangements in the community composition of ice-dwelling microbial eukaryotes, with heterotrophic picoeukaryotes being one of the least studied groups. Here, we report the results of a DNA metabarcoding investigation of heterotrophic picoeukaryote diversity in the ice of the Kandalaksha Gulf of the White Sea by Illumina high-throughput sequencing of the 18S rRNA V4 gene region. In total, 121 operational taxonomic units (OTUs) belonging to heterotrophic protists were revealed. The communities of heterotrophic picoeukaryotes in first-year ice were represented by seven eukaryotic domains (Stramenopiles, Alveolata, Rhizaria, Cryptista, Haptista, Apusozoa, Opisthokonta) and within 15 phyla. Rhizaria was the most dominant domain accounting for 48% of the total relative read abundance and included only Cercozoa. The taxonomic composition of heterotrophic picoeukaryotes was analyzed in detail with attention to rare and important microbial eukaryotes and unusual finds in sea ice habitats, such as the parasitic Perkinsea. Unknown Cercozoa clade was revealed. We have demonstrated that the White Sea heterotrophic picoeukaryote communities are diverse but insufficiently studied. Only 39% of OTUs were classified down to the order, family, or genus level, and only 11% of OTUs were classified to the genus level. This demonstrates that many unsequenced unicellular eukaryotes are found in sea ice and highlights some limitations of the V4 18S rRNA gene metabarcoding approach—the incompleteness of databases (lack of reference sequences) and shortness of the V4 region (inability to classify OTUs to species level). [ABSTRACT FROM AUTHOR]

This study provides a morphological, ultrastructural, and phylogenetic characterization of a novel micro-eukaryotic parasite (2.3-2.6 µm) infecting amphipod genera Echinogammarus and Orchestia. Longitudinal studies across two years revealed that infection prevalence peaked in late April and May, reaching 64% in Echinogammarus sp. and 15% in Orchestia sp., but was seldom detected during the rest of the year. The parasite infected predominantly hemolymph, connective tissue, tegument, and gonad, although hepatopancreas and nervous tissue were affected in heavier infections, eliciting melanization and granuloma formation. Cell division occurred inside walled parasitic cysts, often within host hemocytes, resulting in hemolymph congestion. Small subunit (18S) rRNA gene phylogenies including related environmental sequences placed the novel parasite as a highly divergent lineage within Class Filasterea, which together with Choanoflagellatea represent the closest protistan relatives of Metazoa. We describe the new parasite as Txikispora philomaios n. sp. n. g., the first confirmed parasitic filasterean lineage, which otherwise comprises four free-living flagellates and a rarely observed endosymbiont of snails. Lineage-specific PCR probing of other hosts and surrounding environments only detected T. philomaios in the platyhelminth Procerodes sp. We expand the known diversity of Filasterea by targeted searches of metagenomic datasets, resulting in 13 previously unknown lineages from environmental samples., (© 2021 The International Society of Protistologists.)

The evolution of seeds is a major reason why flowering plants are a dominant life form on Earth. The developing seed is composed of two fertilization products, the embryo and endosperm, which are surrounded by a maternally derived seed coat. Accumulating evidence indicates that efficient communication among all three seed components is required to ensure coordinated seed development. Cell communication within plant seeds has drawn much attention in recent years. In this study, we review current knowledge of cross-talk among the endosperm, embryo, and seed coat during seed development, and highlight recent advances in this field., (© 2021 Institute of Botany, Chinese Academy of Sciences.)

The capacity of haem to transfer electrons, bind diatomic gases, and catalyse various biochemical reactions makes it one of the essential biomolecules on Earth and one that was likely used by the earliest forms of cellular life. Since the description of haem biosynthesis, our understanding of this multi-step pathway has been almost exclusively derived from a handful of model organisms from narrow taxonomic contexts. Recent advances in genome sequencing and functional studies of diverse and previously neglected groups have led to discoveries of alternative routes of haem biosynthesis that deviate from the 'classical' pathway. In this review, we take an evolutionarily broad approach to illuminate the remarkable diversity and adaptability of haem synthesis, from prokaryotes to eukaryotes, showing the range of strategies that organisms employ to obtain and utilise haem. In particular, the complex evolutionary histories of eukaryotes that involve multiple endosymbioses and horizontal gene transfers are reflected in the mosaic origin of numerous metabolic pathways with haem biosynthesis being a striking case. We show how different evolutionary trajectories and distinct life strategies resulted in pronounced tensions and differences in the spatial organisation of the haem biosynthesis pathway, in some cases leading to a complete loss of a haem-synthesis capacity and, rarely, even loss of a requirement for haem altogether., (© 2021 The Authors. Biological Reviews published by John Wiley & Sons Ltd on behalf of Cambridge Philosophical Society.)

An ancestral eukaryote acquired photosynthesis by genetically integrating a cyanobacterial endosymbiont as the chloroplast. The chloroplast was then further integrated into many other eukaryotic lineages through secondary endosymbiotic events of unicellular eukaryotic algae. While photosynthesis enables autotrophy, it also generates reactive oxygen species that can cause oxidative stress. To mitigate the stress, photosynthetic eukaryotes employ various mechanisms, including regulating chloroplast light absorption and repairing or removing damaged chloroplasts by sensing light and photosynthetic status. Recent studies have shown that, besides algae and plants with innate chloroplasts, several lineages of numerous unicellular eukaryotes engage in acquired phototrophy by hosting algal endosymbionts or by transiently utilizing chloroplasts sequestrated from algal prey in aquatic ecosystems. In addition, it has become evident that unicellular organisms engaged in acquired phototrophy, as well as those that feed on algae, have also developed mechanisms to cope with photosynthetic oxidative stress. These mechanisms are limited but similar to those employed by algae and plants. Thus, there appear to be constraints on the evolution of those mechanisms, which likely began by incorporating photosynthetic cells before the establishment of chloroplasts by extending preexisting mechanisms to cope with oxidative stress originating from mitochondrial respiration and acquiring new mechanisms. Numerous unicellular eukaryotes host algal endosymbionts or utilize chloroplasts sequestrated from algal prey. They have developed some mechanisms to mitigate photosynthetic oxidative stress which are similar to those employed by algae and plants. [ABSTRACT FROM AUTHOR]

Macroalgae have been a key ecological component of marine ecosystems since the Proterozoic period and are common fossil forms in Cambrian Burgess Shale‐type Lagerstätten. However, in most cases, it is difficult to place these early fossil algae into modern groups because little distinctive morphology is preserved. Here, we describe a new form of macroalgae, Qingjiangthallus cystocarpium gen. & sp. nov., from the Qingjiang biota of South China. The new taxon is represented by 546 specimens remarkably preserved with characteristics that allow a phylogenetic placement into crown groups of red algae. Centimeter‐sized thalli resemble members of the extant Rhodymeniophycidae (a subclass of the class Florideophyceae), and hence suggest a florideophycean affinity, which indicates that ahnfeltiophycidaen and rhodymeniophycidaen algae may have diverged at least 518 Ma, accordant with estimations of molecular studies. The presence of possible cystocarps on Qingjiangthallus thalli suggests that evolutionary innovation of a triphasic life cycle in red algae may have occurred no later than the Early Cambrian. The branching patterns and branch width of Qingjiangthallus are consistent with the coarsely dichotomously branched morphogroup, which was previously present in the Ediacaran, Ordovician, and afterward, but absent in the Cambrian. [ABSTRACT FROM AUTHOR]

All animals evolved from a single lineage of unicellular precursors more than 600 million years ago. Thus, the biological and genetic foundations for animal sensation, cognition and behavior must necessarily have arisen by modifications of pre-existing features in their unicellular ancestors. Given that the single-celled ancestors of the animal kingdom are extinct, the only way to reconstruct how these features evolved is by comparing the biology and genomic content of extant animals to their closest living relatives. Here, we reconstruct the Umwelt (the subjective, perceptive world) inhabited by choanoflagellates, a group of unicellular (or facultatively multicellular) aquatic microeukaryotes that are the closest living relatives of animals. Although behavioral research on choanoflagellates remains patchy, existing evidence shows that they are capable of chemosensation, photosensation and mechanosensation. These processes often involve specialized sensorimotor cellular appendages (cilia, microvilli, and/or filopodia) that resemble those that underlie perception in most animal sensory cells. Furthermore, comparative genomics predicts an extensive "sensory molecular toolkit" in choanoflagellates, which both provides a potential basis for known behaviors and suggests the existence of a largely undescribed behavioral complexity that presents exciting avenues for future research. Finally, we discuss how facultative multicellularity in choanoflagellates might help us understand how evolution displaced the locus of decision-making from a single cell to a collective, and how a new space of behavioral complexity might have become accessible in the process. [ABSTRACT FROM AUTHOR]

SUMMARY: Arabidopsis thaliana diverged from A. arenosa and A. lyrata at least 6 million years ago. The three species differ by genome‐wide polymorphisms and morphological traits. The species are to a high degree reproductively isolated, but hybridization barriers are incomplete. A special type of hybridization barrier is based on the triploid endosperm of the seed, where embryo lethality is caused by endosperm failure to support the developing embryo. The MADS‐box type I family of transcription factors is specifically expressed in the endosperm and has been proposed to play a role in endosperm‐based hybridization barriers. The gene family is well known for its high evolutionary duplication rate, as well as being regulated by genomic imprinting. Here we address MADS‐box type I gene family evolution and the role of type I genes in the context of hybridization. Using two de‐novo assembled and annotated chromosome‐level genomes of A. arenosa and A. lyrata ssp. petraea we analyzed the MADS‐box type I gene family in Arabidopsis to predict orthologs, copy number, and structural genomic variation related to the type I loci. Our findings were compared to gene expression profiles sampled before and after the transition to endosperm cellularization in order to investigate the involvement of MADS‐box type I loci in endosperm‐based hybridization barriers. We observed substantial differences in type‐I expression in the endosperm of A. arenosa and A. lyrata ssp. petraea, suggesting a genetic cause for the endosperm‐based hybridization barrier between A. arenosa and A. lyrata ssp. petraea. Significance Statement: We address MADS‐box type I gene family evolution using de‐novo assembled genomes of A. arenosa and A. lyrata ssp. petraea and predict orthologs, copy number and structural genomic variation related to the type I loci. We observe substantial differences in MADS‐box type‐I expression in the endosperm suggesting a genetic cause for an endosperm‐based hybridization barrier. [ABSTRACT FROM AUTHOR]

Fruit set is the process by which the ovary develops into a fruit and is an important factor in determining fruit yield. Fruit set is induced by two hormones, auxin and gibberellin, and the activation of their signaling pathways, partly by suppressing various negative regulators. Many studies have investigated the structural changes and gene networks in the ovary during fruit set, revealing the cytological and molecular mechanisms. In tomato (Solanum lycopersicum), SlIAA9 and SlDELLA/PROCERA act as auxin and gibberellin signaling repressors, respectively, and are important regulators of the activity of transcription factors and downstream gene expression involved in fruit set. Upon pollination, SlIAA9 and SlDELLA are degraded, which subsequently activates downstream cascades and mainly contributes to active cell division and cell elongation, respectively, in ovaries during fruit setting. According to current knowledge, the gibberellin pathway functions as the most downstream signal in fruit set induction, and therefore its role in fruit set has been extensively explored. Furthermore, multi-omics analysis has revealed the detailed dynamics of gene expression and metabolites downstream of gibberellins, highlighting the rapid activation of central carbon metabolism. This review will outline the relevant mechanisms at the molecular and metabolic levels during fruit set, particularly focusing on tomato. [ABSTRACT FROM AUTHOR]

Summary: Rhodophyta (or red algae) are a diverse and species‐rich group that forms one of three major lineages in the Archaeplastida, a eukaryotic supergroup whose plastids arose from a single primary endosymbiosis. Red algae are united by several features, such as relatively small intron‐poor genomes and a lack of cytoskeletal structures associated with motility like flagella and centrioles, as well as a highly efficient photosynthetic capacity. Multicellular red algae (or macroalgae) are one of the earliest diverging eukaryotic lineages to have evolved complex multicellularity, yet despite their ecological, evolutionary, and commercial importance, they have remained a largely understudied group of organisms. Considering the increasing availability of red algal genome sequences, we present a broad overview of fundamental aspects of red macroalgal biology and posit on how this is expected to accelerate research in many domains of red algal biology in the coming years. [ABSTRACT FROM AUTHOR]

Background The molecular evolution of organellar genomes in angiosperms has been studied extensively, with some lineages, such as parasitic ones, displaying unique characteristics. Parasitism has emerged 12 times independently in angiosperm evolution. Holoparasitism is the most severe form of parasitism, and is found in ~10 % of parasitic angiosperms. Although a few holoparasitic species have been examined at the molecular level, most reports involve plastomes instead of mitogenomes. Parasitic plants establish vascular connections with their hosts through haustoria to obtain water and nutrients, which facilitates the exchange of genetic information, making them more susceptible to horizontal gene transfer (HGT). HGT is more prevalent in the mitochondria than in the chloroplast or nuclear compartments. Scope This review summarizes current knowledge on the plastid and mitochondrial genomes of holoparasitic angiosperms, compares the genomic features across the different lineages, and discusses their convergent evolutionary trajectories and distinctive features. We focused on Balanophoraceae (Santalales), which exhibits extraordinary traits in both their organelles. Conclusions Apart from morphological similarities, plastid genomes of holoparasitic plants also display other convergent features, such as rampant gene loss, biased nucleotide composition and accelerated evolutionary rates. In addition, the plastomes of Balanophoraceae have extremely low GC and gene content, and two unexpected changes in the genetic code. Limited data on the mitochondrial genomes of holoparasitic plants preclude thorough comparisons. Nonetheless, no obvious genomic features distinguish them from the mitochondria of free-living angiosperms, except for a higher incidence of HGT. HGT appears to be predominant in holoparasitic angiosperms with a long-lasting endophytic stage. Among the Balanophoraceae, mitochondrial genomes exhibit disparate evolutionary paths with notable levels of heteroplasmy in Rhopalocnemis and unprecedented levels of HGT in Lophophytum. Despite their differences, these Balanophoraceae share a multichromosomal mitogenome, a feature also found in a few free-living angiosperms. [ABSTRACT FROM AUTHOR]

Photosynthesis allows for the formation of biomass from inorganic carbon and therefore greatly enhances the amount of organic material on planet Earth. Especially, oxygenic photosynthesis removed a major bottleneck in the formation of biomass by utilising ubiquitous water (H2O) and CO2 molecules as raw materials for organic molecules. This, over billions of years, shaped the world into the form we know today, with an oxygen-containing atmosphere, largely oxygenated water bodies and landmasses consisting of sediment rocks. Oxygenic photosynthesis furthermore enabled the evolution of aerobic energy metabolism, and it would be very difficult to imagine animal (including human) life in the absence of molecular oxygen as an electron acceptor. Oxygenic photosynthesis first, and exclusively, evolved in cyanobacteria. However, eukaryotes also learned to photosynthesise, albeit with a trick, which is the integration of formerly free-living cyanobacteria into the eukaryotic cell. There, the former bacteria became endosymbionts, and from these endosymbionts, the photosynthetic organelles (termed plastids) evolved. In almost all major groups of eukaryotes, plastid-containing members are found. At the same time, plastid-related features also indicate that these plastids form a monophyletic group. This can be explained by the transfer of plastids between the eukaryotic super-groups, leading to plastids being found in groups that are otherwise non-photosynthetic. In this chapter, we discuss the evolutionary origin of plastids, with a special emphasis on the evolution of plankton algae, such as diatoms or dinoflagellates, who acquired their plastids from other photosynthetic eukaryotes. [ABSTRACT FROM AUTHOR]

Acquired photosynthesis transforms genotypically heterotrophic lineages into autotrophs. Transient acquisitions of eukaryotic chloroplasts may provide key evolutionary insight into the endosymbiosis process—the hypothesized mechanism by which eukaryotic cells obtained new functions via organelle retention. Here, we use an eco-evolutionary model to study the environmental conditions under which chloroplast retention is evolutionarily favorable. We focus on kleptoplastidic lineages—which steal functional chloroplasts from their prey—as hypothetical evolutionary intermediates. Our adaptive dynamics analysis reveals a spectrum of evolutionarily stable strategies ranging from phagotrophy to phototrophy to obligate kleptoplasty. Our model suggests that a low-light niche and weak (or absent) trade-offs between chloroplast retention and overall digestive ability favor the evolution of phototrophy. In contrast, when consumers experience strong trade-offs, obligate kleptoplasty emerges as an evolutionary end point. Therefore, the preevolved trade-offs that underlie an evolving lineage's physiology will likely constrain its evolutionary trajectory. [ABSTRACT FROM AUTHOR]

Sigma receptors are non-opiate/non-phencyclidine receptors that bind progesterone and/or heme and also several unrelated xenobiotics/chemicals. They reside in the plasma membrane and in the membranes of the endoplasmic reticulum, mitochondria, and nucleus. Until recently, the biology/pharmacology of these proteins focused primarily on their role in neuronal functions in the brain/retina. However, there have been recent developments in the field with the discovery of unexpected roles for these proteins in iron/heme homeostasis. Sigma receptor 1 (S1R) regulates the oxidative stress-related transcription factor NRF2 and protects against ferroptosis, an iron-induced cell death process. Sigma receptor 2 (S2R), which is structurally unrelated to S1R, complexes with progesterone receptor membrane components PGRMC1 and PGRMC2. S2R, PGRMC1, and PGRMC2, either independently or as protein–protein complexes, elicit a multitude of effects with a profound influence on iron/heme homeostasis. This includes the regulation of the secretion of the iron-regulatory hormone hepcidin, the modulation of the activity of mitochondrial ferrochelatase, which catalyzes iron incorporation into protoporphyrin IX to form heme, chaperoning heme to specific hemoproteins thereby influencing their biological activity and stability, and protection against ferroptosis. Consequently, S1R, S2R, PGRMC1, and PGRMC2 potentiate disease progression in hemochromatosis and cancer. These new discoveries usher this intriguing group of non-traditional progesterone receptors into an unchartered territory in biology and medicine. [ABSTRACT FROM AUTHOR]

Aphelids are a holomycotan group, represented exclusively by parasitoids infecting algae. They form a sister lineage to Fungi in the phylogenetic tree and represent a key group for reconstruction of the evolution of Holomycota and for analysis of the origin of Fungi. The newly assembled genome of Aphelidium insullamus (Holomycota, Aphelida) with a total length of 18.9 Mb, 7820 protein-coding genes and a GC percentage of 52.05% was obtained by a hybrid assembly based on Oxford Nanopore long reads and Illumina paired reads. In order to trace the origin and the evolution of fungal osmotrophy and its presence or absence in Aphelida, we analyzed the set of main fungal transmembrane transporters, which are proteins of the Major Facilitator superfamily (MFS), in the predicted aphelid proteomes. This search has shown an absence of a specific fungal protein family Drug:H+ antiporters-2 (DAH-2) and specific fungal orthologs of the sugar porters (SP) family, and the presence of common opisthokont's orthologs of the SP family in four aphelid genomes. The repertoire of SP orthologs in aphelids turned out to be less diverse than in free-living opisthokonts, and one of the most limited among opisthokonts. We argue that aphelids do not show signs of similarity with fungi in terms of their osmotrophic abilities, despite the sister relationships of these groups. Moreover, the osmotrophic abilities of aphelids appear to be reduced in comparison with free-living unicellular opisthokonts. Therefore, we assume that the evolution of fungi-specific traits began after the separation of fungal and aphelid lineages, and there are no essential reasons to consider aphelids as a prototype of the fungal ancestor. [ABSTRACT FROM AUTHOR]

Polycomb repressive complexes (PRCs) play a pivotal role in the growth and development of eukaryotes. The components of PRCs are well conserved among most eukaryotes, including humans and plants. PRCs-mediated gene silencing in plants has been intensively studied in an effort to capture molecular mechanisms underlying the epigenetic control of developmental programs. Thus, this review intended to describe current knowledge on PcG-mediated gene regulation which dictates many aspects of developmental programs including seed dormancy, leaf and floral organ development, floral transition, and embryogenesis processes. This review is divided into two parts. First, a general introduction of polycomb complexes in eukaryotes in terms of their composition and interacting partners is given. This review then discusses the role of polycomb complexes in the development of Arabidopsis plants, with particular focus placed on the current understanding of how PRCs target their target genes. In addition, this review covers the molecular details of PRCs' role in well-studied vernalization-mediated floral transition in winter annual Arabidopsis plants. [ABSTRACT FROM AUTHOR]

The emergence of animals from their unicellular ancestors is a major evolutionary event. Thanks to the study of diverse close unicellular relatives of animals, we now have a better grasp of what the unicellular ancestor of animals was like. However, it is unclear how that unicellular ancestor of animals became the first animals. To explain this transition, two popular theories, the choanoblastaea and the synzoospore, have been proposed. We will revise and expose the flaws in these two theories while showing that, due to the limits of our current knowledge, the origin of animals is a biological black swan event. As such, the origin of animals defies retrospective explanations. Therefore, we should be extra careful not to fall for confirmation biases based on few data and, instead, embrace this uncertainty and be open to alternative scenarios. With the aim to broaden the potential explanations on how animals emerged, we here propose two novel and alternative scenarios. In any case, to find the answer to how animals evolved, additional data will be required, as will the hunt for microscopic creatures that are closely related to animals but have not yet been sampled and studied. [ABSTRACT FROM AUTHOR]

While glycans underlie many biological processes, such as protein folding, cell adhesion, and cell–cell recognition, deep evolution of glycosylation machinery remains an understudied topic. N-linked glycosylation is a conserved process in which mannosidases are key trimming enzymes. One of them is the glycoprotein endo -α-1,2-mannosidase which participates in the initial trimming of mannose moieties from an N-linked glycan inside the cis -Golgi. It is unique as the only endo-acting mannosidase found in this organelle. Relatively little is known about its origins and evolutionary history; so far it was reported to occur only in vertebrates. In this work, a taxon-rich bioinformatic survey to unravel the evolutionary history of this enzyme, including all major eukaryotic clades and a wide representation of animals, is presented. The endomannosidase was found to be more widely distributed in animals and other eukaryotes. The protein motif changes in context of the canonical animal enzyme were tracked. Additionally, the data show the two canonical vertebrate endomannosidase genes, MANEA and MANEAL , arose at the second round of the two vertebrate genome duplications and one more vertebrate paralog, CMANEAL , is uncovered. Finally, a framework where N-glycosylation co-evolved with complex multicellularity is described. A better understanding of the evolution of core glycosylation pathways is pivotal to understanding biology of eukaryotes in general, and the Golgi apparatus in particular. This systematic analysis of the endomannosidase evolution is one step toward this goal. [ABSTRACT FROM AUTHOR]

The core objective of this study was to genetically and phenotypically characterize subclinical mastitis-causing multidrug-resistant Staphylococcus aureus (MDRSA). In addition, risk factors associated with subclinical mastitis caused by MDRSA were investigated. Bacterial cultures were performed on 2120 mammary quarters, 40 swabs of milk utensils, 5 bulk tank milk samples, and 11 nostril and 11 hand swabs from milkers from five dairy farms. Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) was conducted for S. aureus identification. Antimicrobial resistance was screened phenotypically using the disk diffusion test in all S. aureus isolates. A biofilm formation assay; detection of genes associated with beta-lactam resistance, efflux pump, and biofilm formation; and pulsed-field gel electrophoresis (PFGE) were performed in all MDRSA isolates. Multi-locus sequence typing (MLST) was carried out in cefoxitin-resistant MDRSA isolates. A total of 188 S. aureus isolates from milk as well as two from milking utensils and one from bulk tank milk were identified. Most of the isolates (92.7%; 177 of 191) showed beta-lactam resistance, and 7% (14 of 191) were MDRSA. Interestingly, 36% (5 of 14) of MDRSA isolates were cefoxitin-resistant, but none carried mecA or mecC genes. Based on PFGE results, it was observed that S. aureus strains were more likely to be unique to a specific herd. Two clonal complexes were identified, CC97 (ST126; commonly livestock-associated) and CC1 (ST7440; usually community-associated). To the best of our knowledge, this is the first report of ST7440 isolated from bovine mastitis in Brazil. The risk factor results underscored the importance of considering parity, stage of lactation, SCC, milk production, and herd size when studying the risk of subclinical mastitis and antimicrobial resistance in S. aureus. Thus, to implement effective strategies to prevent subclinical mastitis in dairy herds and to minimize MDRSA spread, it is important to understand MDRSA strains' distribution and their antimicrobial resistance profile. [ABSTRACT FROM AUTHOR]

Several automated molecular methods have emerged for distinguishing eukaryote species based on DNA sequence data. However, there are knowledge gaps around which of these single‐locus methods is more accurate for the identification of microalgal species, such as the highly diverse and ecologically relevant diatoms. We applied genetic divergence, Automatic Barcode Gap Discovery for primary species delimitation (ABGD), Assemble Species by Automatic Partitioning (ASAP), Statistical Parsimony Network Analysis (SPNA), Generalized Mixed Yule Coalescent (GMYC) and Poisson Tree Processes (PTP) using partial cox1, rbcL, 5.8S + ITS2, ITS1 + 5.8S + ITS2 markers to delineate species and compare to published polyphasic identification data (morphological features, phylogeny and sexual reproductive isolation) to test the resolution of these methods. ASAP, ABGD, SPNA and PTP models resolved species of Eunotia, Seminavis, Nitzschia, Sellaphora and Pseudo‐nitzschia corresponding to previous polyphasic identification, including reproductive isolation studies. In most cases, these models identified diatom species in similar ways, regardless of sequence fragment length. GMYC model presented smallest number of results that agreed with previous published identification. Following the recommendations for proper use of each model presented in the present study, these models can be useful tools to identify cryptic or closely related species of diatoms, even when the datasets have relatively few sequences. [ABSTRACT FROM AUTHOR]

The endosymbiotic origin of plastids from cyanobacteria gave eukaryotes photosynthetic capabilities and launched the diversification of countless forms of algae. These primary plastids are found in members of the eukaryotic supergroup Archaeplastida. All known archaeplastids still retain some form of primary plastids, which are widely assumed to have a single origin. Here, we use single-cell genomics from natural samples combined with phylogenomics to infer the evolutionary origin of the phylum Picozoa, a globally distributed but seemingly rare group of marine microbial heterotrophic eukaryotes. Strikingly, the analysis of 43 single-cell genomes shows that Picozoa belong to Archaeplastida, specifically related to red algae and the phagotrophic rhodelphids. These picozoan genomes support the hypothesis that Picozoa lack a plastid, and further reveal no evidence of an early cryptic endosymbiosis with cyanobacteria. These findings change our understanding of plastid evolution as they either represent the first complete plastid loss in a free-living taxon, or indicate that red algae and rhodelphids obtained their plastids independently of other archaeplastids., (© 2021. The Author(s).)

Gregarine apicomplexans are ubiquitous endosymbionts of invertebrate hosts. Despite their ecological and evolutionary importance, inferences about the phylogenetic relationships of major gregarine groups, such as the Lecudinidae and Urosporidae, have been hindered by vague taxonomic definitions and limited molecular and morphological data. In this study, we investigated five gregarine species collected from four families of polychaete hosts (Nereididae, Oenonidae, Hesionidae, and Phyllodocidae) using light microscopy (LM) and scanning electron microscopy (SEM). We also generated small subunit ribosomal DNA sequences from these species and conducted molecular phylogenetic analyses to elucidate the evolutionary relationships within the Lecudinoidea. Our results include new molecular and morphological data for two previously described species (Lecudina cf. platynereidis and Lecudina cf. arabellae), the discovery of a new species of Lecudina (L. oxydromus n. sp.), and the discovery of two novel species, namely Amplectina cordis n. gen. et. n. sp. and Sphinctocystis inclina n. sp. These two species exhibited unique shapes and movements, resembling those of urosporids but with a phylogenetic affinity to lecudinids, blurring the border between lecudinids and urosporids. Our study emphasizes the need for further investigations into this highly diverse group, which has achieved great success across multiple animal phyla with diverse shapes and movements., (© 2024 The Author(s). Journal of Eukaryotic Microbiology published by Wiley Periodicals LLC on behalf of International Society of Protistologists.)

The evolutionary and ecological success of spermatophytes is intrinsically linked to the seed habit, which provides a protective environment for the initial development of the new generation. This environment includes an ephemeral nourishing tissue that supports embryo growth. In gymnosperms this tissue originates from the asexual proliferation of the maternal megagametophyte, while in angiosperms it is a product of fertilization, and is called the endosperm. The emergence of these nourishing tissues is of profound evolutionary value, and they are also food staples for most of the world's population. Here, using Orthofinder to infer orthologue genes among newly generated and previously published datasets, we provide a comparative transcriptomic analysis of seed nourishing tissues from species of several angiosperm clades, including those of early diverging lineages, as well as of one gymnosperm. Our results show that, although the structure and composition of seed nourishing tissues has seen significant divergence along evolution, there are signatures that are conserved throughout the phylogeny. Conversely, we identified processes that are specific to species within the clades studied, and thus illustrate their functional divergence. With this, we aimed to provide a foundation for future studies on the evolutionary history of seed nourishing structures, as well as a resource for gene discovery in future functional studies., (© 2024 The Authors. The Plant Journal published by Society for Experimental Biology and John Wiley & Sons Ltd.)

Chromatin is a dynamic network that regulates genome organization and gene expression. Different types of chromatin regulators are highly conserved among Archaeplastida, including unicellular algae, while some chromatin genes are only present in land plant genomes. Here, we review recent advances in understanding the function of conserved chromatin factors in basal land plants and algae. We focus on the role of Polycomb-group genes which mediate H3K27me3-based silencing and play a role in balancing gene dosage and regulating haploid-to-diploid transitions by tissue-specific repression of the transcription factors KNOX and BELL in many representatives of the green lineage. Moreover, H3K27me3 predominantly occupies repetitive elements which can lead to their silencing in a unicellular alga and basal land plants, while it covers mostly protein-coding genes in higher land plants. In addition, we discuss the role of nuclear matrix constituent proteins as putative functional lamin analogs that are highly conserved among land plants and might have an ancestral function in stress response regulation. In summary, our review highlights the importance of studying chromatin regulation in a wide range of organisms in the Archaeplastida., (© 2023 The Authors. The Plant Journal published by Society for Experimental Biology and John Wiley & Sons Ltd.)

Horizontal gene transfer (HGT), or lateral gene transfer, is the non-sexual movement of genetic information between genomes. It has played a pronounced part in bacterial and archaeal evolution, but its role in eukaryotes is less clear. Behaviours unique to eukaryotic cells - phagocytosis and endosymbiosis - have been proposed to increase the frequency of HGT, but nuclear genomes encode fewer HGTs than bacteria and archaea. Here, I review the existing theory in the context of the growing body of data on HGT in eukaryotes, which suggests that any increased chance of acquiring new genes through phagocytosis and endosymbiosis is offset by a reduced need for these genes in eukaryotes, because selection in most eukaryotes operates on variation not readily generated by HGT., (© 2024. Springer Nature Limited.)

The cytoskeleton has a central role in eukaryotic biology, enabling cells to organize internally, polarize, and translocate. Studying cytoskeletal machinery across the tree of life can identify common elements, illuminate fundamental mechanisms, and provide insight into processes specific to less-characterized organisms. Red algae represent an ancient lineage that is diverse, ecologically significant, and biomedically relevant. Recent genomic analysis shows that red algae have a surprising paucity of cytoskeletal elements, particularly molecular motors. Here, we review the genomic and cell biological evidence and propose testable models of how red algal cells might perform processes including cell motility, cytokinesis, intracellular transport, and secretion, given their reduced cytoskeletons. In addition to enhancing understanding of red algae and lineages that evolved from red algal endosymbioses (e.g., apicomplexan parasites), these ideas may also provide insight into cytoskeletal processes in animal cells., (© 2021 Wiley Periodicals LLC.)

As an obligate intracellular parasite, Toxoplasma gondii must import essential nutrients from the host cell into the parasitophorous vacuole. We previously reported that the parasite scavenges cholesterol from host endocytic organelles for incorporation into membranes and storage as cholesteryl esters in lipid droplets. In this study, we have investigated whether Toxoplasma utilizes cholesterol as a precursor for the synthesis of metabolites, such as steroids. In mammalian cells, steroidogenesis occurs in mitochondria and involves membrane-bound type I cytochrome P450 oxidases that are activated through interaction with heme-binding proteins containing a cytochrome b5 domain, such as members of the membrane-associated progesterone receptor (MAPR) family. Our LC-MS targeted lipidomics detect selective classes of hormone steroids in Toxoplasma, with a predominance for anti-inflammatory hydroxypregnenolone species, deoxycorticosterone and dehydroepiandrosterone. The genome of Toxoplasma contains homologs encoding a single type I CYP450 enzyme (we named TgCYP450mt) and a single MAPR (we named TgMAPR). We showed that TgMAPR is a hemoprotein with conserved residues in a heme-binding cytochrome b5 domain. Both TgCYP450 and TgMAPR localize to the mitochondrion and show interactions in in situ proximity ligation assays. Genetic ablation of cyp450mt is not tolerated by Toxoplasma; we therefore engineered a conditional knockout strain and showed that iΔTgCYP450mt parasites exhibit growth impairment in cultured cells. Parasite strains deficient for mapr could be generated; however, ΔTgMAPR parasites suffer from poor global fitness, loss of plasma membrane integrity, aberrant mitochondrial cristae, and an abnormally long S-phase in their cell cycle. Compared to wild-type parasites, iΔTgCYP450mt and ΔTgMAPR lost virulence in mice and metabolomics studies reveal that both mutants have reduced levels of steroids. These observations point to a steroidogenic pathway operational in the mitochondrion of a protozoan that involves an evolutionary conserved TgCYP450mt enzyme and its binding partner TgMAPR. Author summary: In addition to controlling membrane fluidity, cholesterol serves as a substrate for the synthesis of important biomolecules, in particular steroid hormones. Steroidogenesis involves mitochondrial cholesterol-metabolizing cytochrome P450s activated by membrane-associated progesterone receptor (MAPR) hemoproteins. The intravacuolar parasite Toxoplasma scavenges cholesterol from the host and our targeted lipidomics reveal the presence of pregnenolone and selected steroid hormones in the parasite. We investigated a potential steroidogenic pathway in Toxoplasma by characterizing the single CYP450 (TgCYP450mt) and the MAPR homolog (TgMAPR) in Toxoplama. Both TgCYP450mt and TgMAPR are expressed in the mitochondrion and interact with each other. Parasites lacking mapr are viable in vitro unlike ΔTgCYP450mt parasites. Conditional TgCYP450mt knock-out parasites and ΔTgMAPR suffer from developmental defects, are poorly virulent and have reduced levels of steroids compared to WT parasites. These data suggest that Toxoplasma has the ability to synthesize some steroids in the mitochondrion, using a cholesterol-metabolizing cytochrome P450 and reveal that steroidogenesis is an ancient pathway, conserved in eukaryotic lineages. [ABSTRACT FROM AUTHOR]

Background and aims The MBW complex consist of proteins belonging to three major families (MYB, bHLH and WDR) involved in various processes throughout plant development: epidermal cell development, mucilage secretory cells and flavonoid biosynthesis. Recently, it has been reported that TT8 , encoding a bHLH transcription factor, is involved in the biosynthesis of flavonoids in the seed coat and it also plays a role in bypassing the postzygotic barrier resulting from an unbalance in genetic loads of the parental lines. Here, we focus on the functional evolution, in seed development, of the bHLH proteins that are part of the MBW complex, complemented with a literature review. Methods Phylogenetic analyses performed across seed plants and expression analyses in the reproductive tissues of four selected angiosperms (Arabidopsis thaliana , Brassica napus , Capsella rubella and Solanum lycopersicum) allow us to hypothesize on the evolution of its functions. Key Results TT8 expression in the innermost layer of the seed coat is conserved in the selected angiosperms. However, except for Arabidopsis , TT8 is also expressed in ovules, carpels and fruits. The homologues belonging to the sister clade of TT8 , EGL3 / GL3 , involved in trichome development, are expressed in the outermost layer of the seed coat, suggesting potential roles in mucilage. Conclusions The ancestral function of these genes appears to be flavonoid biosynthesis, and the conservation of TT8 expression patterns in the innermost layer of the seed coat in angiosperms suggests that their function in postzygotic barriers might also be conserved. Moreover, the literature review and the results of the present study suggest a sophisticated association, linking the mechanisms of action of these genes to the cross-communication activity between the different tissues of the seed. Thus, it provides avenues to study the mechanisms of action of TT8 in the postzygotic triploid block, which is crucial because it impacts seed development in unbalanced crosses. [ABSTRACT FROM AUTHOR]

Speciation involves reproductive isolation, which can occur by hybridization barriers acting in the endosperm of the developing seed. The nuclear endosperm is a nutrient sink, accumulating sugars from surrounding tissues, and undergoes coordinated cellularization, switching to serve as a nutrient source for the developing embryo. Tight regulation of cellularization is therefore vital for seed and embryonic development. Here we showthat hybrid seeds from crosses between Arabidopsis thaliana as maternal contributor and A. arenosa or A. lyrata as pollen donors result in an endosperm based post-zygotic hybridization barrier that gives rise to a reduced seed germination rate. Hybrid seeds display opposite endosperm cellularization phenotypes, with late cellularization in crosses with A. arenosa and early cellularization in crosses with A. lyrata. Stage specific endosperm reporters display temporally ectopic expression in developing hybrid endosperm, in accordance with the early and late cellularization phenotypes, confirming a disturbance of the source-sink endosperm phase change.We demonstrate that the hybrid barrier is under the influence of abiotic factors, and show that a temperature gradient leads to diametrically opposed cellularization phenotype responses in hybrid endosperm with A. arenosa or A. lyrata as pollen donors. Furthermore, different A. thaliana accession genotypes also enhance or diminish seed viability in the twohybridcross-types, emphasizing that both genetic and environmental cues control the hybridization barrier.We have identified an A. thalianaMADS-BOX type I family single locus that is required for diametrically opposed cellularization phenotype responses in hybrid endosperm. Loss of AGAMOUS-LIKE 35 significantly affects the germination rate of hybrid seeds in opposite directions when transmitted through the A. thaliana endosperm, and is suggested to be a locus that promotes cellularization as part of an endosperm based mechanism involved in post-zygotic hybrid barriers. The role of temperature inhybrid speciationandthe identification of distinct loci in control of hybrid failure have great potential to aid the introduction of advantageous traits in breeding research and to support models to predict hybrid admixture in a changing global climate. [ABSTRACT FROM AUTHOR]

Endosperm is a key nutritive tissue that supports the developing embryo or seedling, and serves as a major nutritional source for human and livestock feed. In sexually-reproducing flowering plants, it generally develops after fertilization. However, autonomous endosperm (AE) formation (i.e. independent of fertilization) is also possible. Recent findings of AE loci/ genes and aberrant imprinting in native apomicts, together with a successful initiation of parthenogenesis in rice and lettuce, have enhanced our understanding of the mechanisms bridging sexual and apomictic seed formation. However, the mechanisms driving AE development are not well understood. This review presents novel aspects related to AE development in sexual and asexual plants underlying stress conditions as the primary trigger for AE. Both application of hormones to unfertilized ovules and mutations that impair epigenetic regulation lead to AE development in sexual Arabidopsis thaliana , which may point to a common pathway for both phenomena. Apomictic-like AE development under experimental conditions can take place due to auxin-dependent gene expression and/or DNA methylation. [ABSTRACT FROM AUTHOR]

Although discussed by 20th century philosophers in terms drawn from the sciences of non-living systems, in recent decades biological function has been considered in relationship to organismal capability and purpose. Bringing two phenomena generally neglected in evolutionary theory (i.e. inherency and agency) to bear on questions of function leads to a rejection of the adaptationist 'selected effects' notion of biological function. I review work showing that organisms such as the placozoans can thrive with almost no functional embellishments beyond those of their constituent cells and physical properties of their simple tissues. I also discuss work showing that individual tissue cells and their artificial aggregates exhibit agential behaviours that are unprecedented in the histories of their respective lineages. I review findings on the unique metazoan mechanism of developmental gene expression that has recruited, during evolution, inherent ancestral cellular functionalities into specialized cell types and organs of the different animal groups. I conclude that most essential functions in animal species are inherent to the cells from which they evolved, not selected effects, and that many of the others are optional 'add-ons', a status inimical to fitness-based models of evolution positing that traits emerge from stringent cycles of selection to meet external challenges. [ABSTRACT FROM AUTHOR]

In this paper, we follow the evolutionary origins of cells as unicellular organisms and their evolution towards multicellularity, with a focus on plants and animals, both of which have two basic types of organismal self-identities: the immunological and the neuronal. Most cells of the animal immune system and its mesenchymal tissues are amoeba-like without flagella or cilia and form only loose cell–cell contacts. On the other hand, neuronal and epithelial cells are typically ciliated and assemble epithelial or neuronal synapses. In contrast, walled cells of higher plants lack flagella or cilia. However, lower plants up to the gymnosperm tree Ginkgo biloba have flagellated sperm cells. In our symbiotic concept of eukaryogenesis, the first ancient eukaryotic cells emerged from the merger of a large amoeba-like host cell with a small flagellated guest cell which later transformed into the eukaryotic nucleus. This duality at the origin of the eukaryotic cell matches with the duality of sexual gametes. It also corresponds to the immune system/neural dualities of organismal self-identities in both animals and plants. [ABSTRACT FROM AUTHOR]

Photosynthetic microalgae are responsible for an important fraction of CO2 fixation and O2 production on Earth. Three-dimensional (3D) ultrastructural characterization of these organisms in their natural environment can contribute to a deeper understanding of their cell biology. However, the low throughput of volume electron microscopy (vEM) methods along with the complexity and heterogeneity of environmental samples pose great technical challenges. In the present study, we used a workflow based on a specific electron microscopy sample preparation method compatible with both light and vEM imaging in order to target one cell among a complex natural community. This method revealed the 3D subcellular landscape of a photosynthetic dinoflagellate, which we identified as Ensiculifera tyrrhenica, with quantitative characterization of multiple organelles. We show that this cell contains a single convoluted chloroplast and show the arrangement of the flagellar apparatus with its associated photosensitive elements. Moreover, we observed partial chromatin unfolding, potentially associated with transcription activity in these organisms, in which chromosomes are permanently condensed. Together with providing insights in dinoflagellate biology, this proof-of-principle study illustrates an efficient tool for the targeted ultrastructural analysis of environmental microorganisms in heterogeneous mixes. [ABSTRACT FROM AUTHOR]

Simple Summary: Mastitis is one of the most common diseases of the dairy industry and with it brings important economic losses. The most prevalent form of the disease is subclinical mastitis, which leads, in the absence of clinical signs, to decreased milk production, increased somatic cell count, and an increased risk of clinical mastitis during lactation. With the increasing public health concerns for antimicrobial use and its relationship with the development of antimicrobial resistance, nation-specific regulations and general pressure to reduce group-level prophylactic use of antimicrobials have been established. Selective dry therapy reserves antimicrobial treatment for cows or quarters suspected of having an intramammary infection. The treatment is administered after the last milking, while uninfected cows or quarters do not receive antibiotherapy. Since selective dry cow therapy was introduced, different methods of selecting infected cows or quarters have been reported. The aim of this article is to describe the management of mastitis in dairy cows and the main tools for its diagnosis, with a specific focus on on-farm instruments. Mastitis is one of the most important diseases in dairy cattle farms, and it can affect the health status of the udder and the quantity and quality of milk yielded. The correct management of mastitis is based both on preventive and treatment action. With the increasing concern for antimicrobial resistance, it is strongly recommended to treat only the mammary quarters presenting intramammary infection. For this reason, a timely and accurate diagnosis is fundamental. The possibility to detect and characterize mastitis directly on farm would be very useful to choose the correct management protocol. Some on-field diagnostic tools are already routinely applied to detect mastitis, such as the California Mastitis Test and on-farm culture. Other instruments are emerging to perform a timely diagnosis and to characterize mastitis, such as Infra-Red Thermography, mammary ultrasound evaluation and blood gas analysis, even if their application still needs to be improved. The main purpose of this article is to present an overview of the methods currently used to control, detect, and characterize mastitis in dairy cows, in order to perform a timely diagnosis and to choose the most appropriate management protocol, with a specific focus on on-farm diagnostic tools. [ABSTRACT FROM AUTHOR]

SUMMARY: Seed abortion is an important process in the formation of seedless characteristics in citrus fruits. However, the molecular regulatory mechanism underlying citrus seed abortion is poorly understood. Laser capture microdissection‐based RNA‐seq combined with Pacbio‐seq was used to profile seed development in the Ponkan cultivars 'Huagan No. 4' (seedless Ponkan) (Citrus reticulata) and 'E'gan No. 1' (seeded Ponkan) (C. reticulata) in two types of seed tissue across three developmental stages. Through comparative transcriptome and dynamic phytohormone analyses, plant hormone signal, cell division and nutrient metabolism‐related processes were revealed to play critical roles in the seed abortion of 'Huagan No. 4'. Moreover, several genes may play indispensable roles in seed abortion of 'Huagan No. 4', such as CrWRKY74, CrWRKY48 and CrMYB3R4. Overexpression of CrWRKY74 in Arabidopsis resulted in severe seed abortion. By analyzing the downstream regulatory network, we further determined that CrWRKY74 participated in seed abortion regulation by inducing abnormal programmed cell death. Of particular importance is that a preliminary model was proposed to depict the regulatory networks underlying seed abortion in citrus. The results of this study provide novel insights into the molecular mechanism across citrus seed development, and reveal the master role of CrWRKY74 in seed abortion of 'Huagan No. 4'. Significance Statement: The seedless character of citrus has important economic value and is favored by consumers, but the formation process of its internal mechanism still lacks understanding. In this study, the molecular mechanism of seed abortion in seedless Ponkan caused by abnormal programmed cell death was preliminarily analyzed by functional genomics, cytological morphological observation, physiological and biochemical assays, as well as stable genetic transformation. [ABSTRACT FROM AUTHOR]

The first data on the composition and diversity of the summer community of planktonic protists in Usinsky Bay and the adjacent water area of the Kuybyshev Reservoir, obtained using high-throughput sequencing of the 18S ribosomal RNA gene, are presented. In the composition of the protist community, 1150 operational taxonomic units (OTU) were found; among them, representatives of the Stramenopiles–Alveolata–Rhizaria (SAR) supergroup predominate. In the complete library, Stramenopiles predominate by the number of OTU, represented (in descending order) by Chrysophyceae (8.5%), Opalozoa (8.3%), Diatomea (4.7%), and Oomycetes (Peronosporomycetes) (3.7%); by the number of nucleotide sequences, Alveolata (62.0%) and, first of all, Ciliata (56.9%). There are four interconnected communities of protists: of the river area, the bay itself, the mouth zone, and the reservoir outside the influence of the bay (above the mouth). The communities of the river area and the reservoir area above the mouth have the greatest contrast in composition. In general, the estuarine system studied has features of both ecocline and ecotone. The competitive relationships with cyanobacteria have the main effect on the development of the phototrophic component of eukaryotic plankton. Cyanobacterial "bloom" also affects the structure of the heterotrophic part of the community, although this effect is less pronounced. The development of Archaeplastida, Rhizaria, and minor groups of protists positively correlates with the portion of Metazoa sequences in the samples, which reflects the intensity of the metazooplankton press. Sequences belonging to Bolidophyceae and Rhodelphida, the taxa rare for freshwater, were found. These findings expand the biogeography of these groups that were found so far in very few freshwater reservoirs. [ABSTRACT FROM AUTHOR]

The order Protococcidiida is one of the most poorly studied basal groups of Sporozoa (Apicomplexa sensu stricto). To date, the phylogenetic unity of protococcidians and their relationship with other sporozoans are understudied. Only the protococcidian Eleutheroschizon duboscqi has molecular evidence of a sister position to "true" coccidians (Eimeria, Sarcocystis, Toxoplasma). E. duboscqi is characterized by epicellular development in the so-called parasitophorous sac of the host cell origin. The unusual localization of Eleutheroschizon is comparable to that of Cryptosporidium. We describe a new species of the genus, E. planoratum ex Naineris quadricuspida polychaete from the White Sea, using light and electron microscopy. The morphology of attachment apparatus, phylogenetic analyses of concatenated DNA sequences of the nuclear ribosomal operon (SSU rDNA, ITS1, 5.8S rDNA, ITS2, and LSU rDNA), and compensatory base changes in ITS2 secondary structures of both protococcidians confirm the new species. The resulting phylogenies also confirm that Eleutheroschizon is sister to eimeriid coccidians, while Cryptosporidium tends to be grouped with gregarines. We discuss a new type of endoparasitism among sporozoans—the closed epicellular parasitism that evolved convergently in Eleutheroschizon and Cryptosporidium. The diagnosis of the new species and the emended diagnoses of the species E. duboscqi and the genus Eleutheroschizon are presented. [ABSTRACT FROM AUTHOR]

Grain development is a crucial determinant of yield and quality in bread wheat (Triticum aestivum L.). However, the regulatory mechanisms underlying wheat grain development remain elusive. Here we report how TaMADS29 interacts with TaNF-YB1 to synergistically regulate early grain development in bread wheat. The tamads29 mutants generated by CRISPR/Cas9 exhibited severe grain filling deficiency, coupled with excessive accumulation of reactive oxygen species (ROS) and abnormal programmed cell death that occurred in early developing grains, while overexpression of TaMADS29 increased grain width and 1,000-kernel weight. Further analysis revealed that TaMADS29 interacted directly with TaNF-YB1; null mutation in TaNF-YB1 caused grain developmental deficiency similar to tamads29 mutants. The regulatory complex composed of TaMADS29 and TaNF-YB1 exercises its possible function that inhibits the excessive accumulation of ROS by regulating the genes involved in chloroplast development and photosynthesis in early developing wheat grains and prevents nucellar projection degradation and endosperm cell death, facilitating transportation of nutrients into the endosperm and wholly filling of developing grains. Collectively, our work not only discloses the molecular mechanism of MADS-box and NF-Y TFs in facilitating bread wheat grain development, but also indicates that caryopsis chloroplast might be a central regulator of grain development rather than merely a photosynthesis organelle. More importantly, our work offers an innovative way to breed high-yield wheat cultivars by controlling the ROS level in developing grains. [ABSTRACT FROM AUTHOR]

Euglenids are a diverse group of flagellates that inhabit most environments and exhibit many different nutritional modes. The most prominent euglenids are phototrophs, but phagotrophs constitute the majority of phylogenetic diversity of euglenids. They are pivotal to our understanding of euglenid evolution, yet we are only starting to understand relationships amongst phagotrophs, with the backbone of the tree being most elusive. Ploeotids make up most of this backbone diversity—yet despite their morphological similarities, SSU rDNA analyses and multigene analyses show that they are non‐monophyletic. As more ploeotid diversity is sampled, known taxa have coalesced into some subgroups (e.g. Alistosa), but the relationships amongst these are not always supported and some taxa remain unsampled for multigene phylogenetics. Here, we used light microscopy and single‐cell transcriptomics to characterize five ploeotid euglenids and place them into a multigene phylogenetic framework. Our analyses place Decastava in Alistosa; while Hemiolia branches with Liburna, establishing the novel clade Karavia. We describe Hemiolia limna, a freshwater‐dwelling species in an otherwise marine clade. Intriguingly, two undescribed ploeotids are found to occupy pivotal positions in the tree: Chelandium granulatum nov. gen. nov. sp. branches as sister to Olkasia, and Gaulosia striata nov. gen. nov. sp. remains an orphan taxon. [ABSTRACT FROM AUTHOR]

Phago-mixotrophy, the combination of photoautotrophy and phagotrophy in mixoplankton, organisms that can combine both trophic strategies, have gained increasing attention over the past decade. It is now recognized that a substantial number of protistan plankton species engage in phago-mixotrophy to obtain nutrients for growth and reproduction under a range of environmental conditions. Unfortunately, our current understanding of mixoplankton in aquatic systems significantly lags behind our understanding of zooplankton and phytoplankton, limiting our ability to fully comprehend the role of mixoplankton (and phago-mixotrophy) in the plankton food web and biogeochemical cycling. Here, we put forward five research directions that we believe will lead to major advancement in the field: (i) evolution: understanding mixotrophy in the context of the evolutionary transition from phagotrophy to photoautotrophy; (ii) traits and trade-offs: identifying the key traits and trade-offs constraining mixotrophic metabolisms; (iii) biogeography: large-scale patterns of mixoplankton distribution; (iv) biogeochemistry and trophic transfer: understanding mixoplankton as conduits of nutrients and energy; and (v) in situ methods: improving the identification of in situ mixoplankton and their phago-mixotrophic activity. [ABSTRACT FROM AUTHOR]