Distinct Lineages Research Articles

Dominant Malignant Clones Leverage Lineage Restricted Epigenomic Programs to Drive Ependymoma Development.

1. Specific chromatin modules accessible during brain development render distinct cell lineage programs at risk of transformation by pediatric fusion oncoproteins.2. Cross-species single cell ATAC and RNA (scMultiome) of mouse and human ependymoma (EPN) reveals diverse patterns of lineage differentiation programs that restrain oncogenic transformation.3. Early intermediate progenitor-like EPN cells establish a tumor cell hierarchy that mirrors neural differentiation programs.4. ZFTA-RELA transformation is compatible with distinct developmental epigenetic states requiring precise 'goldilocks' levels of fusion oncoprotein expression.5. Dominant tumor clones establish the entire EPN cellular hierarchy that reflects normal gliogenic and neurogenic differentiation programs.

A comparative analysis of chloroplast genomes revealed the chloroplast heteroplasmy of Artemisia annua.

Artemisia annua L. is the main source of artemisinin, an antimalarial drug. High diversity of morphological characteristics and artemisinin contents of A. annua has affected the stable production of artemisinin while efficient discrimination method of A. annua strains is not available. The complete chloroplast (cp) genomes of 38 A. annua strains were assembled and analyzed in this study. Phylogenetic analysis of Artemisia species showed that distinct intraspecific divergence occurred in A. annua strains. A total of 38 A. annua strains were divided into two distinct lineages, one lineage containing widely-distributed strains and the other lineage only containing strains from northern China. The A. annua cp genomes ranged from 150, 953 to 150, 974bp and contained 131 genes, and no presence or absence variation of genes was observed. The IRs and SC junctions were located in rps19 and ycf1, respectively, without IR contraction observed. Rich sequence polymorphisms were observed among A. annua strains, and a total of 60 polymorphic sites representing 14 haplotypes were identified which unfolding the cpDNA heteroplasmy of A. annua. In conclusion, this study provided valuable resource for A. annua strains identification and provided new insights into the evolutionary characteristics of A. annua.

Nonequilibrium Antigen Recognition during Infections and Vaccinations

The initial immune response to an acute primary infection is a coupled process of antigen proliferation, molecular recognition by naive B cells, and their subsequent clonal expansion. This process contains a fundamental problem: the recognition of an exponentially time-dependent antigen signal. Here, we show that an efficient immune response must be stringently constrained to B-cell lineages with high antigen binding affinity. We propose a tuned proofreading mechanism for primary recognition of new antigens, where the molecular recognition machinery is adapted to the complexity of the immune repertoire. We show that this process produces potent, specific, and fast recognition of antigens, maintaining a spectrum of genetically distinct B-cell lineages as input for affinity maturation. Our analysis maps the proliferation-recognition dynamics of a primary infection to a generalized Luria-Delbrück process, akin to the dynamics of the classic fluctuation experiment. This map establishes a link between signal recognition dynamics and evolution. We derive the resulting statistics of the activated immune repertoire: Antigen binding affinity, expected size, and frequency of active B-cell clones are related by power laws, which define the class of generalized Luria-Delbrück processes. Their exponents depend on the antigen and B-cell proliferation rate, the number of proofreading steps, and the lineage density of the naive repertoire. We extend the model to include spatiotemporal processes, including the diffusion-recognition dynamics of a vaccination. Empirical data of activated mouse immune repertoires are found to be consistent with activation involving about three proofreading steps. The model predicts key clinical characteristics of acute infections and vaccinations, including the emergence of elite neutralizers and the effects of immune aging. More broadly, our results establish infections and vaccinations as a new probe into the global architecture and functional principles of immune repertoires. Published by the American Physical Society 2024

Psychrosphaera algicola sp. nov. and Paraglaciecola algarum sp. nov., and reclassification of Pseudoalteromonas elyakovii, Pseudoalteromonas flavipulchra, and Pseudoalteromonas profundi as later heterotypic synonyms of P. distincta, P. maricaloris, and P. gelatinilytica.

Two Gram-negative, obligately aerobic, rod-shaped bacteria, strains G1-22T and G1-23T, were isolated from the phycosphere of a marine brown alga. Both strains exhibited catalase- and oxidase-positive activities. Strain G1-22T displayed optimal growth at 25 °C, pH 8.0, and 2.0-3.0% (w/v) NaCl, while strain G1-23T exhibited optimal growth at 25 °C, pH 8.0, and 4.0% NaCl. Ubiquinone-8 was identified as the sole isoprenoid quinone in both strains. As major fatty acids (> 5%), strain G1-22T contained C16 : 0, summed feature 3 (C16 : 1 ω7c and/or C16 : 1 ω6c), summed feature 8 (C18 : 1 ω7c and/or C18 : 1 ω6c), C12 : 1 3-OH, and C10 : 0 3-OH, while strain G1-23T contained C16 : 0, summed feature 3 (C16 : 1 ω7c and/or C16 : 1 ω6c), and C14 : 0. Phosphatidylethanolamine, phosphatidylglycerol, and diphosphatidylglycerol were major polar lipids in both strains. Strains G1-22T and G1-23T had DNA G+C contents of 40.2 and 38.9 mol%, respectively. Phylogenetic analyses based on 16S rRNA and genome sequences revealed that strains G1-22T and G1-23T formed distinct phylogenetic lineages within the genera Psychrosphaera and Paraglaciecola, respectively. Strain G1-22T showed closest relatedness to Psychrosphaera ytuae MTZ26T with 97.8% 16S rRNA gene sequence similarity, 70.2% average nucleotide identity (ANI), and a 21.5% digital DNA-DNA hybridization (dDDH) value, while strain G1-23T was most closely related to Paraglaciecola aquimarina KCTC 32108T with 95.6% 16S rRNA gene sequence similarity, 74.6% ANI, and a 20.1% dDDH value. Based on phenotypic and molecular characteristics, strains G1-22T and G1-23T are proposed to represent two novel species, namely Psychrosphaera algicola sp. nov. (type strain G1-22T=KACC 22486T=JCM 34971T) and Paraglaciecola algarum sp. nov. (type strain G1-23T=KACC 22490T=JCM 34972T), respectively. Additionally, based on the comparison of whole genome sequences, it is proposed that Pseudoalteromonas elyakovii, Pseudoalteromonas flavipulchra, and Pseudoalteromonas profundi are reclassified as later heterotypic synonyms of Pseudoalteromonas distincta, Pseudoalteromonas maricaloris, and Pseudoalteromonas gelatinilytica, respectively.

Commuting-driven competition between transmission chains shapes seasonal influenza virus epidemics in the United States.

Despite intensive study, much remains unknown about the dynamics of seasonal influenza virus epidemic establishment and spread in the United States (US) each season. By reconstructing transmission lineages from seasonal influenza virus genomes collected in the US from 2014 to 2023, we show that most epidemics consisted of multiple distinct transmission lineages. Spread of these lineages exhibited strong spatiotemporal hierarchies and lineage size was correlated with timing of lineage establishment in the US. Mechanistic epidemic simulations suggest that mobility-driven competition between lineages determined the extent of individual lineages' geographical spread. Based on phylogeographic analyses and epidemic simulations, lineage-specific movement patterns were dominated by human commuting behavior. These results suggest that given the locations of early-season epidemic sparks, the topology of inter-state human mobility yields repeatable patterns of which influenza viruses will circulate where, but the importance of short-term processes limits predictability of regional and national epidemics.

Identification of a Novel ECM Remodeling Macrophage Subset in AKI to CKD Transition by Integrative Spatial and Single-Cell Analysis.

The transition from acute kidney injury (AKI) to chronic kidney disease (CKD) is a critical clinical issue. Although previous studies have suggested macrophages as a key player in promoting inflammation and fibrosis during this transition, the heterogeneity and dynamic characterization of macrophages are still poorly understood. Here, we used integrated single-cell RNA sequencing and spatial transcriptomic to characterize the spatiotemporal heterogeneity of macrophages in murine AKI-to-CKD model of unilateral ischemia-reperfusion injury. A marked increase in macrophage infiltration at day 1 was followed by a second peak at day 14 post AKI. Spatiotemporal profiling revealed that injured tubules and macrophages co-localized early after AKI, whereas in late chronic stages had spatial proximity to fibroblasts. Further pseudotime analysis revealed two distinct lineages of macrophages in this transition: renal resident macrophages differentiated into the pro-repair subsets, whereas infiltrating monocyte-derived macrophages contributed to chronic inflammation and fibrosis. A novel macrophage subset, extracellular matrix remodeling-associated macrophages (EAMs) originating from monocytes, linked to renal fibrogenesis and communicated with fibroblasts via insulin-like growth factors (IGF) signalling. In sum, our study identified the spatiotemporal dynamics of macrophage heterogeneity with a unique subset of EAMs in AKI-to-CKD transition, which could be a potential therapeutic target for preventing CKD development.

Avian phylogenetic and functional diversity are better conserved by land‐sparing than land‐sharing farming in lowland tropical forests

Abstract The transformation of natural habitats for farming is a major driver of tropical biodiversity loss. To mitigate impacts, two alternatives are promoted: intensifying agriculture to offset protected areas (land sparing) or integrating wildlife‐friendly habitats within farmland (land sharing). In the montane and dry tropics, phylogenetic and functional diversity, which underpin evolutionary values and the provision of ecosystem functioning and services, are best protected by land sparing. A key question is how these components of biodiversity are best conserved in the more stable environments of lowland moist tropical forests. Focusing on cattle farming within the Colombian Amazon, we investigated how the occupancy of 280 bird species varies between forest and pasture spanning gradients of wildlife‐friendly features. We then simulated scenarios of land‐sparing and land‐sharing farming to predict impacts on phylogenetic and functional diversity metrics. Predicted metrics differed marginally between forest and pasture. However, community assembly varied significantly. Wildlife‐friendly pastures were inadequate for most forest‐dependent species, while phylogenetic and functional diversity indices showed minimal variation across gradients of wildlife‐friendly features. Land sparing consistently retained higher levels of Faith's phylogenetic diversity (~30%), functional richness (~20%) and evolutionarily distinct lineages (~40%) than land sharing, and did so across a range of landscape sizes. Securing forest protection through land‐sparing practices remains superior for conserving overall community phylogenetic and functional diversity than land sharing. Synthesis and applications: To minimise the loss of avian phylogenetic diversity and functional traits from farming in the Amazon, it is imperative to protect large blocks of undisturbed and regenerating forests. The intensification required within existing farmlands to make space for spared lands while meeting agricultural demand needs to be sustainable, avoiding long‐term negative impacts on soil quality and other ecosystem services. Policies need to secure the delivery of both actions simultaneously.

Patterns of persistence: Genetic and behavioral population complexity of winter flounder amid population declines.

Winter flounder Pseudopleuronectes americanus (Walbaum 1792) are a coastal flatfish species of economic and cultural importance that have dwindled to <15, % of their historic abundance in the southern New England/Mid-Atlantic region of the United States, with evidence indicating near-extirpation of certain local populations. This species exhibits intricate behaviors in spawning and migration that contribute to population complexity and resilience. These behaviors encompass full or partial philopatry to natal estuaries, the generation of multiple pulses of larval delivery, and partial migration. The patterns of genetic diversity within and among estuaries and cohorts presented here carry important implications in understanding the susceptibility to demographic shocks, even if the full extent of genetic diversity within and among winter flounder stocks on the US East Coast remains unresolved. Our findings reveal connectivity between estuaries in Long Island, New York, suggesting the potential for genetic rescue of depleted subpopulations. Family reconstruction and relatedness analysis indicate that split cohorts and migration contingents are not the result of genetically distinct lineages. We found no evidence for genetic structure separating these groups, and in some instances, we were able to detect closely related individuals that belonged to different migratory contingents or cohorts. Characterizing the spatial and behavioral organization of this species at the population level is crucial for comprehending its potential for recovery, not only in terms of biomass but also in reinstating the complex population structure that supports resilience. The search for generality in winter flounder spawning and migration behavior remains elusive, but perhaps the lack of generalities within this species is what has allowed it to persist in the face of decades of environmental and anthropogenic stressors.

Abstract We029: Common and Divergent Cellular Etiologies Underlying Hypoplastic Left Heart Syndrome and Hypoplastic Right Heart Syndrome

Single ventricle heart defects are the most severe forms of congenital heart defects and are classified based on the affected ventricles: hypoplastic left heart syndrome (HLHS) and hypoplastic right heart syndrome (HRHS). Cellular etiologies underlying differential left and right ventricular hypoplasia are unknown and remain intractable without an experimental model to probe common and divergent cellular etiologies between HLHS and HRHS. In this study, we leveraged patient-specific induced pluripotent stem cells (iPSCs) and single-cell transcriptomics to interrogate distinct etiologies of HLHS and HRHS. Both HLHS and HRHS iPSC-derived cardiomyocytes (iPSC-CMs) exhibit a reduced proliferation capacity compared to sex-matched family controls under both static and cyclic stretch conditions. Biological pathways related to cell cycle progression, DNA replication, and cell proliferation are downregulated in both HLHS and HRHS iPSC-CMs, suggesting an intrinsic cardiac proliferation deficiency. Single-cell transcriptomics indicate that differentiation of cardiac mesoderm towards second heart field (SHF) progenitors are compromised in both HLHS and HRHS. However, differentiation of epicardial progenitors is enhanced at the expense of SHF progenitors in HLHS, whereas first heart field (FHF) progenitors are prevalent in HRHS. Trajectory inference analysis uncovers distinct cell lineage determination pathways in FHF and SHF progenitors between HLHS and HRHS. Moreover, HLHS iPSC-CMs exhibit reduced mitochondrial activities whereas HRHS iPSC-CMs show enhanced mitochondrial respiration and ATP production compared to controls. In sum, these common and divergent cellular etiologies of HLHS and HRHS may underlie ventricular hypoplasia in the left side and right side of the heart.

Abstract We028: Decoding m6a RNA methylomes identifies Igf2bp1 as a common barrier to direct reprogramming

Direct reprogramming has revolutionized the fields of stem cell biology and regenerative medicine. Targeted transdifferentiation of cells in situ holds significant promise in treating a large swathe of illness and injury including cardiovascular disease. However, much remains unknown about the molecular mechanisms of direct reprogramming, particularly its post-transcriptional regulation, including the role of m6a RNA modification. Here, by characterizing early changes in the m6a RNA methylome during reprogramming of fibroblasts toward three distinct lineages—cardiac, hepatic and neuronal—we identify lineage-specific features as well as common regulatory patterns. Our data reveal extensive changes in m6a methylome of direct reprogramming with clear impacts on cell fate decisions. Through loss-of-function screening of m6a readers, we uncovered Igf2bp1(insulin-like growth factor 2 mRNA binding protein 1) as a shared barrier to direct reprogramming. Further mechanistic studies will show how Igf2bp1 influences the reprogramming process mediated via m6a modifications. Collectively, our results present a fascinating portrait of m6a RNA methylome during direct reprogramming and reveal a key role of Igf2bp1 in maintaining cell fate, enhancing our mechanistic understanding of the reprogramming process.

Integrative taxonomy of the genus Coridius Illiger, 1807 (Hemiptera: Heteroptera: Dinidoridae) reveals hidden diversity and three new species from North-East India.

The genus Coridius Illiger, 1807 (Heteroptera: Dinidoridae) comprises a group of phytophagous terrestrial bugs consisting of 36 species distributed in the Afrotropical and Indo-Malayan regions. In several communities in northeastern India, insects are recognised as a delicacy, medicine, and a nutritional supplement, with Coridius being a popular delicacy. However, Coridius has received little taxonomic attention to date due to large intraspecific variations, inadequate taxonomic treatments, and the rarity of many species. To address this gap, an integrative taxonomy of the genus was performed. Two mitochondrial genes, viz., cytochrome oxidase subunit 1 (COI) and 16S rRNA, were sequenced to reconstruct the phylogenetic relationships within Coridius. We performed both maximum likelihood (ML) and Bayesian inference (BI) to develop a species tree, followed by the Bayesian implementation of the Poisson tree process (bPTP) and Assemble Species by Automatic Partitioning (ASAP) as an additional test to assess species boundaries and delimit operational taxonomic units. A linear discriminant analysis (LDA) of four key morphological characters was then performed to identify species groups. Overall, our analysis supported the establishment of three new species: Coridius adii sp. nov., Coridius esculentus sp. nov., and Coridius insperatus sp. nov., and revealed six distinct lineages within Coridius chinensis (Dallas, 1851). Linear discriminant analysis of morphological characters indicated the clustering of eight species. The species status of Coridius nigriventris (Westwood, 1837) stat. rev, formerly synonymized under Coridius nepalensis (Westwood, 1837), is reinstated in this study. Further, we revised the genus Coridius from India and rediscovered Coridius assamensis (Distant, 1902) and Coridius fuscus (Westwood, 1837) after 100 years.

Retinoic acid signalling regulates branchiomeric neck muscle development at the head/trunk interface.

Skeletal muscles of the head and trunk originate in distinct lineages with divergent regulatory programmes converging on activation of myogenic determination factors. Branchiomeric head and neck muscles share a common origin with cardiac progenitor cells in cardiopharyngeal mesoderm (CPM). The retinoic acid (RA) signalling pathway is required during a defined early time window for normal deployment of cells from posterior CPM to the heart. Here, we show that blocking RA signalling in the early mouse embryo also results in selective loss of the trapezius neck muscle, without affecting other skeletal muscles. RA signalling is required for robust expression of myogenic determination factors in posterior CPM and subsequent expansion of the trapezius primordium. Lineage-specific activation of a dominant-negative RA receptor reveals that trapezius development is not regulated by direct RA signalling to myogenic progenitor cells in CPM, or through neural crest cells, but indirectly through the somitic lineage, closely apposed with posterior CPM in the early embryo. These findings suggest that trapezius development is dependent on precise spatiotemporal interactions between cranial and somitic mesoderm at the head/trunk interface.

Parallel Evolution at the Regulatory Base-Pair Level Contributes to Mammalian Interspecific Differences in Polygenic Traits.

Parallel evolution occurs when distinct lineages with similar ancestral states converge on a new phenotype. Parallel evolution has been well documented at the organ, gene pathway, and amino acid sequence level but in theory, it can also occur at individual nucleotides within noncoding regions. To examine the role of parallel evolution in shaping the biology of mammalian complex traits, we used data on single-nucleotide polymorphisms (SNPs) influencing human intraspecific variation to predict trait values in other species for 11 complex traits. We found that the alleles at SNP positions associated with human intraspecific height and red blood cell (RBC) count variation are associated with interspecific variation in the corresponding traits across mammals. These associations hold for deeper branches of mammalian evolution as well as between strains of collaborative cross mice. While variation in RBC count between primates uses both ancient and more recently evolved genomic regions, we found that only primate-specific elements were correlated with primate body size. We show that the SNP positions driving these signals are flanked by conserved sequences, maintain synteny with target genes, and overlap transcription factor binding sites. This work highlights the potential of conserved but tunable regulatory elements to be reused in parallel to facilitate evolutionary adaptation in mammals.

Evidence of striking morphological similarity and tissue tropism of phylogenetically distant myxozoan genera: Myxidium and Paramyxidium in the kidney of the European eel.

European eel, Anguilla anguilla (Linnaeus) (Elopomorpha: Anguilliformes), is a critically endangered fish of ecological and economic importance, hosting numerous parasites, including myxozoans (Cnidaria). Since its initial discovery in the kidney of European eel, Myxidium giardi Cépède, 1906 has been reported with numerous spore sizes and shapes from various tissues of multiple anguillid species. Morphological variability, wide host and tissue spectrum, and lack of sequence data raised doubts about the conspecificity of reported isolates. Subsequent studies provided 18S rDNA sequences of several isolates from anguillids and other elopiform fish, and demonstrated a split of parasite data into two distinct phylogenetic lineages, one comprising the M. giardi sequence, and the other all species infecting elopiform fishes classified under the recently established genus Paramyxidium Freeman et Kristmundsson, 2018. Myxidium giardi was, however, transferred to this genus as Paramyxidium giardi n. comb. and designated as the type species of the genus. In line with this change, the sequence originally identified as M. giardi was considered to have been incorrectly associated with this species. To shed light on the status of M. giardi originally described by Cépède (1906), we conducted microscopic and molecular examinations of various organs of 24 individuals of European eel, originating from diverse Czech habitats. Through morphometric and molecular analyses, we demonstrated that spore and polar capsule morphology, morphometry and tissue tropism of our European eel kidney parasite isolates matched the features of the original M. giardi description. Our isolates clustered in the lineage encompassing the first published M. giardi sequence. Thus, the originally described M. giardi indeed represents an existing species within the genus Myxidium Bütschli, 1882, which we formally resurrect and redescribe. Due to the morphological and molecular differences between M. giardi and P. giardi of Freeman et Kristmundsson (2018), we additionally rename the latter species as Paramyxidium freemani nom. nov.

Phylogenomic Analyses of Three Distinct Lineages Uniting Staphylococcus cohnii and Staphylococcus urealyticus from Diverse Hosts.

We sequenced and assembled genomes for 17 isolates of Staphylococcus cohnii isolated from osteomyelitis lesions in young broilers from two separate experiments where we induced lameness using a hybrid wire-litter flooring system. Whole genome comparisons using three different methods support a close relationship of genomes from both S. cohnii and Staphylococcus urealyticus. The data support three different lineages, which we designated as Lineage 1, Lineage 2, and Lineage 3, uniting these two species within an evolving complex. We present evidence for horizontal transfer between lineages of genomic regions from 50-440 kbp. The transfer of a 186 kbp region from Lineage 1 to Lineage 2 appears to have generated Lineage 3. Human-associated isolates appear to be limited to Lineages 2 and 3 but Lineage 2 appears to contain a higher number of human pathogenic isolates. The chicken isolates from our lameness trials included genomically diverse isolates from both Lineage 1 and 2, and isolates from both lineages were obtained from osteomyelitis lesions of individual birds. Our results expand the diversity of Staphylococci associated with osteomyelitis in poultry and suggest a high diversity in the microbiome of day-old chicks. Our data also support a reevaluation and unification of the taxonomic classifications of S. cohnii and S. urealyticus.

Chengkuizengella axinellae sp. nov., a symbiotic bacterium isolated from a marine sponge of the genus Axinella.

A Gram-stain-positive, strictly aerobic, creamy-white colored, endospore-forming and non-motile rods strain, designated as strain 2205SS18-9T, was isolated from a marine sponge, Axinella sp. collected from Seopseom Island, Republic of Korea. Optimal growth of strain 2205SS18-9T was observed at 25-30°C, pH 6.5-7.0, and in the presence of 3.0% (w/v) NaCl. Cells were oxidase-positive and catalase-negative. Negative for nitrate reduction and indole production. Phylogenetic analyses based on the 16S rRNA gene and whole-genome sequences revealed that strain 2205SS18-9T formed a distinct phyletic lineage in the genus Chengkuizengella, and it was most closely related to Chengkuizengella marina YPA3-1-1T and Chengkuizengella sediminis J15A17T with 97.1 and 96.6% 16S rRNA gene sequence similarities, respectively. The average nucleotide identity and digital DNA-DNA hybridization values between strain 2205SS18-9T and Chengkuizengella marina YPA3-1-1T were 79.0 and 21.6%, respectively. The genomic DNA G + C content was 34.1%. The genome harbors a number of host-adhesion and transporter genes, suggested that strain 2205SS18-9T may interact with its sponge host as a symbiont. Menaquinone-7 was the sole isoprenoid quinone and antieiso-C15:0 (28.5%), iso-C16:0 (25.8%), C16:1 ω7c alcohol (15.0%), and iso-C15:0 (11.2%) were detected as the major fatty acids. Polar lipids included diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, two unidentified aminophospholipids, and an unidentified lipid. The cell-wall peptidoglycan contained lysine, alanine, glutamate, and aspartate. Based on these analyses, strain 2205SS18-9T represents a novel species of the genus Chengkuizengella, for which the name Chengkuizengella axinellae sp. nov. is proposed. The type strain is 2205SS18-9T (= KACC 23238T = LMG 33063T).

An insight into the cryptic diversity of Fragilariaceae (Bacillariophyta), with the description of a new Antarctic species, Gedaniella antarctica sp. nov.

ABSTRACT Fragilariaceae is a paraphyletic family of araphid diatoms commonly used as bio-indicators, in environmental assessments and in paleoenvironmental reconstructions, and with various potential industrial applications. Recent molecular taxonomic research has highlighted significant limitations in traditional morphology-based investigations of these diatom species. Most descriptions of species and genera of the Fragilariaceae present broad morphological character definitions and many diagnostic characters are indistinguishable by light microscopy. In this sense, taxon misidentification is common and could have serious implications for environmental surveys and laboratory experiments. To better understand the diversity of the Fragilariaceae, we (1) performed phylogenetic analyses of the small subunit ribosomal RNA (18S rRNA), rbcL and psbC gene sequences, (2) inferred a cladogram from key morphological features used in the traditional identification of Fragilariaceae, (3) tested if the topologies of the tree recovered from the molecular phylogeny, of the tree based on morphology and of the trees constraining to monophyly the genera Sarcophagodes, Pseudostaurosira and Nanofrustulum (together and separately) were significantly different and (4) mapped morphological character states on the ML tree and inferred their evolution based on maximum parsimony. Our results supported the monophyly of a group of Fragilariaceae within small araphid diatoms including the genera Cratericulifera, Plagiostriata, Castoridens, Opephora, Staurosira, Staurosirella, Punctastriata, Psammotaenia, Hendeyella, Stauroforma, Pseudostaurosira sensu Li, Nanofrustulum sensu Li, Serratifera sensu Li and Gedaniella sensu Li. Molecular phylogeny and topology tests suggested that the latest circumscriptions of the genera Sarcophagodes, Pseudostaurosira and Nanofrustulum sensu Morales were not monophyletic. Analyses of the Antarctic strain IMA070A collected during the XXXIV Italian Antarctic Expedition using fine structural features of the frustule and molecular data revealed that this diatom belongs to a distinct lineage within Gedaniella, which we describe here as Gedaniella antarctica sp. nov.

Genome analysis reveals three distinct lineages of the cosmopolitan white shark

The white shark (Carcharodon carcharias) (Linnaeus, 1758), an iconic apex predator occurring in all oceans,1,2 is classified as Vulnerable globally3-with global abundance having dropped to 63% of 1970s estimates,4-and as Critically Endangered in Europe.5 Identification of evolutionary significant units and their management are crucial for conservation,6 especially as the white shark is facing various but often region-specific anthropogenic threats.7,8,9,10,11 Assessing connectivity in a cosmopolitan marine species requires worldwide sampling and high-resolution genetic markers.12 Both are lacking for the white shark, with studies to date typified by numerous but geographically limited sampling, and analyses relying largely on relatively small numbers of nuclear microsatellites,13,14,15,16,17,18,19 which can be plagued by various genotyping artefacts and thus require cautious interpretation.20 Sequencing and computational advances are finally allowing genomes21,22,23 to be leveraged into population studies,24,25,26,27 with datasets comprising thousands of single-nucleotide polymorphisms (SNPs). Here, combining target gene capture (TGC)28 sequencing (89 individuals, 4,000 SNPs) and whole-genome re-sequencing (17 individuals, 391,000 SNPs) with worldwide sampling across most of the distributional range, we identify three genetically distinct allopatric lineages (North Atlantic, Indo-Pacific, and North Pacific). These diverged 100,000-200,000 years ago during the Penultimate Glaciation, when low sea levels, different ocean currents, and water temperatures produced significant biogeographic barriers. Our results show that without high-resolution genomic analyses of samples representative of a species' range,12 the true extent of diversity, presence of past and contemporary barriers to gene flow, subsequent speciation, and local evolutionary events will remain enigmatic.

Recovering Alpine Secale cereale (Rye) Varieties: Insights from Genetic, Agronomic, and Phytochemical Analyses to Support Sustainable Mountain Agriculture Economy

Rye (Secale cereale L.) cultivation has a long history in the Alpine region, where local ecotypes have been honed through generations of human selection. Despite the introduction of commercial varieties during the 20th century, traditional ecotypes are believed to persist in Valtellina, especially in the medium/upper valley (Teglio and Bormio). Our study aims to identify and preserve these local rye ecotypes by comparing them to commercial varieties. We examined 14 rye accessions through population genetic analyses (by using eight SSR makers), agronomic trials (germplasm characters, plant traits, and yields), and phytochemical analyses (total phenolic compound, flavonoids, and the radical scavenging activity). Two commercial varieties were used—one from Poland, previously genetically characterized (C_POL_P1; i.e., P1 ancestry), and one with an unknown origin. Additionally, we analyzed eleven accessions from Valtellina (medium and upper valley) and one from another alpine valley in South Tirol (Laimburg; LAI). Molecular markers analysis revealed the presence of two distinct genetic lineages: the first (P1) comprised all Teglio accessions and the commercial one from Poland, while the second (P2) grouped the two alpine accessions from Bormio (upper Valtellina) and South Tirol, along with a commercial one of uncertain origin. The clusters P2 exhibited significantly lower average values of the number of alleles (z = 2.03; p &lt; 0.05), Shannon index (z = 2.35; p &lt; 0.05), and expected heterozygosity (z = 1.97; p &lt; 0.05) than in P1. Significant differences were observed in plant traits and agronomic performance between P1 and P2 accessions, with the latter displaying superior traits. For instance, the seed weight of germplasm was the highest in P2 (H(chi2) = 22.44; p &lt; 0.001). Phytochemical analyses did not reveal a clear pattern between genetic lineages but identified some very well-performing Valtellina landraces in terms of scavenging activity. Characterizing these local rye varieties helps establish a short food supply chain to support Valtellina’s mountain economy. The medium valley (P1) and upper valley (P2) varieties have the potential for agroecological valorization, benefiting local farmers. Phytochemical analyses identified better accessions within P1 and P2 for nutraceutical use and commercialization. Additionally, selecting and conserving resilient ecotypes can address future challenges from extreme climate conditions.

Microbiome of psyllids of the family Aphalaridae, including Aphalara itadori, a biocontrol agent against Reynoutria spp.

AbstractSeveral European and North American countries have started releasing the Japanese knotweed psyllid, Aphalara itadori (Shinji) (Hemiptera: Aphalaridae), to control the Japanese knotweed, Reynoutria japonica Houtt. (Polygonaceae), and its relatives, which are among the worst invasive exotic plants. However, establishing populations of the currently released strains in the field has not been successful, desiring newly collected lineages. Moreover, little is known about the microbiome of the current strains, which potentially impacts properties as biocontrol agents. Hence, this study analyzed the microbiota of an A. itadori strain newly collected on Honshu Island, Japan, along with related species of the family Aphalaridae, using amplicon sequencing of 16S rRNA genes. The localization of symbionts identified in A. itadori was further analyzed using fluorescence in situ hybridization. The results demonstrated that the A. itadori bacteriome, a specialized organ for microbial symbiosis, maintains a dual symbiotic system with the primary symbiont “Candidatus Carsonella ruddii” (Gammaproteobacteria: Oceanospirillales: Halomonadaceae) and the secondary symbiont Sodalis sp. (Gammaproteobacteria: Enterobacterales: Pectobacteriaceae), suggesting that they are evolutionarily stable obligate mutualists for A. itadori. The central area of the bacteriome containing Sodalis comprised uninucleate bacteriocytes with nuclei larger than those of bacteriocytes harboring Carsonella. This observation contrasted previous reports on various psyllid lineages in which secondary symbionts are housed in a central syncytium with nuclei smaller than those of bacteriocytes for Carsonella. No known plant pathogens or parasitic manipulators of insect reproduction were identified in the analyzed A. itadori strain, indicating its suitability as a biocontrol agent, posing a minimum risk to the ecosystem. Besides distinct Carsonella lineages, Sodalis independently acquired by Craspedolepta miyatakeai Klimaszewski and an ambiguous Enterobacterales symbiont in Epheloscyta kalopanacis Loginova were identified. Only Carsonella was found in Togepsylla matsumurana Kuwayama. These results indicate repeated infections and replacements of bacterial symbionts during the evolution of Psylloidea, providing deeper insights into the microbe‐psyllid interactions.