Species In Clade Research Articles

Chromosome-scale genome assembly of Codonopsis pilosula and comparative genomic analyses shed light on its genome evolution

IntroductionCodonopsis pilosula is a significant plant in traditional Chinese medicine, valued for its edible and medicinal properties. However, the lack of available genomic resources has hindered further research.MethodsThis study presents the first chromosome-scale genome assembly of C. pilosula using PacBio CLR reads and Hi-C scaffolding technology. Additionally, Ks analysis and syntenic depth analysis were performed to elucidate its evolutionary history.ResultsThe final assembly yielded a high-quality genome of 679.20 Mb, which was anchored to 8 pseudo-chromosomes with an anchoring rate of 96.5% and a scaffold N50 of 80.50 Mb. The genome assembly showed a high completeness of 97.6% based on Benchmarking with Universal Single-Copy Orthologs (BUSCO) analysis. Repetitive elements constituted approximately 76.8% of the genome, with long terminal repeat retrotransposons (LTRs) accounting for about 39.17%. Ks and syntenic depth analyses revealed that the polyploidization history of three platycodonoid clade species involved only the γ-WGT event. Karyotype evolutionary analysis identified an ancestral karyotype with 9 protochromosomes for the three platycodonoid clade species. Moreover, non-WGD genes, particularly those arising from tandem duplications, were found to contribute significantly to gene family expansion.DiscussionThese findings provide essential insights into the genetic diversity and evolutionary biology of C. pilosula, aiding its conservation and sustainable use.

Structural Analysis of Virus Regulatory N6-Methyladenosine (m6A) Machinery of the Black Flying Fox (Pteropus alecto) and the Egyptian Fruit Bat (Rousettus aegyptiacus) Shows Evolutionary Conservation Amongst Mammals

Background: N6-methyladenosine (m6A) is an abundant RNA epitranscriptomic modification in eukaryotes. The m6A machinery includes cellular writer, eraser and reader proteins that regulate m6A. Pteropus alecto (P. alecto) (the Australian black flying fox) and Rousettus aegyptiacus (R. aegyptiacus) (the Egyptian fruit bat) are bats associated with several viral zoonoses yet neglected in the field of m6A epigenetics studies. Objectives: This study utilises various bioinformatics and in silico tools to genetically identify, characterise and annotate the m6A machinery in P. alecto and R. aegyptiacus. Methods: A range of bioinformatic tools were deployed to comprehensively characterise all known m6A-associated proteins of P. alecto and R. aegyptiacus. Results: Phylogenetically, the m6A fat mass and obesity-associated protein (FTO) eraser placed the order Chiroptera (an order including all bat species) in a separate clade. Additionally, it showed the lowest identity matrices in P. alecto and R. aegyptiacus when compared to other mammals (74.1% and 72.8%) and Homo sapiens (84.0% and 76.1%), respectively. When compared to humans, genetic loci-based analysis of P. alecto and R. aegyptiacus showed syntenic conservation in multiple flanking genes of 8 out the 10 m6A-associated genes. Furthermore, amino acid alignment and protein tertiary structure of the two bats’ m6A machinery demonstrated conservation in the writers but not in erasers and readers, compared to humans. Conclusions: These studies provide foundational annotation and genetic characterisation of m6A machinery in two important species of bats which can be exploited to study bat–virus interactions at the interface of epitranscriptomics.

Evidence for the proposal that Palisada corallopsis and P. furcata (Ceramiales, Rhodophyta) are conspecific

Abstract Palisada corallopsis has a widely reported distribution in the western and eastern Atlantic and some areas of the Indo-Pacific Ocean, whereas P. furcata has a more restricted distribution, reported only from Brazil and Cuba. Palisada corallopsis and P. furcata were collected from their type localities, Havana, Cuba and Ceará, Brazil, respectively, and compared by morphological and molecular analyses using rbcL and COI-5P genes. The molecular results placed the sequences from the type locality of both species in the same clade, showing low genetic divergence, 0.95 % for rbcL and 1.6 % for COI-5P. Morphologically, the species share similar habits, with branchlets bi-to trifurcated, cortical cells that may be arranged as a palisade and connected by secondary pit-connections. Our detailed morphological observations, including examination of the type specimens, and molecular analyses demonstrate that P. corallopsis and P. furcata are conspecific, P. furcata being a later taxonomic synonym of P. corallopsis.

Global analysis of neuropeptide receptor conservation across phylum Nematoda.

The phylum Nematoda is incredibly diverse and includes many parasites of humans, livestock, and plants. Peptide-activated G protein-coupled receptors (GPCRs) are central to the regulation of physiology and numerous behaviors, and they represent appealing pharmacological targets for parasite control. Efforts are ongoing to characterize the functions and define the ligands of nematode GPCRs, with already most peptide GPCRs known or predicted in Caenorhabditis elegans. However, comparative analyses of peptide GPCR conservation between C. elegans and other nematode species are limited, and many nematode GPCRs remain orphan. A phylum-wide perspective on peptide GPCR profiles will benefit functional and applied studies of nematode peptide GPCRs. We constructed a pan-phylum resource of C. elegans peptide GPCR orthologs in 125 nematode species using a semi-automated pipeline for analysis of predicted proteome datasets. The peptide GPCR profile varies between nematode species of different phylogenetic clades and multiple C. elegans peptide GPCRs have orthologs across the phylum Nematoda. We identified peptide ligands for two highly conserved orphan receptors, NPR-9 and NPR-16, that belong to the bilaterian galanin/allatostatin A (Gal/AstA) and somatostatin/allatostatin C (SST/AstC) receptor families. The AstA-like NLP-1 peptides activate NPR-9 in cultured cells and are cognate ligands of this receptor in vivo. In addition, we discovered an AstC-type peptide, NLP-99, that activates the AstC-type receptor NPR-16. In our pan-phylum resource, the phylum-wide representation of NPR-9 and NPR-16 resembles that of their cognate ligands more than those of allatostatin-like peptides that do not activate these receptors. The repertoire of C. elegans peptide GPCR orthologs varies across phylogenetic clades and several peptide GPCRs show broad conservation in the phylum Nematoda. Our work functionally characterizes the conserved receptors NPR-9 and NPR-16 as the respective GPCRs for the AstA-like NLP-1 peptides and the AstC-related peptide NLP-99. NLP-1 and NLP-99 are widely conserved in nematodes and their representation matches that of their receptor in most species. These findings demonstrate the conservation of a functional Gal/AstA and SST/AstC signaling system in nematodes. Our dataset of C. elegans peptide GPCR orthologs also lays a foundation for further functional studies of peptide GPCRs in the widely diverse nematode phylum.

Comparative Genomics of Conifer‐Associated Fusarium spp.

ABSTRACTRecent studies have shown numerous Fusarium spp. are associated with symptomatic conifer seedlings in both bareroot and container nursery systems. Some of these species have been found pathogenic to conifer seedlings (e.g., F. avenaceum, F. commune, F. oxysporum, F. solani, and F. verticillioides), but the mechanisms and shared evolutionary history of these conifer pathogenic species have not been well studied in these pathosystems. We compared whole genomes of 17 Fusarium spp. associated with conifer seedlings to elucidate putative shared pathogenicity/virulence gene profiles presumably expressed for roles in causing damping‐off and/or root disease of conifer seedlings. In addition, this work provides draft genomes of conifer‐associated Fusarium spp. and genomes not previously referenced in public databases (e.g., F. lactis, F. fredkrugeri, F. ipomoeae, and F. flocciferum). We identified pathogenicity/virulence genes associated with Fusarium spp. pathogens of conifers including effectors, the secreted in xylem (SIX) genes 2, 4, 9 and 14 and secondary metabolites, and the mycotoxins fumonisin and deoxynivalenol. We conclude that gene profiles are shared within Fusarium species complexes and among closely related Fusarium species complexes; however, these shared profiles are widely distributed across all Fusarium pathogens. These findings highlight potential targets for detecting and/or identifying Fusarium pathogens of conifers, but multiple methods and/or targets will be required depending on the species complexes and clades. More research is needed to determine the roles of expressed pathogenicity/virulence genes and the downstream metabolic products that result in pathogenesis to conifers.

Expanded gene and taxon sampling of diplomonads shows multiple switches to parasitic and free-living lifestyle

BackgroundDiplomonads are anaerobic flagellates classified within Metamonada. They contain both host-associated commensals and parasites that reside in the intestinal tracts of animals, including humans (e.g., Giardia intestinalis), as well as free-living representatives that inhabit freshwater and marine anoxic sediments (e.g., Hexamita inflata). The evolutionary trajectories within this group are particularly unusual as the free-living taxa appear to be nested within a clade of host-associated species, suggesting a reversal from host-dependence to a secondarily free-living lifestyle. This is thought to be an exceedingly rare event as parasites often lose genes for metabolic pathways that are essential to a free-living life strategy, as they become increasingly reliant on their host for nutrients and metabolites. To revert to a free-living lifestyle would require the reconstruction of numerous metabolic pathways. All previous studies of diplomonad evolution suffered from either low taxon sampling, low gene sampling, or both, especially among free-living diplomonads, which has weakened the phylogenetic resolution and hindered evolutionary insights into this fascinating transition.ResultsWe sequenced transcriptomes from 1 host-associated and 13 free-living diplomonad isolates; expanding the genome scale data sampling for diplomonads by roughly threefold. Phylogenomic analyses clearly show that free-living diplomonads form several branches nested within endobiotic species. Moreover, the phylogenetic distribution of genes related to an endobiotic lifestyle suggest their acquisition at the root of diplomonads, while traces of these genes have been identified in free-living diplomonads as well. Based on these results, we propose an evolutionary scenario of ancestral and derived lifestyle transitions across diplomonads.ConclusionsFree-living taxa form several clades nested within endobiotic taxa in our phylogenomic analyses, implying multiple transitions between free-living and endobiotic lifestyles. The evolutionary history of numerous virulence factors corroborates the inference of an endobiotic ancestry of diplomonads, suggesting that there have been several reversals to a free-living lifestyle. Regaining host independence may have been facilitated by a subset of laterally transferred genes. We conclude that the extant diversity of diplomonads has evolved from a non-specialized endobiont, with some taxa becoming highly specialized parasites, others becoming free-living, and some becoming capable of both free-living and endobiotic lifestyles.

Phylogenetic and morphological evidence for four new species of Russula (Russulaceae, Basidiomycota) from northwestern China

Four novel species of subgenus Russula crown clade collected from northwestern China are described based on morphological and phylogenetic evidence. Morphologically, R. griseorosea Y.Song sp. nov. (subsection Puellarinae) is characterized by its brown pileus with a grayish pink tint, basidiospores with warts often connected by fine lines, orthochromatic pileipellis with long terminal cells and septate pileocystidia; R. micangshanensis Y.Song sp. nov. (subsection Olivaceinae) is diagnosed by its large basidia, hymenial cystidia and basidiospores, and spore ornamentations with unequal crests and often twinned warts, which give the spore distinctive appearance; R. minirosea Y.Song sp. nov. (subsection Laricinae) has very small basidiocarp with pileus less than 3.3 cm in diameter, basidiospores with fine reticulum, small basidia, and septate pileocystidia; R. purpureomarginalis F.Li & Y.Song sp. nov. (subsection Xerampelinae) has large basidiospores with often isolated ornamentations, slim basidia and often septate flexuous pileocystidia. Differences between the four novel species and their closely related taxa were analyzed. Phylogenetic analyses based on both ITS and multi-locus (LSU, rpb2 and tef1) were carried out to confirm the distinct taxonomic status of the four novel species.

Pangenomic and biochemical analyses of Helcococcus ovis reveal widespread tetracycline resistance and a novel bacterial species, Helcococcus bovis.

Helcococcus ovis (H. ovis) is an opportunistic bacterial pathogen of a wide range of animal hosts including domestic ruminants, swine, avians, and humans. In this study, we sequenced the genomes of 35 Helcococcus sp. clinical isolates from the uterus of dairy cows and explored their antimicrobial resistance and biochemical phenotypes in vitro. Phylogenetic and average nucleotide identity analyses classified four Helcococcus isolates within a cryptic clade representing an undescribed species, for which we propose the name Helcococcus bovis sp. nov. By establishing this new species clade, we also resolve the longstanding question of the classification of the Tongji strain responsible for a confirmed human conjunctival infection. This strain did not neatly fit into H. ovis and is instead a member of H. bovis. We applied whole genome comparative analyses to explore the pangenome, resistome, virulome, and taxonomic diversity of the remaining 31 H. ovis isolates. An overwhelming 97% of H. ovis strains (30 out of 31) harbor mobile tetracycline resistance genes and displayed significantly increased minimum inhibitory concentrations of tetracyclines in vitro. The high prevalence of mobile tetracycline resistance genes makes H. ovis a significant antimicrobial resistance gene reservoir in our food chain. Finally, the phylogenetic distribution of co-occurring high-virulence determinant genes of H. ovis across unlinked and distant loci highlights an instance of convergent gene loss in the species. In summary, this study showed that mobile genetic element-mediated tetracycline resistance is widespread in H. ovis, and that there is evidence of co-occurring virulence factors across clades suggesting convergent gene loss in the species. Finally, we introduced a novel Helcococcus species closely related to H. ovis, called H. bovis sp. nov., which has been reported to cause infection in humans.

Identification of Capsicum species from Colombia by DNA barcoding and high resolution melting (HRM) analysis

AbstractDNA barcoding allows the use of molecular markers to differentiate the species of an interest group. This is especially useful when morphological characters are insufficient due to high similarity between species. The genus Capsicum contains some species that are difficult to determine by taxonomic means, in particular the annuum complex. Thus, the objective of this study was to investigate the discriminatory ability of two molecular markers in Colombian Capsicum accessions, including three wild species belonging to the Andean clade of the genus. A total of 95 Capsicum accessions, representing eight species, were genotyped by high resolution melting analysis (HRM) using the Waxy and C2_At5g04590 markers. Waxy could discriminate the Andean clade species (C. rhomboideum, C. dimorphum and C. lycianthoides), C. baccatum, C. pubescens and C. chinense, while C2_At5g04590 could discriminate C. frutescens, C. annuum var. annuum and C. annuum var. glabriusculum. Hence, a combination of the two markers could be used for discrimination of the eight species including the wild variety of C. annuum: C. annuum var. glabriusculum. Most nucleotide substitutions and indels were found in the sequences of the three Andean species, indicating that the Andean clade has a high genetic diversity compared to the other species. The incorporation of more wild species and varieties in this study allowed to correct the power of both markers to discriminate Capsicum species, besides the registration of new haplotypes.

Wolbachia strain diversity in a complex group of sympatric cryptic parasitoid wasp species

BackgroundMaternally-inherited symbionts can induce pre-mating and/or post-mating reproductive isolation between sympatric host lineages, and speciation, by modifying host reproductive phenotypes. The large parasitoid wasp genus Cotesia (Braconidae) includes a diversity of cryptic species, each specialized in parasitizing one to few related Lepidoptera host species. Here, we characterized the infection status of an assemblage of 21 Cotesia species from 15 countries by several microbial symbionts, as a first step toward investigating whether symbionts may provide a barrier to gene flow between these parasitoid host lineages.ResultsThe symbiotic microbes Arsenophonus, Cardinium, Microsporidium and Spiroplasma were not detected in the Cotesia wasps. However, the endosymbiotic bacterium Wolbachia was present in at least eight Cotesia species, and hence we concentrated on it upon screening additional DNA extracts and SRAs from NCBI. Some of the closely related Cotesia species carry similar Wolbachia strains, but most Wolbachia strains showed patterns of horizontal transfer between phylogenetically distant host lineages.ConclusionsThe lack of co-phylogenetic signal between Wolbachia and Cotesia suggests that the symbiont and hosts have not coevolved to an extent that would drive species divergence between the Cotesia host lineages. However, as the most common facultative symbiont of Cotesia species, Wolbachia may still function as a key-player in the biology of the parasitoid wasps. Its precise role in the evolution of this complex clade of cryptic species remains to be experimentally investigated.

A New Species of Creptotrematina (Trematoda: Allocreadiidae) from the Red Minor Tetra, Hyphessobrycon eques (Steindachner, 1882) (Characidae) from Brazil, with Comments on the Genetic Divergence of C. Aguirrepequenoi Jiménez-Guzmán, 1973 across a Wide Geographical Range in Middle America.

Allocreadiids are relatively small digeneans that appear to be restricted to freshwater systems distributed across the world. Allocreadiids are highly diverse in the Americas, particularly in the Neotropical biogeographical region. Their taxonomic history has been rather controversial, with several taxonomic reassessments and the description of new genera and species. We sampled Creptotrematina specimens from a characid collected in the Pardo River, Paranapanema River basin in Brazil, and specimens of C. aguirrepequenoi, from Astyanax spp. in several localities between northern Mexico and Costa Rica. The specimens were studied through integrative approaches using morphological and molecular analyses of the 28S rDNA gene and two different regions of the COI mtDNA gene. We describe a new species of Creptotrematina which is differentiated from other congeners by the overall body size, but in particular by the size and position of the cirrus-sac, distribution of the vitelline follicles, and extension of uterine loops in the posterior end of body. Phylogenetic analyses of the 28S rDNA and COI mtDNA genes placed the new species in a monophyletic clade together with all other sequenced species of Creptotrematina, and as a sister species of C. batalhensis. Genetic divergences between the new species and other Creptotrematina spp. varied from 1.1 to 1.2% for the 28S rDNA and 12.4-14.3% for the COI mtDNA. Phylogenetic analysis based on COI mtDNA showed the isolates of C. aguirrepequenoi grouped in four monophyletic clades representing populations geographically separated along a wide geographical range spanning between northern Mexico and Costa Rica, with an estimated genetic divergence between 3.9% and 8.9%. Our findings based on integrative analyses recognize Creptotrematina saltograndensis n. sp. from a characid collected in the Pardo River, Paranapanema River basin in Brazil and provide validation of the wide geographical distribution of C. aguirrepequenoi across Middle-America parasitizing Astyanax spp.; the genetic divergence of the species through the analysis of two regions of COI mtDNA points towards considering it represent a species complex, although we refrain at the moment on describing a new species, awaiting for further verification using other molecular markers, and obtaining fresh material for a more detailed taxonomic analyses. This study increases the known diversity of allocreadiids and contributes to the understanding of evolutionary relationships, host-parasite relationships, and biogeographic history of the group.

An evolutionarily distinct Hmgn2 variant influences shape recognition in Medaka Fish

Protein sequence diversification significantly impacts physiological traits. In this study, using medaka fish (Oryzias latipes), we identify a novel protein variant affecting shape preference behavior. Re-analysis of sequencing data reveals that LOC101156433 encodes a unique Hmgn2 variant with unusual subnuclear localization, clustered separately from the Hmgn2 clades of other species. Medaka mutants with this variant showed reduce telencephalic regions and altered shape preference, suggesting a link between protein sequence variation and behavioral changes. Additionally, this Hmgn2 variant is common in Acanthopterygii fishes, which are adapted to a variety of environments, indicating its potential evolutionary significance. Our findings highlight the relationship between amino acid sequence variation and the development of new molecular and behavioral adaptations, providing insights into the visual shape perception system in fish.

Comprehensive Genomic and Evolutionary Analysis of Biofilm Matrix Clusters and Proteins in the Vibrio Genus.

Vibrio cholerae pathogens cause cholera, an acute diarrheal disease resulting in significant morbidity and mortality worldwide. Biofilm formation by V. cholerae enhances its survival in natural ecosystems and facilitates transmission during cholera outbreaks. Critical components of the biofilm matrix are the Vibrio polysaccharide (VPS) produced by the vps-1 and vps-2 gene clusters, and biofilm matrix proteins encoded in the rbm cluster. However, the biofilm matrix clusters and associated matrix proteins in other Vibrio species remain under investigated, and their evolutionary patterns are largely unknown. In this study, we systematically annotated the biofilm matrix clusters across 6,121 Vibrio genomes, revealing their distribution, diversity, and evolution. We found that biofilm matrix clusters not only exist in V. cholerae but also in phylogenetically distant Vibrio species. Additionally, vps-1 clusters tend to co-locate with rbmABC genes, while vps-2 clusters are often adjacent to rbmDEF genes in various Vibrio species, which helps explain the separation of these clusters by the rbm cluster in well-characterized V. cholerae strains. Evolutionary analysis of RbmC and Bap1 reveals that these two major biofilm matrix proteins are sequentially and structurally related and have undergone domain/modular alterations during their evolution. RbmC genes are more prevalent, while bap1 likely resulted from an ancient duplication event of rbmC and is only present in a major clade of species containing rbmC counterparts. Notably, a novel loop-less Bap1 variant, identified in two subspecies clades of V. cholerae, was found to be associated with altered biofilm formation and the loss of antibiotic efflux pumps and chemotaxis. Another rbm cluster gene, rbmB, involved in biofilm dispersal, was found to share a common ancestor with Vibrio prophage pectin lyase-like tail proteins, indicating its functional and evolutionary linkages to Vibriophage proteins. In summary, our findings establish a foundational understanding of the proteins and gene clusters that contribute to Vibrio biofilm formation from an evolutionary perspective across a broad taxonomic scale. This knowledge paves the way for future strategies aimed at engineering and controlling biofilms through genetic modification.

Hyperaccumulation of nickel but not selenium drives floral microbiome differentiation: A study with six species of Brassicaceae.

Intraspecific variation in flower microbiome composition can mediate pollination and reproduction, and so understanding the community assembly processes driving this variation is critical. Yet the relative importance of trait-based host filtering and dispersal in shaping among-species variation in floral microbiomes remains unknown. Within two clades of Brassicaceae, we compared diversity and composition of floral microbiomes in natural populations of focal nickel and selenium hyperaccumulator species and two of their non-accumulating relatives. We assessed the relative strengths of floral elemental composition, plant phylogenetic distance (host filtering), and geography (dispersal) in driving floral microbiome composition. Species in the nickel hyperaccumulator clade had strongly divergent floral microbiomes, the most of that variation driven by floral elemental composition, followed by geographic distance between plant populations and, lastly, phylogenetic distance. Conversely, within the selenium hyperaccumulator clade, floral microbiome divergence was much lower among the species and elemental composition, geography, and plant phylogeny were far weaker determinants of microbiome variation. Our results show that the strength of elemental hyperaccumulation's effect on floral microbiomes differs substantially among plant clades, possibly due to variation in elements as selective filters or in long-distance dispersal probability in different habitats.

Postcephalic segmentation and spines of the Siluro-Devonian odontopleurine trilobites Leonaspis Richter & Richter and Kettneraspis Prantl & Přibyl, with description of Bruthansovaspis gen. nov. from the Wenlock to Ludlow of the Prague Basin

Species of the odontopleurine trilobites Leonaspis Richter & Richter, 1917 and Kettneraspis Prantl & Přibyl, 1949 from the Silurian and the Devonian have been studied. Dorsal tubercle and spine patterns are highly variable and deemed of restricted use. The pygidial segmentation of Leonaspis is consistent among species in the development of a rudimentary inner pleural ridge or wide space between the pleural ridge and the axis. In Kettneraspis, an inner pleural ridge is never developed but the primitive condition is to have a space here. The formation of this ridge and an auxiliary interior border spine pair was arrested prematurely during ontogeny in species assigned to Kettneraspis at present. The type species of the monotypic Rupbachella Alberti, 2021 is regarded as a juvenile Leonaspis. Bruthansovaspis gen. nov. (type species: Acidaspis roemeri Barrande, 1852) is proposed for a Silurian clade of former Kettneraspis species from peri-Gondwana, that are principally distinct in lacking the combination of stunted anterior and macropleural posterior, thoracic segments synapomorphic of Kettneraspis and Leonaspis. The types of Bruthansovaspis roemeri, Bruthansovaspis dormitzeri (Hawle & Corda, 1847), Bruthansovaspis dumortieri (Hawle & Corda, 1847), Kettneraspis propinqua (Barrande, 1852), Kettneraspis lindackeri (Hawle & Corda, 1847) and Bruthansovaspis zenkeri (Hawle & Corda, 1847) (= B. dormitzeri) from the Silurian of the Barrandian, all of which had previously been lumped as dormitzeri, are figured and their classifications revisited. Exceptionally well-preserved odontopleurine material from the Devonian in the Tafilalt (southern Morocco) is described as Kettneraspis freitagi sp. nov. Leonaspis? strix Lütke, 1965 from the Devonian of the Harz Mountains is in need of revision; a previously tentatively assigned pygidium does not belong in that genus.

Diversity, virulence and antibiotic resistance of Vibrio Harveyi clade species associated with bivalve aquaculture within marine protected areas

The aim of the present study was to investigate the diversity, distribution of virulence factor genes and antimicrobial resistance phenotypes of Vibrio Harveyi clade species from two distinct and spatially distant near-shore bivalve farming environments located in protected marine reserves of the eastern Adriatic. Tissues of farmed Mediterranean mussel Mytilus galloprovincialis and European flat oyster Ostrea edulis, seawater and sediment samples were collected during six bi-monthly sampling events conducted over one year from farming locations in Lim Bay and Mali Ston Bay, Croatia. Eight distinctive Harveyi subclades, namely, V. harveyi, V. alginolyticus, V. diabolicus, V. jasicida, V. parahaemolyticus, V. rotiferianus, V. campbellii and V. communis, were detected by Phylogenetic Multilocus Sequence Analysis (MLSA) based on rpoD, toxR and rctB concatenated genes sequences. Genomic fingerprinting of MLSA-classified samples revealed substantial diversity of environmental isolates. The virulence-related genes considered typical for the Harveyi clade and their homologues were represented in all subclades with varying frequencies. Of twelve antibiotics commonly used in human and veterinary medicine, the most frequent resistance phenotypes were resistance to ampicillin (90%), erythromycin (39%), imipenem (29%) and streptomycin (22%). >60% of isolates were resistant to at least two classes of antibiotics. Seasonal or site-specific differences were found in the proportion of isolates carrying virulence genes and displaying specific antibiotic resistance phenotype.This study is the first to provide a broader perspective on the properties of Vibrio Harveyi clade species associated with ecosystems under presumably low anthropogenic pressures, such as marine protected areas. New data on virulence and antibiotic resistance are presented of Harveyi clade species coexisting in different environmental compartments, including those that have been largely overlooked or understudied in the context of bivalve aquaculture. Taken together, these results highlight the importance of monitoring the presence of potentially pathogenic strains in the natural Vibrio population of bivalve farming areas to reduce the risk to seafood consumers.

Karyotype diversity and genome size in the Cyphomandra clade of Solanum L. (Solanaceae)

Abstract The Cyphomandra clade, a distinct group within the Solanum L. genus, is characterized by remarkable traits, including large chromosomes and big genome sizes. We aimed to investigate whether these features are conserved within the Cyphomandra clade and how they differentiate this group from other Solanum species. We elaborated karyotypes based on CMA/DAPI banding and rDNA fluorescence in situ hybridization (FISH) and estimated the genome size from 12 species, eight belonging to Cyphomandra and four from related clades. All species showed metacentric or submetacentric chromosomes and symmetrical karyotypes, with 2n = 24, except S. mammosum L. (2n = 22). CMA/DAPI banding in combination with rDNA FISH revealed three distinct patterns of heterochromatin distribution (number and position of bands, all CMA+). Most species showed one pair of 35S and 5S rDNA on different chromosomes, except S. mammosum (one of the two pairs was observed in the same chromosome). Notable, the Cyphomandra clade species showed larger chromosomes and genome sizes than other species of Solanum, corroborating that these karyotype attributes are valuable to characterize the clade. The number of CMA/DAPI bands and rDNA sites does not justify the differences in the genome size. Therefore, the accumulation and dispersion of other repetitive sequences, like transposable elements, may be associated with the karyotype changes.

Liquorilactobacillus: A Context of the Evolutionary History and Metabolic Adaptation of a Bacterial Genus from Fermentation Liquid Environments.

In the present work, we carried out a comparative genomic analysis to trace the evolutionary trajectory of the bacterial species that make up the Liquorilactobacillus genus, from the identification of genes and speciation/adaptation mechanisms in their unique characteristics to the identification of the pattern grouping these species. We present phylogenetic relationships between Liquorilactobacillus and related taxa such as Bacillus, basal lactobacilli and Ligilactobacillus, highlighting evolutionary divergences and lifestyle transitions across different taxa. The species of this genus share a core genome of 1023 genes, distributed in all COGs, which made it possible to characterize it as Liquorilactobacillus sensu lato: few amino acid auxotrophy, low genes number for resistance to antibiotics and general and specific cellular reprogramming mechanisms for environmental responses. These species were divided into four clades, with diversity being enhanced mainly by the diversity of genes involved in sugar metabolism. Clade 1 presented lower (< 70%) average amino acid identity with the other clades, with exclusive or absent genes, and greater distance in the genome compared to clades 2, 3 and 4. The data pointed to an ancestor of clades 2, 3 and 4 as being the origin of the genus Ligilactobacillus, while the species of clade 1 being closer to the ancestral Bacillus. All these traits indicated that the species of clade 1 could be soon separated in a distinct genus.

Host specificity in the fungal plant parasite Anthracoidea sempervirentis (Anthracoideaceae, Ustilaginales) reveals three new species and indicates a potential split in the host plant Carex sempervirens.

The smut fungal genus Anthracoidea contains more than 100 species that parasitize hosts predominantly in the sedge genus Carex. Anthracoidea species are mainly found in the boreal zones of the Northern Hemisphere and many species have an arctic-alpine distribution. Recent re-organization of the taxonomy of the main host genus Carex questions current understanding of host associations in Anthracoidea. Host specificity for many of the species in this genus is considered to be quite broad and a host spectrum of over 10 host species is common. One aim of the study is to understand the potential influence that host taxonomy has on the evolutionary patterns of Anthracoidea. Additionally, by including more specimens, we clarify host specificity and species delimitation in Anthracoidea sempervirentis, a prevalent species occurring on different host species in different Carex subgroups using molecular data. Host colonization patterns within Anthracoidea are complex, and different subclades of Carex have been colonized several times independently, whereas clades of related Anthracoidea species often occur on Carex species from the same host clade. Parasites previously thought to be Anthracoidea sempervirentis occurring on the different Carex host are shown to be at least four distinct species that are restricted to individual host species. Three new species, Anthracoidea ferrugineae on Carex ferruginea from the Alps and the Carpathians, A. firmae on Carex firma from the Alps, and A. kitaibelianae on Carex kitaibeliana from mountains in the Balkan Peninsula, are described and illustrated. An emended description of Anthracoidea sempervirentis is also provided. Anthracoidea sempervirentis in its emended circumscription consists of two clades that correspond to respective clades within Carex sempervirens. The study shows that host colonization in Anthracoidea is more complex than current host taxonomy suggests. Further, including several specimens per host species results in a much higher diversity within Anthracoidea than previously assumed. Citation: Kemler M, Denchev TT, Feige A, Denchev CM, Begerow D (2024). Host specificity in the fungal plant parasite Anthracoidea sempervirentis (Anthracoideaceae, Ustilaginales) reveals three new species and indicates a potential split in the host plant Carex sempervirens. Fungal Systematics and Evolution 13: 91-110. doi: 10.3114/fuse.2024.13.04.

Molecular delimitation of cryptic Australian squid species of the genus Uroteuthis Rehder, 1945 (Cephalopoda: Loliginidae), provides a baseline of diversity to resolve classification challenges throughout the Indo-Pacific

ABSTRACT This study provides a comprehensive molecular phylogenetic analysis of Uroteuthis squid from the Indo-Pacific region. The main aim was to increase sample coverage from northern and eastern Australian waters to resolve the identity and distribution of Uroteuthis species taken by local fisheries. Two mitochondrial regions, cytochrome c oxidase subunit I (COI) and 16S ribosomal RNA (16S rRNA), were sequenced from 220 new specimens and analysed with a further 51 sequences from GenBank to create a combined phylogeny for the genus. Three nuclear regions, 18S ribosomal DNA (18S rDNA), 28S ribosomal DNA (28S rDNA) and rhodopsin, were also sequenced from representatives of each species. Based on the mitochondrial phylogeny plus distance and tree-based delimitation models, a COI species barcode gap of 4–5% is proposed for discriminating Uroteuthis species. Applying this gap partitioned many described species into species complexes; for example, U. duvaucelii, U. noctiluca and U. edulis resolved into 10 species. Although more conserved, mitochondrial 16S rRNA sequences differentiated all new species clades, whereas none of the nuclear markers resolved the closest species. Results confirm that neither U. chinensis nor U. edulis occurs in Australian waters. Five undescribed species are identified from northern and eastern Australia, of which four are consistent with earlier allozyme studies (and two align with existing DNA sequences). One is a new southeastern, deeper shelf species differentiated in this study, along with a sixth undescribed species from Indonesian waters. Results of the molecular analysis are now being used to inform complementary morphometric analyses for new species descriptions, and genetic stock structure assessments of these important fisheries resources.