Monophyletic Clade Research Articles

Facivitalis istanbulensis gen. nov., sp. nov., a novel member of the family Sphingomonadaceae with the potential for aromatic-degradation isolated from Jet A1 fuel.

A novel gram-stain-indeterminate, rod-shaped, endospore-forming, motile, aerobic bacterium, designated JETA1-E2T, was isolated from aircraft fuel Jet A1 sample. The strain showed high pairwise similarity values of partial 16S rRNA gene sequences to Sphingomonas paucimobilis (MT367853) (99.42%), Sphingomonas sanguinis (MF319771) (99.34%), and Sphingomonas pseudosanguinis (HE716953) (99.27%) within the family Sphingomonadaceae. However, API test results revealed that the strain JETA1-E2T differed from these type strains. The phylogenetic tree based on the whole genome and the phylogenomic tree generated with the UBCG tool showed that the strain JETA1-E2T formed a distinct monophyletic clade within the family Sphingomonadaceae, and clustered distantly with the genera Sphingomonas and Sphingobium. The predominant respiratory quinone is Q-10. The major fatty acids are C16:0 and summed feature 8 (C18:1ω7c and/or C18:1ω6c). C19:0 is present in small amounts. The polar lipids are diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine, aminophospholipid, unidentified glycolipid, and two unidentified sphingoglycolipids. The only polyamine is putrescine in minor amounts. The DNA G + C content of the type strain is 66.5mol%. Several unique genes in the strain JETA1-E2T may contribute to fight against various stressors, virulence and pathogenicity, as well as survival in challenging conditions. The strain JETA1-E2T contains 100 of the characterised proteins available in the HADEG database of which 58% of these are involved in metabolic process of aromatics degradation. The findings indicate that the strain JETA1-E2T has the potential to metabolise hydrocarbons such as fuel, especially aromatic compounds. Based on the results of polyphasic taxonomic analyses, the strain JETA1-E2T represents a novel species in a new genus in the family Sphingomonadaceae for which the name Facivitalis istanbulensis gen. nov., sp. nov. is proposed. The type strain of Facivitalis istanbulensis is JETA1-E2T (DSM 117971T = LMG 33634T = KUEN 1206 (B) F3-1-1T).

Chloroplast genome of four Amorphophallus species: genomic features,comparative analysis, and phylogenetic relationships among Amorphophallus species

BackgroundThe genus Amorphophallus (Araceae) contains approximately 250 species, most of which have high ecological and economic significance. The chloroplast genome data and the comprehensive analysis of the chloroplast genome structure of Amorphophallus is limited. In this study, four chloroplast genomes of Amorphophallus were sequenced and assembled. For the first time, comparative analyses of chloroplast genomes were conducted on the 13 Amorphophallus species in conjunction with nine published sequences.ResultsThe Amorphophallus chloroplast genomes exhibited typical quadripartite structures with lengths ranging from 164,417 to 177,076 bp. These structures consisted of a large single copy (LSC, 90,705 − 98,561 bp), a small single copy (SSC, 14,172 − 21,575 bp), and a pair of inverted repeats (IRs, 26,225 − 35,204 bp). The genomes contain 108 − 113 unique genes, including 76 − 79 protein-coding genes, 28 − 29 tRNA genes, and 4 rRNA genes. The molecular structure, gene order, content, codon usage, long repeats, and simple sequence repeats (SSRs) within Amorphophallus were generally conserved. However, several variations in intron loss and gene expansion on the IR-SSC boundary regions were found among these 13 genomes. Four mutational hotspot regions, including trnM-atpE, atpB, atpB-rbcL and ycf1 were identified. They could identify and phylogeny future species in the genus Amorphophallus. Positive selection was found for rpl36, ccsA, rpl16, rps4, rps8, rps11, rps12, rps14, clpP, rps3, ycf1, rpl20, rps2, rps18, rps19, atpA, atpF, rpl14, rpoA, rpoC1, rpoC2 and rps15 based on the analyses of Ka/Ks ratios. Phylogenetic inferences based on the complete chloroplast genomes revealed a sister relationship between Amorphophallus and Caladieae. All Amorphophallus species formed a monophyletic evolutionary clade and were divided into three groups, including CA-II, SEA, and CA-I. Amorphophallus albus, A. krausei, A. kachinensis and A. konjac were clustered into the CA-II clade, A. paeoniifolius and A. titanum were clustered into the SEA clade, A. muelleri ‘zhuyajin1’, Amorphophallus sp, A. coaetaneus, A. tonkinensis and A. yunnanensis were clustered into CA- I clade.ConclusionsThe genome structure and gene content of Amorphophallus chloroplast genomes are consistent across various species. In this study, the structural variation and comparative genome of chloroplast genomes of Amorphophallus were comprehensively analyzed for the first time. The results provide important genetic information for species classification, identification, molecular breeding, and evolutionary exploration of the genus Amorphophallus.

First report of Hexametra angusticaecoides Chabaud & Brygoo, 1960 (Nematoda: Ascarididae) in a population of captive central bearded dragons, Pogona vitticeps Ahl (Squamata: Agamidae).

Between 2022 and 2023 ascaridoid nematodes of the genus Hexametra were recovered from two captive central bearded dragons (Pogona vitticeps Ahl) in the Extremadura region of Spain. These nematodes were identified by an integrative approach combining morpho-anatomical and molecular data. We used two rRNA regions (D2-D3 expansion segments of the 28S, and ITS fragments), and the partial region of the cytochrome oxidase I gene (COI mtDNA) sequences. Hexametra angusticaecoides Chabaud & Brygoo, 1960 (Ascarididae) was morphologically characterized and illustrated using light and scanning electron microscopy. Bayesian inference (BI) and Maximum Likelihood (ML) phylogenetic trees for these genetic markers established relationships that highlight the importance of using molecular and phylogenetic data for accurate species identification within the genus Hexametra. Phylogenetic trees indicated that the Spanish isolates of H. angusticaecoides were clustered in a well-supported clade together with other isolates from Central Europe of the same species. Molecular phylogenetic findings also reflect that there was a higher intraspecific variation for ITS genetic markers at the intraspecific level. Phylogenetic results based on 28S rRNA suggest that Ascarididea was divided into three monophyletic major clades. To our knowledge, this is the first report of this species parasitizing bearded dragons, extending the host range of this species. These findings represent the first formal record of H. angusticaecoides in Spain.

Genetic Diversity and Demographic History of Wax Moths, Galleria mellonella Linnaeus, 1758 and Achroia grisella Fabricius, 1794 (Lepidoptera: Pyralidae)

Wax moths, Galleria mellonella Linnaeus, 1758 and Achroia grisella Fabricius, 1794 are the key pests of honeybee colonies worldwide. They cause wax comb damages which lead to colony perishing and absconding. To control these pests, their genetic background and evolution should be considered. In this study, genetic diversity and demographic history of 2 species of wax moth were explored based on mitochondrial genes (COI). Wax moths were collected from northeatern part of Thailand for morphological and DNA analyses. G. mellonella and A. grisella sequences from GenBank were included for genetic diversity and demographic history analyses (total of 80 and 26 sequences, respectively). Overall genetic diversity for A. grisella samples from Northeastern Thailand was relatively low (h = 0.467 ± 0.132 and π = 0.00150 ± 0.00042). Likewise, low genetic diversity was also observed in G. mellonella samples (h = 0.280 ± 0.101 and π = 0.00046 ± 0.00017). Among samples from different global regions, the haplotype and nucleotide diversity of A. grisella were 0.834 ± 0.050 and 0.00996 ± 0.00124, respectively. The haplotype and nucleotide diversity of G. mellonella were 0.709 ± 0.034 and 0.01084 ± 0.00279, respectively. The ML tree revealed that these 2 species were separated into 2 major clades (G. mellonella clade and A. grisella clade). All sequences corresponding to G. mellonella formed to a single monophyletic clade, while all the sequences corresponding to A. grisella formed another single monophyletic clade. Clade G. mellonella was divided into 4 subclades designated as Clade Gm1, Gm2, Gm3 and Gm4, whereas A. grisella clade was divided into 3 subclades designated as Clade Ag1, Ag2 and Ag3. The sum of squares deviation (SSD) and Harpending’s raggedness index (rg) and the results of Tajima’s D and Fu’s Fs tests indicated population expansion was not found in either species. HIGHLIGHTS This study highlighted the genetic diversity of wax moths Galleria mellonella Linnaeus, 1758 and Achroia grisella Fabricius, 1794 in Thailand and other parts of the world. Population expansion was not observed in either species. The results will be useful to predict directions of population distribution of wax moths under certain factors. GRAPHICAL ABSTRACT

Parasalinivibrio latis gen. nov., sp. nov., isolated from the distal gut of healthy farmed Asian Seabass (Lates calcarifer).

Asian Seabass (Lates calcarifer) is widely farmed as a sustainable source of protein for countries in the tropical Indo-West Pacific region. However, microbial species of the gut microbiome of healthy Asian Seabass remain largely uncharacterized and uncultured. Here, we analysed the microbial composition along the gastrointestinal tract of a farmed healthy Asian Seabass. We used different cultivation approaches to obtain isolates from the seabass intestinal tract and describe the isolation and characterization of a novel strain, TLL-SE01T. Analysis of the strain's 16S rRNA gene indicates that the strain belongs to the family Vibrionaceae with Photobacterium damselae as its closest relative, albeit sharing only 94.8% (aligned region 1553bp) nucleotide identity. Comparative genomic analysis with all validly published Vibrionaceae species with available genomes revealed average nucleotide identity (ANI) and DNA-DNA hybridisation (DDH) values of around 70% and 24% respectively to strain TLL-SE01T, which are well below proposed thresholds for species delineation (ANI, 95-96%; DDH, 70%). The alignment fraction and ANI genus demarcation boundaries for all genera in the Vibrionaceae family were determined for which strain TLL-SE01T is well below the calculated values, indicating that it belongs to a novel genus. Single- and core-gene phylogenetic analysis places strain TLL-SE01T in a monophyletic clade, further supporting its designation to a novel genus. Phenotypic comparison between strain TLL-SE01T and its close relatives indicated additional differences, such as growth response at different salt concentrations and different metabolic capabilities. Based on genotypic, phylogenetic and phenotypic differences to other Vibrionaceae species, we propose a novel species in a new genus, Parasalinivibrio latis gen. nov. sp. nov. and strain TLL-SE01T (= BCRC 81435T = JCM 36283T) as the type strain.

Genetic potential for aerobic respiration and denitrification in globally distributed respiratory endosymbionts

The endosymbiont Candidatus Azoamicus ciliaticola was proposed to generate ATP for its eukaryotic host, an anaerobic ciliate of the Plagiopylea class, fulfilling a function analogous to mitochondria in other eukaryotic cells. The discovery of this respiratory endosymbiosis has major implications for both evolutionary history and ecology of microbial eukaryotes. However, with only a single species described, knowledge of its environmental distribution and diversity is limited. Here we report four complete, circular metagenome assembled genomes (cMAGs) representing respiratory endosymbionts inhabiting groundwater in California, Ohio, and Germany. These cMAGs form two lineages comprising a monophyletic clade within the uncharacterized gammaproteobacterial order UBA6186, enabling evolutionary analysis of their key protein complexes. Strikingly, all four cMAGs encode a cytochrome cbb3 oxidase, which indicates that these endosymbionts have the capacity for aerobic respiration. Accordingly, we detect these respiratory endosymbionts in diverse habitats worldwide, thus further expanding the ecological scope of this respiratory symbiosis.

Phylogenomic insights and geographic distribution of the New World genus Amphibolips Reinhard (Hymenoptera: Cynipidae, Cynipini) using ultraconserved elements

AbstractIn recent years, new wasp species and genera of Cynipidae have been described, and their species delimitation and evolutionary relationships have been supported using molecular markers. However, few studies have included comprehensive and extensive sampling of specimens across the complete distribution of a single genus. In this study, we analysed the phylogenetic relationships of the genus Amphibolips throughout its range using ultraconserved elements (UCEs). We collected 520 adult wasps from 401 sites in various geographic locations, predominantly in Mexico, and used 78 wasps for UCE analysis. Our results demonstrate that Amphibolips forms a monophyletic clade. Amphibolips can be further subdivided into four genetically well‐differentiated clades. Each clade had morphological traits that could be collectively characterised. Species delimitation using molecular sequencing highlights the taxonomic complexity involved in separating and assigning species using exclusively morphological criteria. This approach offers an opportunity to refine current morphological taxonomic criteria or propose new criteria to establish more accurate classifications. The rich diversity of host species and geographic regions in Mexico represents a biodiversity hotspot for Amphibolips. The number of undescribed species remains high. This study facilitates the determination of appropriate boundaries for putative new Amphibolips species.

Microsatellite Markers & Mitochondrial D-Loop Based Phylogenetic And Diversity Analysis In Gabrali Cattle.

The Gabrali cattle is a multipurpose breed, native to Khyber Pakhtunkhwa, Pakistan. Despite its economic importance, scientific data about its phylogeny and genetic diversity is scarce. To address this issue, the present study was conducted on thirty (30) unrelated Gabrali male and female animals, from which blood samples were collected and DNA was extracted. Twelve (12) microsatellite loci and 1159bp of D-loop region were amplified via PCR and visualized on a 2% agarose gel. Sanger sequencing technique was used to sequence the D-loop amplicons. The microsatellite loci revealed 83 alleles with MNA (mean no of alleles per locus) = 8.8, the Ho (observed heterozygosity) and He (expected heterozygosity) of all loci were 0.58 and 0.50 respectively, mean PIC (Polymorphic Information content) = 0.59 and FIS (Inbreeding coefficient) = 0.056 using GeneAlEx® software. Microsatellite analysis revealed a normal allelic distribution across the breed, consistent with Hardy-Weinberg equilibrium. D-loop sequencing revealed eight haplotypes with 30 SNPs using DNA SP 6.0 software. High AT content was observed than GC content i.e. 55.9% and 44.1% respectively, while the transition to transversion ratio was R = 10:1. The value of Haplotype and Nucleotides diversity was Hd = 0.8601 ± SD = 0.0895 and Π = 0.0136 ± SD = 0.00197 respectively. Phylogenetic analysis done using Neighbor-joining method with bootstraps value of 1000, revealed the monophyletic clade of both Gabrali and Bos indicus haplotypes. Furthermore, the introgression of genes from national cattle breeds into Gabrali cattle was observed. It is concluded that Gabrali cattle have common ancestry with Bos indicus having no threats of genetic bottleneck having substantial genetic diversity.

Dickeya ananae sp. nov., pectinolytic bacterium isolated from pineapple (Ananas comosus).

Recently, species clustering within Dickeya zeae has been identified as complex, encompassing validly published names, including D. oryzae and D. parazeae, with some strains potentially delineating new species. In this study, genomes of strains isolated from a bacterial heart rot outbreak in pineapple (Ananas comosus var. comosus) on Oahu, Hawaii, along with two strains from pineapple in Malaysia, were sequenced. Orthologous average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values among the sequenced genomes ranged from 98.93-99.9% and 91.8-99.9%, respectively, supporting the classification of seven strains within the same species. Comparisons of ANI and dDDH values between these seven strains and type strains of D. zeae, D. parazeae, and D. oryzae ranged from 94.4-95.9% and 57.2-66.5%, respectively. These values fall below the proposed boundaries for new species designation, supporting the delineation of a novel species. Phylogenetic analyses, including 16S rRNA, gapA, multi-locus sequence analysis (MLSA) of 10 housekeeping genes, whole-genome, and pangenome analyses, were concordant and revealed a distinct monophyletic clade, separating these strains from other members of the D. zeae complex, with D. oryzae as the closest relative. Notably, a nitrogen fixation gene cluster comprising 28 genes, similar to the Klebsiella spp. nitrogenase gene cluster, was found in the genome of the seven pineapple strains. Based on polyphasic approaches, including ANI, dDDH, biochemical, physiological, and phylogenomic analyses, we propose the reclassification in a new species of the five pineapple strains from Hawaii A5391, A5410T, A5611, A6136, and A6137, together with the two pineapple strains from Malaysia CFBP 1272 and CFBP 1278, previously classified as D. zeae. We propose the name Dickeya ananae sp. nov. for this taxon, represented by the type strain A5410T (= ICMP 25020T = LMG 33197T).

Expanding the Triangle of U: Comparative analysis of the Hirschfeldia incana genome provides insights into chromosomal evolution, phylogenomics and high photosynthesis-related traits.

The Brassiceae tribe encompasses many economically important crops and exhibits high intraspecific and interspecific phenotypic variation. After a shared whole-genome triplication (WGT) event (Br-α, ~15.9 million years ago), differential lineage diversification and genomic changes contributed to an array of divergence in morphology, biochemistry, and physiology underlying photosynthesis-related traits. Here, the C3 species Hirschfeldia incana is studied as it displays high photosynthetic rates under high-light conditions. Our aim was to elucidate the evolution that gave rise to the genome of H. incana and its high-photosynthesis traits. We reconstructed a chromosome-level genome assembly for H. incana (Nijmegen, v2.0) using nanopore and chromosome conformation capture (Hi-C) technologies, with 409Mb in size and an N50 of 52Mb (a 10× improvement over the previously published scaffold-level v1.0 assembly). The updated assembly and annotation was subsequently employed to investigate the WGT history of H. incana in a comparative phylogenomic framework from the Brassiceae ancestral genomic blocks and related diploidized crops. Hirschfeldia incana (x=7) shares extensive genome collinearity with Raphanus sativus (x=9). These two species share some commonalities with Brassica rapa and B. oleracea (A genome, x=10 and C genome, x=9, respectively) and other similarities with B. nigra (B genome, x=8). Phylogenetic analysis revealed that H. incana and R. sativus form a monophyletic clade in between the Brassica A/C and B genomes. We postulate that H. incana and R. sativus genomes are results of hybridization or introgression of the Brassica A/C and B genome types. Our results might explain the discrepancy observed in published studies regarding phylogenetic placement of H. incana and R. sativus in relation to the "Triangle of U" species. Expression analysis of WGT retained gene copies revealed sub-genome expression divergence, likely due to neo- or sub-functionalization. Finally, we highlighted genes associated with physio-biochemical-anatomical adaptive changes observed in H. incana which likely facilitate its high-photosynthesis traits under high light. The improved H. incana genome assembly, annotation and results presented in this work will be a valuable resource for future research to unravel the genetic basis of its ability to maintain a high photosynthetic efficiency in high-light conditions and thereby improve photosynthesis for enhanced agricultural production.

Beyond natural language: an ontology-based description of a new Scarabaeus dung beetle from Madagascar (Coleoptera, Scarabaeinae).

The dung beetle genus Scarabaeus (Coleoptera, Scarabaeinae, Scarabaeini), predominantly found in the arid regions of the Old World, includes three endemic species inhabiting the dry ecosystems of western and southern Madagascar. These species are presumed to form a monophyletic clade nested within the African Scarabaeus.Semantic modelling of phenotypes using ontologies represents a transformative approach to species description in biology, making phenotypic data FAIR and computable. The recently developed Phenoscript language enables the creation of semantic, computable species descriptions using a syntax akin to human natural language (NL). However, Phenoscript has not yet been tested as a tool for describing new taxa. In this study, we test the utility of Phenoscript by describing a new species, Scarabaeus (sensu lato) sakalava sp. nov. from Madagascar. The initial description is composed directly in Phenoscript, replacing the traditional natural language format. This Phenoscript description is then translated into a human-readable form using the Phenospy tool for publication purposes. Additionally, the Phenoscript description is converted into an RDF graph, making it understandable by computers using semantic technologies.Scarabaeussakalava sp. nov. is found in western central Madagascar and is closely related to S.viettei (Paulian, 1953) from north-western Madagascar. We provide an updated identification key and distribution map for all Malagasy Scarabaeus and discuss their systematic placement.

Sorlinia euscelidii gen. nov., sp. nov., a novel acetic acid bacterium isolated from the leafhopper Euscelidius variegatus (Hemiptera: Cicadellidae).

Acetic acid bacteria - belonging to the Acetobacteraceae family - are found in the gut of many sugar-feeding insects. In this study, six strains have been isolated from the hemipteran leafhopper Euscelidius variegatus. While they exhibit high 16S rRNA gene sequence similarities to uncultured members of the Acetobacteraceae family, they could not be unequivocally assigned to any particular type species. Considering the clonality of the six isolates, the EV16PT strain was used as a representative of this group of isolates. The genome sequence of EV16PT is composed of a 2.388 Mbp chromosome, with a DNA G+C content of 57 mol%. Phylogenetic analyses based on the 16S rRNA gene sequence and whole-genome multilocus sequence analysis indicate that EV16PT forms a monophyletic clade with the uncultivated endosymbiont of Diaphorina citri, the Candidatus Kirkpatrickella diaphorinae. Such a phylogenetic clade is positioned between those of Asaia-Swaminathania and Kozakia. The genomic distance metrics based on gene and protein sequences support the proposal that EV16PT is a new species belonging to a yet-undescribed genus. It is a rod-shaped Gram-stain-negative bacterium, strictly aerobic, non-motile, non-spore-forming, showing optimal growth without salt (NaCl) at 30 °C and pH of 6-7. The major quinone is Q10, and the dominant cellular fatty acids (>10%) are C18:l ω7c, C19 : 0 cyclo ω6c, C16 : 0 and C19 : 1 2OH. The polar lipid profile comprises diphosphatidylglycerol, phosphatidylethanolamine and phosphatidylcholine, along with unidentified aminophospholipids, glycophospholipids, aminolipids and lipids. Based on a polyphasic approach, including phylogenetic, phylogenomic, genome relatedness, phenotypic and chemotaxonomic characterisations, EV16PT (= KCTC 8296T, = DSM 117028T) is proposed as a representative of a novel species in a novel genus with the proposed name Sorlinia euscelidii gen. nov., sp. nov., in honour of Prof. Claudia Sorlini, an Italian environmental microbiologist at the University of Milan who inspired the research on microbial diversity, including symbiosis in plants and animals.

Novel isolates expand the physiological diversity of Prochlorococcus and illuminate its macroevolution.

Prochlorococcus is a diverse picocyanobacterial genus and the most abundant phototroph on Earth. Its photosynthetic diversity divides it into high-light (HL)- or low-light (LL)-adapted groups representing broad phylogenetic grades-each composed of several monophyletic clades. Here, we physiologically characterize four new Prochlorococcus strains isolated from below the deep chlorophyll maximum in the North Pacific Ocean. We combine these physiological properties with genomic analyses to explore the evolution of photosynthetic antennae and discuss potential macroevolutionary implications. The isolates belong to deeply branching low-light-adapted clades that have no other cultivated representatives and display some unusual characteristics. For example, despite its otherwise low-light-adapted physiological characteristics, strain MIT1223 has low chl b2 content similar to high-light-adapted strains. Isolate genomes revealed that each strain contains a unique arsenal of pigment biosynthesis and binding alleles that have been horizontally acquired, contributing to the observed physiological diversity. Comparative genomic analysis of all picocyanobacteria reveals that Pcb, the major pigment carrying protein in Prochlorococcus, greatly increased in copy number and diversity per genome along a branch that coincides with the loss of facultative particle attachment. Collectively, these observations support a recently developed macroevolutionary model, in which niche-constructing radiations allowed ancestral lineages of picocyanobacteria to transition from a particle-attached to planktonic lifestyle and broadly colonize the euphotic zone.IMPORTANCEThe marine cyanobacterium, Prochlorococcus, is among the Earth's most abundant organisms, and much of its genetic and physiological diversity remains uncharacterized. Although field studies help reveal the scope of diversity, cultured isolates allow us to link genomic potential to physiological processes, illuminate eco-evolutionary feedbacks, and test theories arising from comparative genomics of wild cells. Here, we report the isolation and characterization of novel low-light (LL)-adapted Prochlorococcus strains that fill in multiple evolutionary gaps. These new strains are the first cultivated representatives of the LLVII and LLVIII paraphyletic grades of Prochlorococcus, which are broadly distributed in the lower regions of the ocean euphotic zone. Each of these grades is a unique, highly diverse section of the Prochlorococcus tree that separates distinct ecological groups: the LLVII grade branches between monophyletic clades that have facultatively particle-associated and constitutively planktonic lifestyles, whereas the LLVIII grade lies along the branch that leads to all high-light (HL)-adapted clades. Characterizing strains and genomes from these grades yields insights into the large-scale evolution of Prochlorococcus. The new LLVII and LLVIII strains are adapted to growth at very low irradiance levels and possess unique light-harvesting gene signatures and pigmentation. The LLVII strains represent the most basal Prochlorococcus group with a major expansion in photosynthetic antenna genes. Furthermore, a strain from the LLVIII grade challenges the paradigm that all LL-adapted Prochlorococcus exhibit high ratios of chl b:a2. These findings provide insights into the photophysiological evolution of Prochlorococcus and redefine what it means to be a low- vs high-light-adapted Prochlorococcus cell.

An internal loop region is responsible for inherent target specificity of bacterial Cold-shock proteins.

Cold shock proteins (Csps), of around 70 amino acids, share a protein fold for the cold shock domain (CSD) that contains RNA binding motifs, RNP1 and RNP2, and constitute one family of bacterial RNA-binding proteins. Despite similar amino acid composition, Csps have been shown to individually possess inherent specific functions. Here we identify the molecular differences in Csps that allow selective recognition of RNA targets. Using chimeras and mutants of Escherichia coli CspD and CspA, we demonstrate that Lys43-Ala44 in an internal loop of CspD and the N-terminal portion with Lys4 of CspA are important for determining their target specificities. Pull-down assays suggest these distinct specificities reflect differences in the ability to act on the target RNAs rather than differences in binding to the RNA targets. A phylogenetic tree constructed from 1,573 Csps reveals that the Csps containing Lys-Ala in the loop form a monophyletic clade, and the members in this clade are shown to have target specificities similar to E. coli CspD. The phylogenetic tree also finds a small cluster of Csps containing Lys-Glu in the loop, and these exhibit different specificity than E. coli CspD. Examination of this difference suggests a role of the loop of CspD type proteins in recognition of specific targets. Additionally, each identified type of Csp shows a different distribution pattern among bacteria. Our findings provide a basis for subclassification of Csps based on target RNA specificity, which will be useful for understanding of the functional specialization of Csps.

Investigating the evolution of green algae with a large transcriptomic data set.

The colonization of land by plants approximately 450-500 million years ago (Mya) is one of the most important events in the history of life on Earth. Land plants, hereafter referred to as "embryophytes," comprise the foundation of every terrestrial biome, making them an essential lineage for the origin and maintenance of biodiversity. The embryophytes form a monophyletic clade within one of the two major phyla of the green algae (Viridiplantae), the Streptophyta. Estimates from fossil data and molecular clock analyses suggest the Streptophyte algae (Charophytes) diverged from the other main phylum of green algae, the Chlorophyta, as much as 1500 Mya. Here we present a phylogenetic analysis using transcriptomic and genomic data of 62 green algae and embryophyte operational taxonomic units, 31 of which were assembled de novo for this project. We have focused on identifying the charophyte lineage that is sister to embryophytes, and show that the Zygnematophyceae have the strongest support, followed by the Charophyceae. Furthermore, we have examined amino acid and codon usage across the tree and determined these data broadly follow the phylogenetic tree. We concluded by searching the data set for protein domains and gene families known to be important in embryophytes. Many of these domains and genes have homologous sequences in the charophyte lineages, giving insight into the processes that underlay the colonization of the land by plants. This provides new insights into green algal diversification, identifies previously unknown attributes of genome evolution within the group, and shows how functional mechanisms have evolved over time.

Integrative morphological, cytogenetic and molecular characterization of the Andean climbing catfish Astroblepus mindoensis (Regan, 1916) (Siluriformes:Astroblepidae).

Astroblepus species, commonly known as Andean climbing catfish, exhibit a unique challenge in species delimitation, leading to ongoing taxonomic debates. Here we report data on Astroblepus mindoensis, a vulnerable species endemic to Ecuador, obtained by an integrative approach that includes cytogenetic analysis, molecular identification of the specimens, and recording of morphological and morphometric characters useful for species diagnosis. Thus, this study aimed to associate the karyotype data of the specimens analyzed with morphological and molecular characters, improving and expanding the existing taxonomic information, thus contributing to the systematics of the species. Our morphology results, unlike Regan's original description, which is brief and ambiguous, provide a more detailed morphometric and meristic description. Molecular phylogenetic reconstruction and genetic distance based on a fragment of the cytochrome c oxidase subunit I (COI) showed that our samples constitute a well-supported and monophyletic clade within the A. grixalvii species complex. The cytogenetic analysis identified distinct chromosomal markers, including a single cluster of major ribosomal genes (on chromosome pair 3) and of minor ribosomal genes (on chromosome pair 12) with their localization differing from those reported in other Astroblepus species analyzed. Additionally, the presence of a heteromorphic chromosome pair in males suggests the presence of an XX/XY sex-determination system that has not been identified in other congeneric species. Further investigation is necessary to determine if these chromosomes are associated with the accumulation of repeated sequences, as typically occurs with sex chromosomes, and to assess their presence in other species of the genus.

Full Genome Characterization of the First Oropouche Virus Isolate Imported in Europe from Cuba.

On 27 May 2024, the Cuban Ministry of Health reported the first outbreak of Oropouche fever on the island. The etiologic agent, Oropouche virus (OROV), is a poorly understood arbovirus that has been known since the 1960s and represents a public health burden in Latin America. We report the whole-genome characterization of the first European OROV isolate from a returning traveler from Cuba with Oropouche fever-like symptoms. The isolate was obtained from the patient's serum; whole-genome sequencing was performed by next-generation sequencing, followed by phylogenetic analysis and genetic variability studies. The analysis showed that the most closely related sequence was from the French Guiana 2020 outbreak. Interestingly, our isolate is a reassortant virus, included in a highly supported monophyletic clade containing recent OROV cases (Brazil 2015-Colombia 2021), separated from the other four previously known genotypes. More deeply, it was found to be included in a distinct branch containing the sequences of the Brazil 2022-2024 outbreak. The reassortment event involved the S and L segments, which have high similarity with sequences belonging to a new cluster (here defined as OROV_SCDC_2024), while the M segment shows high similarity with older sequences. These results likely describe the viral strain responsible for the current outbreak in Cuba, which may also reflect the ongoing outbreak in Latin America. Further studies are needed to understand how OROV evolves towards traits that facilitate its spread and adaptation outside its original basin, and to track its spread and evolution in the European continent.

Leaf Rust Pathogens on Hypericum pseudohenryi: Describing Melampsora danbaensis sp. nov. and M. hyperici-pseudohenryi sp. nov. from China.

Based on morphological and phylogenetic evidence, two novel species of Melampsora were discovered on Hypericum pseudohenryi in China and have been thoroughly characterized. One of these species, designated as M. danbaensis, exhibits distinct features such as aecia of Uredo-type, typically appearing in gregarious or grouped arrangements, and presenting a shallowly pulvinate structure. Aeciospores exhibit tremendous variations in size, ranging in shape from globose to ellipsoidal and bearing pronounced verrucose texture. Telia resemble crusts one-spore deep, covering nearly the entire abaxial leaf surface, with sessile teliospores reaching sizes of up to 65.8 µm, and exhibiting a clavate to cylindrical shape. Another species, designated as M. hyperici-pseudohenryi, is distinguished by Uredo-type uredinia, which are hypophyllous, scattered or grouped, and interspersed with numerous paraphyses. Its urediniospores tend to be globose, ellipsoidal or obovoid, echinulate, and are accompanied by clavate to capitate paraphyses reaching lengths up to 77.6 µm. Phylogenetically, both species form a novel monophyletic clade within the Melampsora genus, with robust support demonstrated by a high Maximum likelihood bootstrap support (MLBS) value of 100% and a Bayesian posterior probability (BPP) of 1. This study enriches our understanding of the diversity and geographical distribution of Melampsora species that infect Hypericum plants in China.

Phylogeographic structure of Italian Formica pratensis (Retzius 1783) populations in the framework of the species Eurasian range

AbstractThe phylogeography and demographical history of Italian Formica pratensis populations were examined and compared with the Eurasian-wide dataset available for this species and the other red wood ant species Formica lugubris. Forty-eight workers belonging to eight populations from both Alps and Apennines were analysed sequencing a 1.5-kilobase mitochondrial DNA fragment, including the cytochrome b gene and part of the NADH dehydrogenase subunit 6 gene. A total of 127 sequences were screened, scoring 53 different haplotypes amongst all specimens, with five new haplotypes discovered in the Italian populations. All the Italian haplotypes clustered in a monophyletic clade, underlining a clear phylogeographical separation of this group from the other Eurasian groups and suggesting a glacial separate forest refugia and different post-glacial colonisation patterns. The haplotypes from the Alps and the Apennines showed a high genetic proximity, pointing out an ancient (Pleistocene) wide distribution of this species across all these areas and common ancestral lineages. No shared haplotypes were scored between Northern and Central Apennine populations, but the low inter-population genetic distance indicated similar post-glacial selective processes acting on these groups. The diversity we recorded may be influenced by the actual fragmentation of F. pratensis populations across its entire Eurasian range, and by the limited geographical origin and sample dimension of the dataset analysed. Future studies with a more extensive sampling in the Alps and Eastern Europe are needed to confirm our result.

Discovery of the first sea turtle adenovirus and turtle associated circoviruses

Turtles are an evolutionarily unique and morphologically distinctive order of reptiles, and many species are globally endangered. Although a high diversity of adenoviruses in scaled reptiles is well-documented, turtle adenoviruses remain largely understudied. To investigate their molecular diversity, we focused on the identification and characterisation of adenoviruses in turtle-derived organ, swab and egg samples. Since reptile circoviruses have been scarcely reported and no turtle circoviruses have been documented to date, we also screened our samples for circoviruses. Host−virus coevolution is a common feature of these viral families, so we aimed to investigate possible signs of this as well. Two screening projects were conducted: one on Brazilian samples collected from animals in their natural habitat, and the other on Hungarian pet shop samples. Nested PCR systems were used for the detection of adeno- and circoviruses and purified PCR products were Sanger sequenced. Phylogenetic trees for the viruses were reconstructed based on the adenoviral DNA polymerase and hexon genes, circoviral Rep genes, and for the turtle hosts based on mitochondrial cytochrome b amino acid sequences. During the screening, testadeno-, siadeno-, and circovirus strains were detected. The circovirus strains were classified into the genus Circovirus, exhibiting significant evolutionary divergence but forming a monophyletic clade within a group of fish circoviruses. The phylogenetic tree of turtles reflected their taxonomic relationships, showing a deep bifurcation between suborders and distinct monophyletic clades corresponding to families. A similar clustering pattern was observed among the testadenovirus strains in their phylogenetic tree. As a result, this screening of turtle samples revealed at least three new testadenoviruses, including the first sea turtle adenovirus, evidence of coevolution between testadenoviruses and their hosts, and the first turtle associated circoviruses. These findings underscore the need for further research on viruses in turtles, and more broadly in reptiles, to better understand their viral diversity and the evolutionary processes shaping host–virus interactions.