Streptomyces profundus sp. nov., a novel marine actinobacterium isolated from deep-sea sediment of Madeira Archipelago, Portugal

A novel strain, MA3_2.13T, was isolated from deep-sea sediment of Madeira Archipelago, Portugal, and characterized using a polyphasic approach. This strain produced dark brown soluble pigments, bronwish black substrate mycelia and an aerial mycelium with yellowish white spores, when grown on GYM 50SW agar. The main respiratory quinones were MK-10(H4), MK-10(H6) and MK-10(H8). Diphosphatidylglycerol, phosphatidylethanolamine, three unidentified phospholipids and two glycophospholipids were identified as the main phospholipids. The major cellular fatty acids were iso-C16 : 1, iso-C16 : 0, anteiso-C17 : 1 and anteiso-C17 : 0. Phylogenetic analyses based on 16S rRNA gene showed that strain MA3_2.13T is a member of the genus Streptomyces and was most closely related to Streptomyces triticirhizae NEAU-YY642T (NR_180032.1; 16S rRNA gene similarity 97.9 %), Streptomyces sedi YIM 65188T (NR_044582.1; 16S rRNA gene similarity 97.4 %), Streptomyces mimosae 3MP-10T (NR_170412.1; 16S rRNA gene similarity 97.3 %) and Streptomyces zhaozhouensis NEAU-LZS-5T (NR_133874.1; 16S rRNA gene similarity 97.0 %). Genome pairwise comparisons with closest related type strains retrieved values below the threshold for species delineation suggesting that strain MA3_2.13T represents a new branch within the genus Streptomyces. Based on these results, strain MA3_2.13T (=DSM 115980T=LMG 33094T) is proposed as the type strain of a novel species of the genus Streptomyces, for which the name Streptomyces profundus sp. nov. is proposed.

Genome sequences of the first Autographiviridae phages infecting marine Roseobacter

The ubiquitous and abundant marine phages play critical roles in shaping the composition and function of bacterial communities, impacting biogeochemical cycling in marine ecosystems. Autographiviridae is among the most abundant and ubiquitous phage families in the ocean. However, studies on the diversity and ecology of Autographiviridae phages in marine environments are restricted to isolates that infect SAR11 bacteria and cyanobacteria. In this study, ten new roseophages that infect marine Roseobacter strains were isolated from coastal waters. These new roseophages have a genome size ranging from 38 917 to 42 634 bp and G+C content of 44.6-50 %. Comparative genomics showed that they are similar to known Autographiviridae phages regarding gene content and architecture, thus representing the first Autographiviridae roseophages. Phylogenomic analysis based on concatenated conserved genes showed that the ten roseophages form three distinct subgroups within the Autographiviridae, and sequence analysis revealed that they belong to eight new genera. Finally, viromic read-mapping showed that these new Autographiviridae phages are widely distributed in global oceans, mostly inhabiting polar and estuarine locations. This study has expanded the current understanding of the genomic diversity, evolution and ecology of Autographiviridae phages and roseophages. We suggest that Autographiviridae phages play important roles in the mortality and community structure of roseobacters, and have broad ecological applications.

First Canadian report of transmission of fluconazole-resistant Candida parapsilosis within two hospital networks confirmed by genomic analysis

Candida parapsilosis is a common cause of non-albicans candidemia. It can be transmitted in healthcare settings resulting in serious healthcare-associated infections and can develop drug resistance to commonly used antifungal agents. Following a significant increase in the percentage of fluconazole (FLU)-nonsusceptible isolates from sterile site specimens of patients in two Ontario acute care hospital networks, we used whole genome sequence (WGS) analysis to retrospectively investigate the genetic relatedness of isolates and to assess potential in-hospital spread. Phylogenomic analysis was conducted on all 19 FLU-resistant and seven susceptible-dose dependent (SDD) isolates from the two hospital networks, as well as 13 FLU susceptible C. parapsilosis isolates from the same facilities and 20 isolates from patients not related to the investigation. Twenty-five of 26 FLU-nonsusceptible isolates (resistant or SDD) and two susceptible isolates from the two hospital networks formed a phylogenomic cluster that was highly similar genetically and distinct from other isolates. The results suggest the presence of a persistent strain of FLU-nonsusceptible C. parapsilosis causing infections over a 5.5-year period. Results from WGS were largely comparable to microsatellite typing. Twenty-seven of 28 cluster isolates had a K143R substitution in lanosterol 14-α-demethylase (ERG11) associated with azole resistance. As the first report of a healthcare-associated outbreak of FLU-nonsusceptible C. parapsilosis in Canada, this study underscores the importance of monitoring local antimicrobial resistance trends and demonstrates the value of WGS analysis to detect and characterize clusters and outbreaks. Timely access to genomic epidemiological information can inform targeted infection control measures.

Genomic analysis of multidrug-resistant Delftia tsuruhatensis isolated from raw bovine milk

Delftia tsuruhatensis is a gram-negative, aerobic bacterium mostly known as an organic pollutant degrading and growth-promoting microorganism. However, it recently emerged as an opportunistic human pathogen. To date, the source of D. tsuruhatensis infection is not clear. The majority of studies of D. tsuruhatensis have focused on environmental or clinical strains, while investigations of D. tsuruhatensis strains isolated from food sources are limited. In the present study, we report the case of D. tsuruhatensis isolation from raw bovine milk. Classical bacteriology approaches, as well as next-generation sequencing and comparative genomics, were used to characterize the features of the D. tsuruhatensis MR-6/3H strain. The MR-6/3H strain was resistant to 19 antimicrobials among 23 tested, including all aminoglycosides, phenicol, trimethoprim-sulfamethoxazole, and almost all β-lactams. Phylogenetically, the MR-6/3H was close to clinical origin strains, including those previously isolated in Russia. Comparative genomics revealed the presence of putative antimicrobial resistance genes in the MR-6/3H isolate, mostly associated with efflux systems. Notably, genus-specific OXA-926-like β-lactamase was also detected. In all, 27 putative virulence factors were predicted, the majority of which were associated with motility, adherence, stress survival, siderophore synthesis, and immunomodulation. In the MR-6/3H genome, the five prophage regions were identified, including two with intact levels. Integrons and CRISPR-Cas systems were not detected in the MR-6/3H isolate. Thus, our findings suggest that raw milk can be the potential source of and transmission route for the dissemination of multidrug-resistant D. tsuruhatensis.

Distinct evolution of ST11 KL64 Klebsiella pneumoniae in Taiwan

Carbapenem-resistant ST11_KL64 Klebsiella pneumoniae emerged as a significant public health concern in Taiwan, peaking between 2013 and 2015, with the majority of isolates exhibiting OXA-48 as the sole carbapenemase. In this study, we employed whole-genome sequencing to investigate the molecular underpinnings of ST11_KL64 isolates collected from 2013 to 2021. Phylogenomic analysis revealed a notable genetic divergence between the ST11_KL64 strains in Taiwan and those in China, suggesting an independent evolutionary trajectory. Our findings indicated that the ST11_KL64_Taiwan lineage originated from the ST11_KL64 lineage in Brazil, with recombination events leading to the integration of ICEKp11 and a 27-kb fragment at the tRNAASN sites, shaping its unique genomic landscape. To further elucidate this unique sublineage, we examined the plasmid contents. In contrast to ST11_KL64_Brazil strains, which predominantly carried blaKPC-2, ST11_KL64_Taiwan strains exhibited the acquisition of an epidemic blaOXA-48-carrying IncL plasmid. Additionally, ST11_KL64_Taiwan strains consistently harbored a multi-drug resistance IncC plasmid, along with a collection of gene clusters that conferred resistance to heavy metals and the phage shock protein system via various Inc-type plasmids. Although few, there were still rare ST11_KL64_Taiwan strains that have evolved into hypervirulent CRKP through the horizontal acquisition of pLVPK variants. Comprehensive characterization of the high-risk ST11_KL64 lineage in Taiwan not only sheds light on its epidemic success but also provides essential data for ongoing surveillance efforts aimed at tracking the spread and evolution of ST11_KL64 across different geographical regions. Understanding the molecular underpinnings of CRKP evolution is crucial for developing effective strategies to combat its emergence and dissemination.

Comparative Plastid Genome and Phylogenomic Analyses of Potamogeton Species

Potamogetonaceae are aquatic plants divided into six genera. The largest genus in the family is Potamogeton, which is morphologically diverse with many hybrids and polyploids. Potamogetonaceae plastomes were conserved in genome size (155,863 bp-156,669 bp), gene contents (113 genes in total, comprising 79 protein-coding genes and 30 tRNA and 4 rRNA genes), and GC content (36.5%). However, we detected a duplication of the trnH gene in the IR region of the Potamogeton crispus and P. maakianus plastomes. A comparative analysis of Alismatales indicated that the plastomes of Potamogetonaceae, Cymodaceae, and Ruppiaceae have experienced a 6-kb inversion of the rbcL-trnV region and the ndh complex has been lost in the Najas flexilis plastome. Five divergent hotspots (rps16-trnQ, atpF intron, rpoB-trnC, trnC-psbM, and ndhF-rpl32) were identified among the Potamogeton plastomes, which will be useful for species identification. Phylogenetic analyses showed that the family Potamogetonaceae is a well-defined with 100% bootstrap support and divided into two different clades, Potamogeton and Stuckenia. Compared to the nucleotide substitution rates among Alismatales, we found neutral selection in all plastid genes of Potamogeton species. Our results reveal the complete plastome sequences of Potamogeton species, and will be helpful for taxonomic identification, the elucidation of phylogenetic relationships, and the plastome structural analysis of aquatic plants.

Dynamics of the MRSA Population in a Chilean Hospital: a Phylogenomic Analysis (2000-2016)

The global dissemination of methicillin-resistant Staphylococcus aureus (MRSA) is associated with the emergence and establishment of clones in specific geographic areas. The Chilean-Cordobes clone (ChC) (ST5-SCCmecI) has been the predominant MRSA clone in Chile since its first description in 1998, despite the report of other emerging MRSA clones in recent years. Here, we characterize the evolutionary history of MRSA from 2000 to 2016 in a Chilean tertiary health care center using phylogenomic analyses. We sequenced 469 MRSA isolates collected between 2000 and 2016. We evaluated the temporal trends of the circulating clones and performed a phylogenomic reconstruction to characterize the clonal dynamics. We found a significant increase in the diversity and richness of sequence types (STs; Spearman r = 0.8748, P < 0.0001) with a Shannon diversity index increasing from 0.221 in the year 2000 to 1.33 in 2016, and an effective diversity (Hill number; q = 2) increasing from 1.12 to 2.71. The temporal trend analysis revealed that in the period 2000 to 2003 most of the isolates (94.2%; n = 98) belonged to the ChC clone. However, since then, the frequency of the ChC clone has decreased over time, accounting for 52% of the collection in the 2013 to 2016 period. This decline was accompanied by the rise of two emerging MRSA lineages, ST105-SCCmecII and ST72-SCCmecVI. In conclusion, the ChC clone remains the most frequent MRSA lineage, but this lineage is gradually being replaced by several emerging clones, the most important of which is clone ST105-SCCmecII. To the best of our knowledge, this is the largest study of MRSA clonal dynamics performed in South America. IMPORTANCE Methicillin-resistant Staphylococcus aureus (MRSA) is a major public health pathogen that disseminates through the emergence of successful dominant clones in specific geographic regions. Knowledge of the dissemination and molecular epidemiology of MRSA in Latin America is scarce and is largely based on small studies or more limited typing techniques that lack the resolution to represent an accurate description of the genomic landscape. We used whole-genome sequencing to study 469 MRSA isolates collected between 2000 and 2016 in Chile providing the largest and most detailed study of clonal dynamics of MRSA in South America to date. We found a significant increase in the diversity of MRSA clones circulating over the 17-year study period. Additionally, we describe the emergence of two novel clones (ST105-SCCmecII and ST72-SCCmecVI), which have been gradually increasing in frequency over time. Our results drastically improve our understanding of the dissemination and update our knowledge about MRSA in Latin America.

Comparative Genomics Identifies Conserved and Variable TAL Effectors in African Strains of the Cotton Pathogen Xanthomonas citri pv. malvacearum

Strains of Xanthomonas citri pv. malvacearum cause bacterial blight of cotton, a potentially serious threat to cotton production worldwide, including in sub-Saharan countries. Development of disease symptoms, such as water soaking, has been linked to the activity of a class of type 3 effectors, called transcription activator-like (TAL) effectors, which induce susceptibility genes in the host's cells. To gain further insight into the global diversity of the pathogen, to elucidate their repertoires of TAL effector genes, and to better understand the evolution of these genes in the cotton-pathogenic xanthomonads, we sequenced the genomes of three African strains of X. citri pv. malvacearum using nanopore technology. We show that the cotton-pathogenic pathovar of X. citri is a monophyletic lineage containing at least three distinct genetic subclades, which appear to be mirrored by their repertoires of TAL effectors. We observed an atypical level of TAL effector gene pseudogenization, which might be related to resistance genes that are deployed to control the disease. Our work thus contributes to a better understanding of the conservation and importance of TAL effectors in the interaction with the host plant, which can inform strategies for improving resistance against bacterial blight in cotton.

Widespread Reassortment Contributes to Antigenic Shift in Bluetongue Viruses from South Africa

Bluetongue (BT), a viral disease of ruminants, is endemic throughout South Africa, where outbreaks of different serotypes occur. The predominant serotypes can differ annually due to herd immunity provided by annual vaccinations using a live attenuated vaccine (LAV). This has led to both wild-type and vaccine strains co-circulating in the field, potentially leading to novel viral strains due to reassortment and recombination. Little is known about the molecular evolution of the virus in the field in South Africa. The purpose of this study was to investigate the genetic diversity of field strains of BTV in South Africa and to provide an initial assessment of the evolutionary processes shaping BTV genetic diversity in the field. Complete genomes of 35 field viruses belonging to 11 serotypes, collected from different regions of the country between 2011 and 2017, were sequenced. The sequences were phylogenetically analysed in relation to all the BTV sequences available from GenBank, including the LAVs and reference strains, resulting in the analyses and reassortment detection of 305 BTVs. Phylogenomic analysis indicated a geographical selection of the genome segments, irrespective of the serotype. Based on the initial assessment of the current genomic clades that circulate in South Africa, the selection for specific clades is prevalent in directing genome segment reassortment, which seems to exclude the vaccine strains and in multiple cases involves Segment-2 resulting in antigenic shift.

Origin and Early Diversification of the Papain Family of Cysteine Peptidases

Peptidases of the papain family play a key role in protein degradation, regulated proteolysis, and the host-pathogen arms race. Although the papain family has been the subject of many studies, knowledge about its diversity, origin, and evolution in Eukaryota, Bacteria, and Archaea is limited; thus, we aimed to address these long-standing knowledge gaps. We traced the origin and expansion of the papain family with a phylogenomic analysis, using sequence data from numerous prokaryotic and eukaryotic proteomes, transcriptomes, and genomes. We identified the full complement of the papain family in all prokaryotic and eukaryotic lineages. Analysis of the papain family provided strong evidence for its early diversification in the ancestor of eukaryotes. We found that the papain family has undergone complex and dynamic evolution through numerous gene duplications, which produced eight eukaryotic ancestral paralogous C1A lineages during eukaryogenesis. Different evolutionary forces operated on C1A peptidases, including gene duplication, horizontal gene transfer, and gene loss. This study challenges the current understanding of the origin and evolution of the papain family and provides valuable insights into their early diversification. The findings of this comprehensive study provide guidelines for future structural and functional studies of the papain family.

Evolutionary dynamics of plastomes in coscinodiscophycean diatoms revealed by comparative genomics

To understand the evolution of coscinodiscophycean diatoms, plastome sequences of six coscinodiscophycean diatom species were constructed and analyzed in this study, doubling the number of constructed plastome sequences in Coscinodiscophyceae (radial centrics). The platome sizes varied substantially in Coscinodiscophyceae, ranging from 119.1 kb of Actinocyclus subtilis to 135.8 kb of Stephanopyxis turris. Plastomes in Paraliales and Stephanopyxales tended to be larger than those in Rhizosoleniales and Coscinodiacales, which were due to the expansion of the inverted repeats (IRs) and to the marked increase of the large single copy (LSC). Phylogenomic analysis indicated that Paralia and Stephanopyxis clustered tightly to form the Paraliales-Stephanopyxales complex, which was sister to the Rhizosoleniales-Coscinodiscales complex. The divergence time between Paraliales and Stephanopyxales was estimated at 85 MYA in the middle Upper Cretaceous, indicating that Paraliales and Stephanopyxales appeared later than Coscinodiacales and Rhizosoleniales according to their phylogenetic relationships. Frequent losses of housekeeping protein-coding genes (PCGs) were observed in these coscinodiscophycean plastomes, indicating that diatom plastomes showed an ongoing reduction in gene content during evolution. Two acpP genes (acpP1 and acpP2) detected in diatom plastomes were found to be originated from an early gene duplication event occurred in the common progenitor after diatom emergence, rather than multiple independent gene duplications occurring in different lineages of diatoms. The IRs in Stephanopyxis turris and Rhizosolenia fallax-imbricata exhibited a similar trend of large expansion to the small single copy (SSC) and slightly small contraction from the LSC, which eventually led to the conspicuous increase in IR size. Gene order was highly conserved in Coscinodiacales, while multiple rearrangements were observed in Rhizosoleniales and between Paraliales and Stephanopyxales. Our results greatly expanded the phylogenetic breadth in Coscinodiscophyceae and gained novel insights into the evolution of plastomes in diatoms.

Pseudomonas solani sp. nov. isolated from the rhizosphere of eggplant in Japan

The search for bacteria that can be used as biocontrol agents to control crop diseases yielded a promising candidate, Sm006^T, which was isolated from the rhizosphere of eggplant (Solanum melongena) growing in a field in Aichi Prefecture, Japan, in 2006. The cells were Gram-stain-negative, aerobic, non-spore-forming, rod-shaped and motile with one polar flagellum. The results of homology searches and phylogenetic analyses based on the 16S rRNA gene sequence indicated that Sm006^T represents a member of the genus Pseudomonas. The genomic DNA G+C content was 66.3 mol% and the major cellular fatty acids (more than 5 % of the total fatty acids) were summed feature 8 (C_18 : 1ω7c and/or C_18 : 1ω6c), summed feature 3 (C_16 : 1ω7c and/or C_16 : 1ω6c), C_16 : 0 and C_12 : 0. Phylogenetic analyses using the rpoD gene sequence and phylogenomic analysis of the whole genome sequence revealed that Sm006^T represents a member of the Pseudomonas resinovorans group; however, its phylogenetic position does not match that of any known species of the genus Pseudomonas. The average nucleotide identity and digital DNA-DNA hybridisation values between the strain and closely related species were lower than the thresholds for prokaryotic species delineation (95-96 and 70 %, respectively), with the highest values observed for Pseudomonas tohonis TUM18999^T (92.05 and 46.3 %, respectively). Phenotypic characteristics, cellular fatty acid composition and possession of 2,4-diacetylphloroglucinol biosynthetic gene cluster could be used to differentiate the strain from its closest relatives. The phenotypic, chemotaxonomic and genotypic data obtained during this study indicated that Sm006^T represents a novel species of the genus Pseudomonas, for which we propose the name Pseudomonas solani sp. nov., with Sm006^T (= MAFF 212523^T = ICMP 24689^T) as the type strain.

The complete chloroplast genome of Primula vialii (Primulaceae), an ornamental plant

Primula vialii Delavay ex Franch. (1905) is an alpine species with an ornamental value. In this study, we sequenced, assembled, and annotated the chloroplast genome of P. vialii. The results showed that it was a double-stranded, closed circular DNA with 154,897 bp in length, comprising a small single-copy (SSC) region of 17,766 bp, a large single-copy (LSC) region of 85,379 bp and a pair of inverted repeat (IR) regions of 25,876 bp. A total of 113 unique genes were annotated, including 79 protein-coding genes, 30 tRNA genes, and 4 rRNA genes. The phylogenetic analysis revealed that P. vialii is closely related to Primula flaccida. The cp genomic data will be useful for systematics and evolutionary studies of Primula.

Comparative genomics provides insights into the phylogeny and environmental adaptations of Peritrichia (Protista, Ciliophora) - a potential resource for environmental pollution control and bioremediation

Peritrichs are one of the largest groups within the class Oligohymenophorea. They have a worldwide distribution and a high degree of species diversity. Using the single-cell genome sequencing technique, we obtained the genomes of five sessilid peritrichs. Combining both genomic and transcriptomic data of other publicly available oligohymenophorean ciliates (including the genomes of three sessilid peritrichs from our team's previous study), we conducted a comparative genomics study. Our phylogenomic analyses using both maximum likelihood and Bayesian inference methods recovered the subclass Peritrichia and each of its two orders (Sessilida and Mobilida) as being monophyletic. The non-monophyly of two families (Vorticellidae and Zoothamniidae) was also well supported in both trees. Molecular clock analysis showed that the origin of the subclass Peritrichia was estimated to be during the late Proterozoic. We also analyzed the stop codon usage of 44 oligohymenophoreans. The results showed that most of these species used TGA as the biased stop codon and reassigned the other two stop codons (TAA and TAG) to code amino acids. In addition, we found that the presence of a typical peritrich lorica is a plesiomorphic character of the family Vaginicolidae. Through GO enrichment analysis for group-specific orthogroups of Vaginicolidae, we successfully identified the biological process and molecular function GO terms that were linked with the typical peritrich lorica, including three glycosaminoglycan-related and two chitin-related GO terms. Finally, our enrichment analyses of significantly expanded gene families in Peritrichia found that sessilids were more tolerant to environmental stress (mainly organic matter) than mobilids, suggesting that peritrich lineages (especially sessilids) may have the potential for application in environmental pollution control and bioremediation. Together, the results presented in this study will facilitate wider genome-scale phylogenetic analyses of Peritrichia and deepen the understanding of their unique advantages for environmental pollution control bioremediation.

Georgenia halotolerans sp. nov., a halotolerant actinobacterium isolated from Taklamakan desert soil

A Gram-stain-positive, aerobic, non-motile, non-spore-forming and rod-shaped actinobacterium, designated strain 10Sc9-8^T, was isolated from Taklamakan desert soil sampled in the Xinjiang Uygur Autonomous Region, China. Strain 10Sc9-8^T grew at 8‒37 °C (optimum, 28‒30 °C), pH 6.0‒10.0 (optimum, pH 7.0-8.0) and in the presence of 0‒15 % (w/v) NaCl (optimum, 0-3 %). Phylogenetic analysis based on 16S rRNA gene sequence suggested that strain 10Sc9-8^T was affiliated with members of the genus Georgenia and showed the highest 16S rRNA gene sequence similarity to Georgenia yuyongxinii Z443^T (97.4 %). Phylogenomic analysis based on the whole genome sequences indicated that strain 10Sc9-8^T should be assigned into the genus Georgenia. The average nucleotide identity and digital DNA-DNA hybridization values calculated from the whole genome sequences indicated that strain 10Sc9-8^T was clearly separated from other closely related species of the genus Georgenia with values below the thresholds for species delineation. Chemotaxonomic analyses showed that the cell-wall peptidoglycan was in a variant of A4α type with an interpeptide bridge comprising l-Lys-l-Ala-Gly-l-Asp. The predominant menaquinone was MK-8(H₄). The polar lipids comprised diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol, phosphatidylinositol mannoside, several unidentified phospholipids, glycolipids and one unidentified lipid. The major fatty acids were anteiso-C_15 : 0, anteiso-C_15 : 1 A and C_16 : 0. The genomic DNA G+C content was 72.7 mol%. On the basis of phenotypic, phylogenetic and phylogenomic data, strain 10Sc9-8^T represents a novel species of the genus Georgenia, for which the name Georgenia halotolerans sp. nov. is proposed. The type strain is 10Sc9-8^T (=JCM 33946^T=CPCC 206219^T).

Molecular evolutionary model based on phylogenetic and mutation analysis of SARS-CoV-2 spike protein sequences from Asian countries: A phylogenomic approach

The lethal pathogenic severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) infection has caused the COVID-19 pandemic, posing serious risks to people. The clove-like spike (S) protein that distinguishes coronaviruses from other viruses is important for viral pathogenicity, evolution, and transmission. The investigation of the unique structural mutations of the SARS-CoV-2 spike protein among 34 Asian countries, as well as the resulting phylogenetic relationship, provided critical information in understanding the pathogenesis. This can be utilized for the discovery of possible treatments and vaccine development. The current study analyzed and depicted phylogenetic and evolutionary models useful for understanding SARS-CoV-2 human-human transmission dynamics in Asian regions with shared land borders. Further, integrated bioinformatics analysis was performed to predict the pathogenic potential and stability of 53 mutational positions among 34 coronavirus strains. Mutations at positions N969K, D614G and S884F have deleterious effects on protein function. These findings are crucial because the Asian mutations could potentially provide a vaccine candidate with co-protection against all SARS-CoV-2 strains. This region is vulnerable because of the high population density and the volume of domestic and international travel for business and tourism. These discoveries would also aid in the development of plans for governments and the general populace to implement all required biocontainment protocols common to all countries.

Chelativorans petroleitrophicus sp. nov., a paraffin oil-degrading bacterium isolated from a mixture of oil-based drill cuttings and paddy soil

We isolated a paraffin oil-degrading bacterial strain from a mixture of oil-based drill cutting and paddy soil, and characterized the strain using a polyphasic approach. The Gram-positive, aerobic, rod-shaped and non-spore-forming strain (SCAU 2101^T) grew optimally at 50 °C, pH 7.0 and 0.5 % (w/v) NaCl. Phylogenetic analysis based on 16S rRNA gene sequence indicated that the strain represented a distinct clade in the genus Chelativorans, neighbouring Chelativorans intermedius LMG 28482^T (97.1 %). The genome size and DNA G+C content of the strain were 3 969 430 bp and 63.1 mol%, respectively. Whole genome based phylogenomic analyses showed that the average nucleotide identity and digital DNA-DNA hybridization values between strain SCAU 2101^T and C. intermedius LMG 28482^T were 77.5 and 21.2 %, respectively. The major respiratory quinone was Q-10. The dominant fatty acids were C_19 : 0 cyclo ω8c (50.6 %), summed feature 8 (C_18 : 1  ω7c and/or C_18 : 1  ω6c; 22.5 %) and C_18 : 0 (13.8 %). The polar lipids of the strain included phosphatidylethanolamine, phosphatidylmonomethylethanolamine, phosphatidylglycerol, phosphatidylcholine and diphosphatidylglycerol. Based on the results, strain SCAU 2101^T was considered to represent a novel species in the genus Chelativorans, for which the name Chelativorans petroleitrophicus sp. nov. is proposed. The type strain is SCAU 2101^T (= CCTCC AB 2021125^T=KCTC 92067^T).

Dyadobacter chenhuakuii sp. nov., Dyadobacter chenwenxiniae sp. nov., and Dyadobacter fanqingshengii sp. nov., isolated from soil of the Qinghai-Tibetan Plateau

Six novel bacterial strains, designated CY22^T, CY357, LJ419^T, LJ53, CY399^T and CY107 were isolated from soil samples collected from the Qinghai-Tibetan Plateau, PR China. Cells were aerobic, rod-shaped, yellow-pigmented, catalase- and oxidase-positive, Gram-stain-negative, non-motile and non-spore-forming. All strains were psychrotolerant and could grow at 0 °C. The results of phylogenetic and phylogenomic analyses, based on 16S rRNA gene sequences and core genomic genes, indicated that the three strain pairs (CY22^T/CY357, LJ419^T/LJ53 and CY399^T/CY107) were closely related to members of the genus Dyadobacter and clustered tightly with two species with validly published names, Dyadobacter alkalitolerans 12116^T and Dyadobacter psychrophilus BZ26^T. Values of digital DNA-DNA hybridization between genome sequences of the isolates and other strains from the GenBank database in the genus Dyadobacter were far below the 70.0 % threshold. The genomic DNA G+C content of these six strains ranged from 45.2 to 45.8 %. The major cellular fatty acids of all six strains were iso-C_15 : 0 and summed feature 3 (comprising C_16 : 1 ω7c and/or C_16 : 1 ω6c). MK-7 was the only respiratory quinone, and phosphatidylethanolamine was the predominant polar lipid for strains CY22^T, LJ419^T and CY399^T. On the basis of the phenotypic, phylogenetic and genomic evidence presented, these six strains represent three novel members of the genus Dyadobacter, for which the names Dyadobacter chenhuakuii sp. nov., Dyadobacter chenwenxiniae sp. nov. and Dyadobacter fanqingshengii sp. nov. are proposed. The type strains are CY22^T (= GDMCC 1.3045^T = KCTC 92299^T), LJ419^T (= GDMCC 1.2872^T = JCM 33794^T) and CY399^T (= GDMCC 1.3052^T = KCTC 92306^T), respectively.

Plastomes of Garcinia mangostana L. and Comparative Analysis with Other Garcinia Species

The two varieties of mangosteen (Garcinia mangostana L.) cultivated in Malaysia are known as Manggis and Mesta. The latter is preferred for its flavor, texture, and seedlessness. Here, we report a complete plastome (156,580 bp) of the Mesta variety that was obtained through a hybrid assembly approach using PacBio and Illumina sequencing reads. It encompasses a large single-copy (LSC) region (85,383 bp) and a small single-copy (SSC) region (17,137 bp) that are separated by 27,230 bp of inverted repeat (IR) regions at both ends. The plastome comprises 128 genes, namely, 83 protein-coding genes, 37 tRNA genes, and 8 rRNA genes. The plastome of the Manggis variety (156,582 bp) obtained from reference-guided assembly of Illumina reads was found to be nearly identical to Mesta except for two indels and the presence of a single-nucleotide polymorphism (SNP). Comparative analyses with other publicly available Garcinia plastomes, including G. anomala, G. gummi-gutta, G. mangostana var. Thailand, G. oblongifolia, G. paucinervis, and G. pedunculata, found that the gene content, gene order, and gene orientation were highly conserved among the Garcinia species. Phylogenomic analysis divided the six Garcinia plastomes into three groups, with the Mesta and Manggis varieties clustered closer to G. anomala, G. gummi-gutta, and G. oblongifolia, while the Thailand variety clustered with G. pedunculata in another group. These findings serve as future references for the identification of species or varieties and facilitate phylogenomic analysis of lineages from the Garcinia genus to better understand their evolutionary history.

Genomic and Metabolite Profiling Reveal a Novel Streptomyces Strain, QHH-9511, from the Qinghai-Tibet Plateau

The prevalence of superbugs, represented by methicillin-resistant Staphylococcus aureus (MRSA), has become a serious clinical and public safety concern with rising incidence in hospitals. Polyketides with diverse chemical structures harbor many antimicrobial activities, including those of rifampin and rapamycin against MRSA. Streptomyces sp. QHH-9511 was isolated from a niche habitat in the Qinghai-Tibet Plateau and used to produce antibacterial metabolites. Herein, an integrated approach combining genome mining and metabolic analysis were employed to decipher the chemical origin of the antibacterial components with pigmented properties in strain QHH-9511, a novel Streptomyces species from a lichen symbiont on the Qinghai-Tibet Plateau. Genomic phylogeny assembled at the chromosome level revealed its unique evolutionary state. Further genome mining uncovered 36 candidate gene clusters, most of which were uncharacterized. Meanwhile, based on liquid chromatography coupled to diode array detection mass spectrometry, a series of granaticins, BSMs, chromones, phaeochromycins, and related molecules were discovered by using the Global Natural Product Social molecular networking platform. Subsequently, several pigment compounds were isolated and identified by high-resolution mass spectrometry and/or nuclear magnetic resonance, among which the structure-activity relationships of seven aromatic polyketides showed that the fused lactone ring of the C-2 carboxyl group could increase antibacterial activity. Genetic experiments indicated that all seven aromatic polyketides are a series of metabolic shunts produced by a single type II polyketide synthase (PKS) cluster. Comparative genomic analysis of granaticin producers showed that the granaticin gene cluster is widely distributed. This study provides an efficient method to combine genome mining and metabolic profiling techniques to uncover bioactive metabolites derived from specific habitats, while deepening our understanding of aromatic polyketide biosynthesis. IMPORTANCE Undescribed microorganisms from special habitats are being screened for anti-superbug drug molecules. In a project to screen actinomycetes for anti-MRSA activity, we isolated a Streptomyces strain from Qinghai Lake lichens. The phylogeny based on the genome assembled at the chromosome level revealed this strain's unique evolutionary state. The chemical origins of the antibacterial components with pigment properties in strain QHH-9511 were determined using an integrated approach combining genome mining and metabolic analysis. Further genome mining uncovered 36 secondary metabolite gene clusters, the majority of which were previously unknown. A series of aromatic compounds were discovered using molecular network analysis, separation, and extraction. Genetic experiments revealed that all seven aromatic polyketides are a series of metabolic shunts produced by a single cluster of type II PKSs. This study describes a method for identifying novel Streptomyces from specific habitats by combining genome mining with metabolic profiling techniques.

Phylogeny and Historical Biogeography of the East Asian Clematis Group, Sect. Tubulosae, Inferred from Phylogenomic Data

The evolutionary history of Clematis section Tubulosae, an East Asian endemic lineage, has not been comprehensively studied. In this study, we reconstruct the phylogeny of this section with a complete sampling using a phylogenomic approach. The genome skimming method was applied to obtain the complete plastome sequence, the nuclear ribosomal DNA (nrDNA), and the nuclear SNPs data for phylogenetic reconstruction. Using a Bayesian molecular clock approach and ancestral range reconstruction, we reconstruct biogeographical history and discuss the biotic and abiotic factors that may have shaped the distribution patterns of the section. Both nuclear datasets better resolved the phylogeny of the sect. Tubulosae than the plastome sequence. Sect. Tubulosae was resolved as a monophyletic group sister to a clade mainly containing species from the sect. Clematis and sect. Aspidanthera. Within sect. Tubulosae, two major clades were resolved by both nuclear datasets. Two continental taxa, C. heracleifolia and C. tubulosa var. ichangensis, formed one clade. One continental taxon, C. tubulosa, and all the other species from Taiwan island, the Korean peninsula, and the Japanese archipelago formed the other clade. Molecular dating results showed that sect. Tubulosae diverged from its sister clade in the Pliocene, and all the current species diversified during the Pleistocene. Our biogeographical reconstruction suggested that sect. Tubulosae evolved and began species diversification, most likely in mainland China, then dispersed to the Korean peninsula, and then expanded its range through the Japanese archipelago to Taiwan island. Island species diversity may arise through allopatric speciation by vicariance events following the range fragmentation triggered by the climatic oscillation and sea level change during the Pleistocene epoch. Our results highlight the importance of climatic oscillation during the Pleistocene to the spatial-temporal diversification patterns of the sect. Tubulosae.

A comparative plastomic analysis of Ziziphus jujuba var. spinosa (Bunge) Hu ex H. F. Chow and implication of the origin of Chinese jujube

Comparative plastomics can be used to explicitly dissect various types of plastome variation. In the present study, the plastome variation pattern of Ziziphus jujuba var. spinosa (also called sour jujube) and its phylogenomic relationship with Chinese jujube were investigated. Plastomes of 21 sour jujube individuals were sequenced and assembled. The length of the sour jujube plastomes ranged between 159399 and 161279 bp. The plastomes exhibited collinearity of structure, gene order and content. The most divergent regions were located in the intergenic spacers, such as trnR-UCU-atpA and psbZ-trnG-UCC. Sliding window analysis demonstrated that the sequence variation among the sour jujube plastomes was relatively low. Sixty-two to 76 SSRs with 4 motif types were identified in the sour jujube plastomes with a predominant motif type of A/T. Three protein-coding genes exhibited higher nonsynonymous/synonymous substitution ratios, indicating that these genes may undergo positive selection. A total of 80 SNPs were detected and 1266 potential RNA editing sites of 23 protein-coding genes were predicted. In the phylogenomic tree constructed, sour jujube has a sister relationship to Chinese jujube, which indicates that Chinese jujube may have originated or been domesticated from sour jujube. The present study explicitly investigated the individual-level plastome variation of sour jujube and provides potential valuable molecular markers for future genetic-related study of this lineage.

The complete chloroplast genome of Primula calliantha subsp. bryophila, an ornamental alpine plant from China

Primula calliantha subsp. bryophila (Balf. f. et Farrer) W.W. Smith and Forrest (1928) is a perennial alpine species with ornamental value. It is distributed in northwestern Yunnan and adjacent eastern Tibet of China, and northern Myanmar. Here, we sequenced and assembled complete plastid genome of P. calliantha subsp. bryophila, which is a circular molecule of 152,045 bp in length, including a large single-copy region (83,966 bp), a small single-copy region (17,663 bp), and a pair of inverted repeats (25,208 bp). The chloroplast genome contained 113 genes, including 79 protein-coding genes, four rRNA genes, and 30 tRNA genes. The phylogenetic tree based on chloroplast genomes showed the relative relationship of P. calliantha subsp. bryophila and P. calliantha, which further supports P. calliantha subsp. bryophila as a subspecies of P. calliantha in taxonomy. The complete chloroplast (cp) genome of P. calliantha subsp. bryophila provides valuable data for further phylogenetic studies of Primulaceae.

Characterization of the complete chloroplast genome of Trailliaedoxa gracilis (Rubiaceae)

Trailliaedoxa gracilis (Rubiaceae) is a Chinese endemic monotypic genus distributed in southwestern China. This study reported the complete chloroplast genome of T. gracilis assembled from Illumina sequencing reads. The chloroplast genome size is 152,407 bp, containing a single large copy (LSC) region of 82,957 bp, a short single copy (SSC) region of 17,936 bp, and a pair of inverted repeats (IRs) of 25,757 bp. A total of 127 genes were found, including 82 protein-coding genes, 37 tRNA genes, and eight rRNA genes. A phylogenetic analysis using the maximum likelihood algorithm revealed that T. gracilis belonged to the subfamily Ixoroideae and had the closest relationship with Scyphiphora hydrophyllacea.

Genetic characteristics, antimicrobial resistance, and prevalence of Arcobacter spp. isolated from various sources in Shenzhen, China

Arcobacter spp. is a globally emerging zoonotic and foodborne pathogen. However, little is known about its prevalence and antimicrobial resistance in China. To investigate the prevalence of Arcobacter spp. isolated from various sources, 396 samples were collected from human feces, chicken cecum, and food specimens including chicken meat, beef, pork, lettuce, and seafood. Arcobacter spp. was isolated by the membrane filtration method. For 92 strains, the agar dilution method and next-generation sequencing were used to investigate their antimicrobial resistance and to obtain whole genome data, respectively. The virulence factor database (VFDB) was queried to identify virulence genes. ResFinder and the Comprehensive Antibiotic Resistance Database (CARD) were used to predict resistance genes. A phylogenetic tree was constructed using the maximum likelihood (ML) method with core single-nucleotide polymorphisms (SNPs). We found that 27.5% of the samples (n = 109) were positive for Arcobacter spp., comprising Arcobacter butzleri (53.0%), Arcobacter cryaerophilus (39.6%), and Arcobacter skirrowii (7.4%). Chicken meat had the highest prevalence (81.2%), followed by seafood (51.9%), pork (43.3%), beef (36.7%), lettuce (35.5%), chicken cecum (8%), and human fecal samples (0%, 0/159). Antimicrobial susceptibility tests revealed that 51 A. butzleri and 40 A. cryaerophilus strains were resistant to streptomycin (98.1, 70%), clindamycin (94.1, 90%), tetracycline (64.7, 52.5%), azithromycin (43.1%, 15%), nalidixic acid (33.4, 35%), and ciprofloxacin (31.3, 35%) but were susceptible to erythromycin, gentamicin, chloramphenicol, telithromycin, and clindamycin (≤10%). A. skirrowii was sensitive to all experimental antibiotics. The virulence factors tlyA, mviN, cj1349, ciaB, and pldA were carried by all Arcobacter spp. strains at 100%, and the following percentages were cadF (95.7%), iroE (23.9%), hecB (2.2%), hecA, and irgA (1.1%). Only one A. butzleri strain (F061-2G) carried a macrolide resistance gene (ereA). One A. butzleri and one A. cryaerophilus harbored resistance island gene clusters, which were isolated from pork and chicken. Phylogenetic tree analysis revealed that A. butzleri, A. cryaerophilus, and A. skirrowii were separated from each other. To our knowledge, this is the first report of the isolation of Arcobacter spp. from vegetables and seafood in China. The resistance island gene cluster found in pork and chicken meat and the presence of virulence factors could be a potential risk to human health.

Pseudomonas aegrilactucae sp. nov. and Pseudomonas morbosilactucae sp. nov., pathogens causing bacterial rot of lettuce in Japan

Phytopathogenic bacterial strains (MAFF 301350T, MAFF 302030T and MAFF 302046), isolated from lettuce (Lactuca sativa var. capitata) with bacterial rot disease in Japan, were subjected to polyphasic characterization to determine their taxonomic affiliations. The cells were Gram-reaction-negative, aerobic, non-spore-forming, motile with polar flagella and rod-shaped. The results of similarity searches and phylogenetic analyses based on the 16S rRNA gene sequences, as well as the analysis results of the cellular fatty acid composition and genomic DNA G+C content indicated that these strains belong to the genus Pseudomonas . Phylogenetic analyses using the rpoD gene sequences and phylogenomic analyses of the whole genome sequences grouped them into the Pseudomonas putida group (MAFF 301350T) and the Pseudomonas fluorescens group (MAFF 302030T and MAFF 302046), but the phylogenetic positions of the strains did not match those of any known Pseudomonas species. The average nucleotide identity and digital DNA–DNA hybridization values between the strains and their closely related species were lower than the thresholds for prokaryotic species delineation (95–96 and 70 %, respectively). Phenotypic characteristics, pathogenicity toward lettuce, cellular fatty acid composition and whole-cell MALDI-TOF mass spectrometry profiles could differentiate the strains from their closest relatives. The phenotypic, chemotaxonomic and genotypic data obtained in this study showed that the strains represent two novel species of the genus Pseudomonas , Pseudomonas aegrilactucae sp. nov. for MAFF 301350T and Pseudomonas morbosilactucae sp. nov. for MAFF 302030T and MAFF 302046. The respective type strains are MAFF 301350T (= ICMP 23989T) and MAFF 302030T (= ICMP 24377T).

Genomic evidence for two pathways of formaldehyde oxidation and denitrification capabilities of the species Paracoccus methylovorus sp. nov

Three strains (H4-D09^T, S2-D11 and S9-F39) of a member of the genus Paracoccus attributed to a novel species were isolated from topsoil of temperate grasslands. The genome sequence of the type strain H4-D09^T exhibited a complete set of genes required for denitrification as well as methylotrophy. The genome of H4-D09^T included genes for two alternative pathways of formaldehyde oxidation. Besides the genes for the canonical glutathione (GSH)-dependent formaldehyde oxidation pathway, all genes for the tetrahydrofolate-formaldehyde oxidation pathway were identified. The strain has the potential to utilize methanol and/or methylamine as a single carbon source as evidenced by the presence of methanol dehydrogenase (mxaFI) and methylamine dehydrogenase (mau) genes. Apart from dissimilatory denitrification genes (narA, nirS, norBC and nosZ), genes for assimilatory nitrate (nasA) and nitrite reductases (nirBD) were also identified. The results of phylogenetic analysis based on 16S rRNA genes coupled with riboprinting revealed that all three strains represented the same species of genus Paracoccus. Core genome phylogeny of the type strain H4-D09^T indicated that Paracoccus thiocyanatus and Paracoccus denitrificans are the closest phylogenetic neighbours. The average nucleotide index (ANI) and digital DNA-DNA hybridization (dDDH) with the closest phylogenetic neighbours revealed genetic differences at the species level, which were further substantiated by differences in several physiological characteristics. The major respiratory quinone is Q-10, and the predominant cellular fatty acids are C_18 : 1ω7c, C_19 : 0cyclo ω7c, and C_16 : 0, which correspond to those detected in other members of the genus. The polar lipid profile consists of a diphosphatidylglycerol (DPG), phosphatidylethanolamine (PE), phosphatidylglycerol (PG), phosphatidylcholine (PC), aminolipid (AL), glycolipid (GL) and an unidentified lipid (L).On the basis of our results, we concluded that the investigated isolates represent a novel species of the genus Paracoccus, for which the name Paracoccus methylovorus sp. nov. (type strain H4-D09^T=LMG 31941^T= DSM 111585^T) is proposed.

Genomic Diversity of SARS-CoV-2 Omicron Variant in South American Countries

Genomic surveillance of SARS-CoV-2 is one of the tools that provide genomic information on circulating variants. Given the recent emergence of the Omicron (B.1.1.529) variant, this tool has provided data about this lineage's genomic and epidemiological characteristics. However, in South America, this variant's arrival and genomic diversity are scarcely known. Therefore, this study determined the genomic diversity and phylogenetic relationships of 21,615 Omicron genomes available in public databases. We found that in South America, BA.1 (n = 15,449, 71%) and BA.1.1 (n = 6257, 29%) are the dominant sublineages, with several mutations that favor transmission and antibody evasion. In addition, these lineages showed cryptic transmission arriving on the continent in late September 2021. This event may have contributed to the dispersal of Omicron sublineages and the acquisition of new mutations. Considering the genomic and epidemiological characteristics of these lineages, especially those with a high number of mutations in their genome, it is important to conduct studies and surveillance on the dynamics of these lineages to identify the mechanisms of mutation acquisition and their impact on public health.

Pufferfish (Tetraodon cutcutia) Sampled from a Freshwater River Serves as an Intermediate Reservoir of a Sucrose Nonfermenting Variant of Vibrio cholerae PS-4

We describe the genomic characteristics of Vibrio cholerae strain PS-4 that is unable to ferment sucrose on a thiosulfate citrate bile salt sucrose (TCBS) agar medium. This bacterium was isolated from the skin mucus of a freshwater pufferfish. The genome of strain PS-4 was sequenced to understand the sucrose nonfermenting phenotype. The gene encoding the sucrose-specific phosphotransferase system IIB (sucR) was absent, resulting in the defective sucrose fermenting phenotype. In contrast, genes encoding the glucose-specific transport system IIB (ptsG) and fructose-specific transport system IIB (fruA) showed acid production while growing with respective sugars. The overall genome relatedness indices (OGRI), such as in silico DNA-DNA hybridization (isDDH), average nucleotide identity (ANI), and average amino acid identity (AAI), were above the threshold value, that is, 70% and 95 to 96%, respectively. Phylogenomic analysis based on genome-wide core genes and the nonrecombinant core genes showed that strain PS-4 clustered with Vibrio cholerae ATCC 14035T. Further, genes encoding cholera toxin (ctx), zonula occludens toxin (zot), accessory cholera enterotoxin (ace), toxin-coregulated pilus (tcp), and lipopolysaccharide biosynthesis (rfb) were absent. PS-4 showed hemolytic activity and reacted strongly to the R antibody. Therefore, the Vibrio cholerae from the pufferfish adds a new ecological niche of this bacterium. IMPORTANCE Vibrio cholerae is native of aquatic environments. In general, V. cholerae ferments sucrose on thiosulfate citrate bile salt sucrose (TCBS) agar and produces yellow colonies. V. cholerae strain PS-4 described in this study is a sucrose nonfermenting variant associated with pufferfish skin and does not produce yellow colonies on TCBS agar. Genes encoding sucrose-specific phosphotransferase system IIB (sucR) were absent. The observed phenotype in the distinct metabolic pathway indicates niche-specific adaptive evolution for this bacterium. Our study suggests that the nonfermenting phenotype of V. cholerae strains on TCBS agar may not always be considered for species delineation.

DNA Barcoding and Phylogenomic Analysis of the Genus Fritillaria in China Based on Complete Chloroplast Genomes

The Fritillaria is an extremely complicated genus in taxonomy and phylogeny, which contains numerous medicinal species in China. Both traditional characteristic-based taxonomy and universal DNA barcodes (ITS, trnH-psbA, and rbcL) are difficult to effectively identify the species. Here, we generated a large dataset of chloroplast genomes from multiple accessions per species of Fritillaria to evaluate their effectiveness in species discrimination. Moreover, phylogeny of species in China was explored based on the complete chloroplast genomes, and then divergence times of each node were estimated. The results showed that all 21 species in Fritillaria here (including two suspicious species) could be correctly discriminated using cpDNA genomes except F. cirrhosa, which suggested that DNA super-barcode could greatly enhance species discriminatory resolution for complicated genera. Furthermore, four regions (ycf1, matK-trnG-GCC, rpoC1, and matK) gained remarkably higher resolution than that of other plastid regions, but only matK might be suitable to identify Fritillaria species in consideration of its lengths. Phylogenomic analysis showed that the subgenus Fritillaria in China was divided into four major clades with obvious geographic structure. Among them, Clade I, mainly distributed in southwest China, was a young and complicated group. Moreover, according to the analysis, taxonomic treatments of the two suspicious species, namely "F. omeiensis" and "F. hupehensis" in Flora of China (2000) are questionable and might need further revision. Molecular dating revealed that both origin and divergence of subgenus Fritillaria, as well as its four major clades, were significantly associated with geological and climatic fluctuations during the Middle to Late Miocene. This study would enrich case studies of DNA super-barcode and provide new insights on speciation, lineage diversification, and biogeography of the Fritillaria in China.

Phylogenetic Analysis Reveals Distinct Evolutionary Trajectories of the Fluoroquinolones-Resistant Escherichia coli ST1193 From Fuzhou, China

Escherichia coli (E. coli) ST1193 is an emerging fluoroquinolones-resistant and virulent lineage. Large gaps remain in our understanding of the evolutionary processes and differences of this lineage. Therefore, we used 76 E. coli ST1193 genomes to detect strain-level genetic diversity and phylogeny of this lineage globally. All E. coli ST1193 possessed fimH64, filCH5, and fumC14. There was 94.7% of isolates classified as O-type O75. There was 9.33% of E. coli ST1193 that possessed K5 capsular, while 90.67% of isolates possessed K1 capsular. The core genome analysis revealed that all isolates were divided into two phylogenetic clades (clade A and B). Clade A included 25 non-Chinese E. coli ST1193, and clade B contained all isolates collected from Fuzhou, China, respectively. The results of comparative genomics indicated Indels were identified in 150 clade-specific genes, which were enriched into the biological process and molecular function. Accessory genome phylogenetic tree showed a high degree of correlation between accessory genome clusters and core genome clades. There was significant difference in antibiotic resistance genes (ARGs) [bla _CTX-M-55 , bla _TEM-1 , sul2, tet(B), tet(R), APH(6)-Id, and AAC(3)-IId], virulence factors (cia, neuC, gad, and traT), and plasmid replicon types (IncQ1, Col156, and IncB/O/K/Z) between clade A (non-Chinese isolates) and clade B (Chinese isolates) (p < 0.05). Further analysis of the genetic environments of bla _CTX-M-55 demonstrated that the flanking contexts of bla _CTX-M-55 were diverse. In conclusion, our results reveal the distinct evolutionary trajectories of the spread of E. coli ST1193 in Fuzhou, China and non-China regions. This supports both global transmission and localized lineage expansion of this lineage following specific introductions into a geographic locality.

Phylogenomic Analysis Substantiates the gyrB Gene as a Powerful Molecular Marker to Efficiently Differentiate the Most Closely Related Genera Myxococcus, Corallococcus, and Pyxidicoccus

Rapid and accurate strain identification of the most closely related genera Myxococcus, Corallococcus, and Pyxidicoccus can enhance the efficiency of the mining of novel secondary metabolites through dereplication. However, the commonly used 16S rRNA gene sequencing cannot accurately differentiate members of the three genera above, and the whole-genome sequencing is unable to rapidly and inexpensively provide species assignation toward a large number of isolates. To overcome the limitations, the gyrB gene was investigated as a candidate genetic marker for exploring the phylogenetic relationships of bacteria within the three genera and for developing the gyrB-based typing method. Here, the bacterial phylogeny and species affiliations of the three genera were determined based on the phylogenomic reconstruction and the analysis of digital DNA–DNA hybridization values among 90 genomes, further confirming nine novel taxa and assigning over one-third of genomes to defined species. The phylogenetic relationships of these strains based on the gyrB gene sequences were congruent with those based on their genome sequences, allowing the use of the gyrB gene as a molecular marker. The gyrB gene-specific primers for the PCR-amplification and sequencing of bacteria within the three genera were designed and validated for 31 isolates from our group collection. The gyrB-based taxonomic tool proved to be able to differentiate closely related isolates at the species level. Based on the newly proposed 98.6% identity threshold for the 966-bp gyrB gene and the phylogenetic inference, these isolates were assigned into two known species and eight additional putative new species. In summary, this report demonstrated that the gyrB gene is a powerful phylogenetic marker for taxonomy and phylogeny of bacteria within the closely related genera Myxococcus, Corallococcus, and Pyxidicoccus, particularly in the case of hundreds or thousands of isolates in environmental studies.

The complete chloroplast genome of Dendrobium comatum (Orchidaceae)

Dendrobium comatum is a rare orchid plant. To further its research and conservation, we reported and characterized its complete chloroplast (cp) genome by using Illumina paired-end sequencing data. We also analyzed its characteristics and studied its clustering relationships. The total chloroplast genome size was 158,008 bp, including inverted repeats (IRs) of 27,032 bp separated by a large single copy (LSC) region and a small single copy (SSC) region of 85,592 and 18,352 bp, respectively. A total of 132 genes, including 38 tRNA, 8 rRNA, and 87 protein-coding genes, were identified. Phylogenetic analysis showed that D. comatum is sister to D. kingianum with sufficient support.

The complete chloroplast genome sequence of Japanese buttercup Ranunculus japonicus Thunb

Ranunculus japonicus is an important medicinal herb widely used in East Asia. In this study, we report the first complete chloroplast genome sequence of Ranunculus japonicus using next-generation sequencing technology. The chloroplast genome size of R. japonicus was 156,981 bp. A total of 129 genes were included, consisting 84 protein-coding genes, eight rRNA genes, and 37 tRNA genes. Thirteen protein-coding genes had intron (ycf3 gene, rps12 gene, rps12 gene, clpP gene contained two introns). A further phylogenomic analysis of Ranunculaceae, including 10 taxa, was conducted for assessing the placement of R. japonicus. It will provide valuable genetic information for this medicinally important species.

Complete chloroplast genome of Chondria tumulosa (Ceramiales, Rhodophyta), a recently described cryptogenic species with invasive traits from Papahānaumokuākea Marine National Monument, Hawai'i

The complete chloroplast genome of Chondria tumulosa, a red alga from Manawai (Pearl and Hermes Atoll), Hawai‘i, was determined and analyzed using next-generation sequencing and de novo assembly approaches. The chloroplast genome sequence of C. tumulosa was 172,617 bp and contained 231 genes, consisting of 197 protein-coding genes, 29 transfer RNA genes, three ribosomal RNA genes, one transfer-messenger RNA gene, one non-coding RNA gene, and one intron inserted into the trnM gene. The number of genes and genome structure was largely similar to other members of the family Rhodomelaceae. The phylogenomic analysis of 32 complete cpDNA from the red algal order Ceramiales showed that C. tumulosa is a distinct species within the Chondrieae tribe, and is a diverging early relative to the other three available Chondria chloroplast genomes.

Natural Hybrid Origin of the Controversial "Species" Clematis × pinnata (Ranunculaceae) Based on Multidisciplinary Evidence

Interspecific hybridization is common and has often been viewed as a driving force of plant diversity. However, it raises taxonomic problems and thus impacts biodiversity estimation and biological conservation. Although previous molecular phylogenetic studies suggested that interspecific hybridization may be rather common in Clematis, and artificial hybridization has been widely applied to produce new Clematis cultivars for nearly two centuries, the issue of natural hybridization of Clematis has never been addressed in detail. In this study, we tested the hybrid origin of a mesophytic and cold-adapted vine species, Clematis pinnata, which is a rare and taxonomically controversial taxon endemic to northern China. Using field investigations, flow cytometry (FCM), phylogenomic analysis, morphological statistics, and niche modeling, we tested hybrid origin and species status of C. pinnata. The FCM results showed that all the tested species were homoploid (2n = 16). Phylonet and HyDe analyses based on transcriptome data showed the hybrid origins of C. × pinnata from either C. brevicaudata × C. heracleifolia or C. brevicaudata × C. tubulosa. The plastome phylogeny depicted that C. × pinnata in different sampling sites originated by different hybridization events. Morphological analysis showed intermediacy of C. × pinnata between its putative parental species in many qualitative and quantitative characters. Niche modeling results suggested that C. × pinnata had not been adapted to a novel ecological niche independent of its putative parents. These findings demonstrated that plants of C. × pinnata did not formed a self-evolved clade and should not be treated as a species. The present study also suggests that interspecific hybridization is a common mechanism in Clematis to generate diversity and variation, and it may play an important role in the evolution and diversification of this genus. Our study implies that morphological diversity caused by natural hybridization may overstate the real species diversity in Clematis.

Phylogenomic analysis of the chloroplast genome of the green-tide forming macroalga Ulva intestinalis Linnaeus (Ulvophyceae, Chlorophyta)

Ulva intestinalis Linnaeus 1753 (Ulvophyceae, Chlorophyta) is a marine green macroalga that is distributed on coasts of the Yellow Sea and the Bohai Sea in China. Here, the complete chloroplast genome of U. intestinalis was constructed and analyzed comparatively. The chloroplast genome of U. intestinalis is a 99,041-bp circular molecule that harbors a total of 112 genes including 71 protein-coding genes (PCGs), 26 transfer RNA genes (tRNAs), three ribosomal RNA genes (rRNAs), three free-standing open reading frames (orfs) and nine intronic orfs, and ten introns in seven genes (atpA, infA, psbB, psbC, petB, rrnL, and rrnS). The maximum likelihood (ML) phylogenomic analysis shows that U. intestinalis firstly groups with Ulva compressa, and then these two species together with the Ulva australis–Ulva fenestrata–Ulva rotundata subclade form a monophyletic clade, Ulva lineage II. U. intestinalis chloroplast genome is the only one in Ulva lineage II where the reversal of a collinear block of two genes (psbD–psbC) did not occur, and its genome structure is consistent with that of most chloroplast genomes in Ulva lineage I, indicating that the similarity of genome structure is not completely related to the genetic relationship of Ulva species. Our genomic data will facilitate the development of specific high-resolution chloroplast molecular markers for rapid identification of U. intestinalis, and help us understand its population diversity and genetic characteristics on a global scale.

Lentzea tibetensis sp. nov., a novel Actinobacterium with antimicrobial activity isolated from soil of the Qinghai-Tibet Plateau

A novel filamentous Actinobacterium, designated strain FXJ1.1311^T, was isolated from soil collected in Ngari (Ali) Prefecture, Qinghai-Tibet Plateau, western PR China. The strain showed antimicrobial activity against Gram-positive bacteria and Fusarium oxysporum. Results of phylogenetic analysis based on 16S rRNA gene sequences indicated that strain FXJ1.1311^T belonged to the genus Lentzea and showed the highest sequence similarity to Lentzea guizhouensis DHS C013^T (98.04%). Morphological and chemotaxonomic characteristics supported its assignment to the genus Lentzea. The genome-wide average nucleotide identity between strain FXJ1.1311^T and L. guizhouensis DHS C013^T as well as other Lentzea type strains was <82.2 %. Strain FXJ1.1311^T also formed a monophyletic line distinct from the known Lentzea species in the phylogenomic tree. In addition, physiological and chemotaxonomic characteristics allowed phenotypic differentiation of the novel strain from L. guizhouensis. Based on the evidence presented here, strain FXJ1.1311^T represents a novel species of the genus Lentzea, for which the name Lentzea tibetensis sp. nov. is proposed. The type strain is FXJ1.1311^T (=CGMCC 4.7383^T=DSM 104975^T).

The complete chloroplast genome of balsam aster (Aster ageratoides Turcz. var. scaberulus (Miq.) Ling., Asteraceae)

The first complete chloroplast genome of Aster ageratoides Turcz. var. scaberulus (Miq.) Ling. is reported in this study. The total chloroplast genome size of A. ageratoides var. scaberulus was 153,071 bp and comprised of a large single-copy region (LSC with 84,896 bp), a small single-copy region (SSC with 18,269 bp), and two inverted repeat regions (IR with 24,953 bp). A total of 122 genes were included in the genome, including 83 protein-coding genes, 8 rRNA genes, and 37 tRNA genes. Eleven protein-coding genes had intron (ycf3, clpP and rps12 gene contained two introns. Further phylogenomic analysis of Asteraceae, including 13 taxa, was conducted for the placement of A. ageratoides var. scaberulus.

Pseudomonas lactucae sp. nov., a pathogen causing bacterial rot of lettuce in Japan

Two phytopathogenic bacteria, MAFF 301380T and MAFF 301381, isolated from rot lesions of lettuce (Lactuca sativa L. var. capitata L.) in Japan, were characterized using a polyphasic approach. The cells were Gram-reaction-negative, aerobic, non-spore-forming, rod-shaped and motile with one to three polar flagella. Analysis of the 16S rRNA gene sequences showed that the strains belong to the genus Pseudomonas and are closely related to Pseudomonas cedrina subsp. cedrina CFML 96-198T (99.72 %), Pseudomonas cedrina subsp. fulgida P515/12T (99.65 %), Pseudomonas gessardii DSM 17152T (99.51 %), Pseudomonas synxantha DSM 18928T (99.44 %), Pseudomonas libanensis CIP 105460T (99.44 %) and Pseudomonas lactis DSM 29167T (99.44 %). The genomic DNA G+C content was 60.4 mol% and the major fatty acids consisted of summed feature 3 (C16 : 1  ω7c/C16 : 1  ω6c), C16 : 0 and summed feature 8 (C18 : 1  ω7c/C18 : 1  ω6c). Phylogenetic analysis using the rpoD gene sequences and phylogenomic analyses based on the whole genome sequences demonstrated that the strains are members of the Pseudomonas fluorescens subgroup but formed a monophyletic and robust clade separated from their closest relatives. The average nucleotide identity and digital DNA-DNA hybridization values between the strains and their closely related species were 88.65 % or less and 36.3 % or less, respectively. The strains could be distinguished from their closest relatives by phenotypic characteristics, pathogenicity towards lettuce and whole-cell MALDI-TOF MS profiles. The evidence presented in this study supports the classification of the strains as representing a novel Pseudomonas species, for which we propose the name Pseudomonas lactucae sp. nov., with the type strain MAFF 301380T (=ICMP 23838T).

Pseudomonas campi sp. nov., a nitrate-reducing bacterium isolated from grassland soil

A novel strain was isolated from grassland soil that has the potential to assimilate ammonium by the reduction of nitrate in the presence of oxygen. Whole genome sequence analysis revealed the presence of an assimilatory cytoplasmic nitrate reductase gene nasA and the assimilatory nitrite reductase genes nirBD which are involved in the sequential reduction of nitrate to nitrite and further to ammonium, respectively. Phylogenetic analysis based on 16S rRNA gene sequences revealed that the isolate represents a member of the genus Pseudomonas. The closest phylogenetic neighbours based on 16S rRNA gene sequence analysis are the type strains of Pseudomonas peli (98.17%) and Pseudomonas guineae (98.03%). In contrast, phylogenomic analysis revealed a close relationship to Pseudomonas alcaligenes. Computation of the average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) with the closest phylogenetic neighbours of S1-A32-2^T revealed genetic differences at the species level, which were further substantiated by differences in several physiological characteristics. On the basis of these results, it was concluded that the soil isolate represents a novel species of the genus Pseudomonas, for which the name Pseudomonas campi sp. nov. (type strain S1-A32-2^T=LMG 31521^T=DSM 110222^T) is proposed.

The complete chloroplast genome of Pluchea pteropoda Hemsl, a mangrove associate plant

Pluchea pteropoda Hemsl is a mangrove associate plant of Asteraceae with medicinal properties such as anti-inflammation and fever-relieving. Here, our study presented the complete chloroplast (cp) genome of Pluchea pteropoda Hemsl. The cp genome of P. pteropoda was 152,300 bp in length, including a large single copy (LSC) region of 84,127 bp, a small single copy (SSC) region of 18,093 bp and a pair of inverted repeats (IR) regions of 25,040 bp. A total of 111 unique genes were found, comprising 79 protein-coding genes, 28 tRNA genes, and 4 rRNA genes. The GC content of the cp genome was 37.5%. Phylogenetic analysis suggested that P. pteropoda nested in Pluchea clade, which was closely related to Ageratina adenophora and Senecio scandens. The work provides beneficial data for following researches on the genetic variation, species delimitation, phylogeny and classification of Pluchea genus.

Phylogenomic Analyses of Nucleotide-Sugar Biosynthetic and Interconverting Enzymes Illuminate Cell Wall Composition in Fungi

The fungi are an enormously successful eukaryotic lineage that has colonized every aerobic habitat on Earth. This spectacular expansion is reflected in the dynamism and diversity of the fungal cell wall, a matrix of polysaccharides and glycoproteins pivotal to fungal life history strategies and a major target in the development of antifungal compounds. Cell wall polysaccharides are typically synthesized by Leloir glycosyltransferases, enzymes that are notoriously difficult to characterize, but their nucleotide-sugar substrates are well known and provide the opportunity to inspect the monosaccharides available for incorporation into cell wall polysaccharides and glycoproteins. In this work, we have used phylogenomic analyses of the enzymatic pathways that synthesize and interconvert nucleotide-sugars to predict potential cell wall monosaccharide composition across 491 fungal taxa. The results show a complex evolutionary history of these cell wall enzyme pathways and, by association, of the fungal cell wall. In particular, we see a significant reduction in monosaccharide diversity during fungal evolution, most notably in the colonization of terrestrial habitats. However, monosaccharide distribution is also shown to be varied across later-diverging fungal lineages.IMPORTANCE This study provides new insights into the complex evolutionary history of the fungal cell wall. We analyzed fungal enzymes that convert sugars acquired from the environment into the diverse sugars that make up the fundamental building blocks of the cell wall. Species-specific profiles of these nucleotide-sugar interconverting (NSI) enzymes for 491 fungi demonstrated multiple losses and gains of NSI proteins, revealing the rich diversity of cell wall architecture across the kingdom. Pragmatically, because cell walls are essential to fungi, our observations of variation in sugar diversity have important implications for the development of antifungal compounds that target the sugar profiles of specific pathogens.

The complete mitochondrial genome of Downesia tarsata (Coleoptera: Chrysomelidae: Cassidinae)

Downesia species are leaf-mining beetles mainly feed on Poaceae plants in the tropical and subtropical areas in Asia. In this study, we firstly sequenced and reported the complete mitochondrial genome for the genus. The complete mitogenome of Downesia tarsata is 18,557 bp in length, including 13 protein-coding genes (PCG), 22 transfer RNA (tRNA), two ribosomal RNA (rRNA), and one AT-rich region. Phylogenomic analysis indicated that D. tarsata is closely related to Agonita chinensis, and the two species belong to the same tribe of Gonophorini. The complete mitochondrial genome of D. tarsata could help clarify the phylogenetic relationship among Cassidinae species.

The complete chloroplast genome sequence of Metabriggsia ovalifolia W. T. Wang (Gesneriaceae), a national key protected plant endemic to Karst areas in China

Metabriggsia ovalifolia W. T. Wang is one of the first-class national protected plants endemic to Karst areas in China. In this study, the complete chloroplast genome was sequenced using Illumina pair-end sequencing data. The chloroplast genome was 153,333 bp in length, consisting of a pair of inverted repeats (IRa and IRb: 25,448 bp), separated by a large single copy region (LSC: 84,381 bp) and a small single copy region (SSC: 18,056 bp). The chloroplast genome encodes 131 genes, including 87 protein-coding genes, 36 transfer RNA, and eight ribosomal RNA genes. The overall GC content of the chloroplast genome was 37.55%. M. ovalifolia phylogenetic analysis indicated close relationship with Oreocharis mileensis of Gesneriaceae family. These genomic resources will be helpful for conservation of this endemic plant species.

Pseudomonas cyclaminis sp. nov., a pathogen causing bacterial bud blight of cyclamen in Japan

Five phytopathogenic bacterial strains, MAFF 301449^T, MAFF 301450, MAFF 301451, MAFF 301452, and MAFF 301453, which were isolated from bud blight lesions of cyclamen (Cyclamen persicum Mill.) in Miyagi, Japan, were subjected to polyphasic taxonomic characterisation. The cells were Gram-reaction-negative, aerobic, non-spore-forming, motile with one to five polar flagella, and rod-shaped. Analysis of 16S rRNA gene sequences showed that they belong to the genus Pseudomonas, with Pseudomonas extremaustralis 14-3^T (99.79 % sequence similarity), Pseudomonas trivialis DSM 14937^T (99.79 %), Pseudomonas poae DSM 14936^T (99.72 %), and Pseudomonas antarctica CMS 35^T (99.72 %) as their relatives. The genomic DNA G+C content was 60.3 mol% and the major fatty acids (>5 % of the total fatty acids) were C_16 : 0, summed feature 3 (C_16 : 1 ω7c/C_16 : 1 ω6c), summed feature 8 (C_18 : 1 ω7c/C_18 : 1 ω6c), and C_17 : 0 cyclo. Phylogenetic analysis using the rpoD gene sequences and phylogenomic analyses based on the whole genome sequences demonstrated that the strains are members of the Pseudomonas fluorescens subgroup, but form a monophyletic and robust clade separated from their relatives. Average nucleotide identity and digital DNA-DNA hybridisation analyses with the closely related Pseudomonas species corroborated their novel species status. The strains were differentiated from their relatives by phenotypic characteristics, pathogenicity towards cyclamen, cellular fatty acid composition, and whole-cell MALDI-TOF mass spectrometry profiles. Based on the phenotypic, chemotaxonomic, and genotypic data obtained, we conclude that the strains represent a novel Pseudomonas species, for which we propose the name Pseudomonas cyclaminis sp. nov.; the type strain is MAFF 301449^T (=ICMP 23720^T).