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Abstract Cyathus olla, belonging to the genus Cyathus within the order Agaricales, is renowned for its bird's nest-like fruiting bodies and has been utilized in folk medicine. However, its genome remains poorly understood. To investigate genomic diversity within the genus Cyathus and elucidate biosynthetic pathways for medicinal compounds, we generated a high-quality genome assembly of C. olla with fourteen chromosomes. The comparative genome analysis revealed variations in both genomes and specific functional genes within the genus Cyathus. Phylogenomic and gene family variation analyses provided insights into evolutionary divergence, as well as genome expansion and contraction in individual Cyathus species and 36 typical Basidiomycota. Furthermore, analysis of LTR-RT and Ka/Ks revealed apparent whole-genome duplication (WGD) events its genome. Through genome mining and metabolite profiling, we identified the biosynthetic gene cluster (BGC) for cyathane diterpenes from C. olla. Furthermore, we predicted 32 BGCs, containing 41 core genes, involved in other bioactive metabolites. These findings represent a valuable genomic resource that will enhance our understanding of Cyathus species genetic diversity. The genome analysis of C. olla provides insights into the biosynthesis of medicinal compounds and establishes a fundamental basis for future investigations into the genetic basis of chemodiversity in this significant medicinal fungus.

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Cyathus olla, belonging to the genus Cyathus within the order Agaricales, is renowned for its bird's nest-like fruiting bodies and has been utilized in folk medicine. However, its genome remains poorly understood. To investigate genomic diversity within the genus Cyathus and elucidate biosynthetic pathways for medicinal compounds, we generated a high-quality genome assembly of C. olla with fourteen chromosomes. The comparative genome analysis revealed variations in both genomes and specific functional genes within the genus Cyathus. Phylogenomic and gene family variation analyses provided insights into evolutionary divergence, as well as genome expansion and contraction in individual Cyathus species and 36 typical Basidiomycota. Furthermore, analysis of LTR-RT and Ka/Ks revealed apparent whole-genome duplication (WGD) events its genome. Through genome mining and metabolite profiling, we identified the biosynthetic gene cluster (BGC) for cyathane diterpenes from C. olla. Furthermore, we predicted 32 BGCs, containing 41 core genes, involved in other bioactive metabolites. These findings represent a valuable genomic resource that will enhance our understanding of Cyathus species genetic diversity. The genome analysis of C. olla provides insights into the biosynthesis of medicinal compounds and establishes a fundamental basis for future investigations into the genetic basis of chemodiversity in this significant medicinal fungus. [ABSTRACT FROM AUTHOR]

Tomato grey leaf spot is a fungal disease that provokes losses in tomato yield. The aim of this work is to analyse genomic differences among three isolates of Stemphylium lycopersici that differ in virulence and sporulation. The bioinformatics analysis led us to predict the identity of putative effectors, pathogenesis and virulence factors. Like the genome of other necrotrophic pathogens, Stemphylium encodes a wide spectrum of effectors, including an ample and diverse array of carbohydrate‐degrading enzymes. Interestingly, the number of predicted effectors was unrelated to virulence. Low virulence appeared to be associated with the presence of several double‐stranded RNAs from viruses as well as cellular processes related to protein degradation, redox and detoxifying processes and monoterpenes production. This is the first identification of the potential effectors of tomato–S. lycopersici interaction; nonetheless functional studies should be done. [ABSTRACT FROM AUTHOR]

Bamboo witches’ broom disease (WBD), caused by Aciculosporium take Miyake, devastates bamboo forests. Understanding the genome and pathogenic factors of pathogen is crucial for disease control. We employed single-molecule real-time sequencing, Illumina paired-end sequencing, and chromatin interaction mapping techniques to assemble the genome of A. take CCTCC-M2023413, analyze pathogenicity- and phytohormone-biosynthesis-related genes, and compare it to 12 other WBD pathogens. The genome of A. take is 59.24 Mb in size, with 54.32% repeats, 7 chromosomes, 7,105 protein-coding genes, 84 ribosomal RNAs, and 115 transfer RNAs. Predictive analysis of pathogenicity genes found 237 carbohydrate-active enzymes, 1,069 membrane transport proteins, 1,040 pathogen-host interaction genes, 315 virulence factors, and 70 effectors. Most of pathogenicity genes overlapped with repeat-rich regions. Additionally, 172 genes were linked to auxin biosynthesis, 53 to brassinosteroid biosynthesis, and 2 to cis-zeatin biosynthesis. Comparative genomic analysis identified 77 core orthogroups shared by 13 WBD pathogens, played roles in metabolites, genetic information processing, pathogenesis, cis-zeatin biosynthesis, lifespan, and quorum sensing. The miaA gene, crucial for cis-zeatin biosynthesis, is structurally conserved and sequence-diverse among 13 WBD pathogens, with upregulated expression during bamboo WBD pathogenesis. This highlights that cis-zeatin is significant contributor to host pathogenesis, and miaA is a new potential target for controlling WBD. This study provides important insights on preventing and controlling bamboo WBD.

Desert environments harbor unique microbial communities. This study focuses on Cellulosimicrobium funkei isolate RVMD1, isolated from rock varnish in the Ma’an Desert. Initial identification was achieved using 16S rRNA gene sequencing, followed by whole-genome sequencing (WGS) for comprehensive characterization. The genome comprises 4,264,015 base pairs (857 contigs) with a high G + C content of 74.59%. A total of 4,449 proteins were predicted. Comparative analysis utilizing OrthoANI, ANI, AAI, and dDDH metrics suggests that RVMD1 belongs to the C. cellulans group, with the highest similarity to C. funkei (97.71% ANI). Phylogenomic analysis of 43 Cellulosimicrobium genomes revealed significant heterogeneity within the genus. Our results challenge current systematics, with C. cellulans potentially representing up to 9 distinct genomospecies. Isolate RVMD1 shows genetic adaptations to its desert environment, including genes for denitrification, oxygen and sulfur cycling, and diverse hydrogen metabolism. Pangenomic analysis uncovered a considerable number of unique genes within RVMD1, highlighting its genetic distinctiveness. Gene family expansions suggest evolution in response to stressors like UV radiation and nutrient limitation. This study represents the first whole-genome analysis of a bacterium isolated from Jordanian rock varnish, emphasizing the value of WGS in understanding microbial diversity and adaptation in extreme environments.

The Pseudomonas aeruginosa genome can change to adapt to different ecological niches. We compared four genomes from a Mexican hospital and 59 genomes from GenBank from different niches, such as urine, sputum, and environmental. The ST analysis showed that high-risk STs (ST235, ST773, and ST27) were present in the genomes of the three niches from GenBank, and the STs of Mexican genomes (ST167, ST2731, and ST549) differed from the GenBank genomes. Phylogenetic analysis showed that the genomes were clustering according to their ST and not their niche. When analyzing the genomic content, we observed that environmental genomes had genes involved in adapting to the environment not found in the clinics and that their mechanisms of resistance were mutations in antibiotic resistance-related genes. In contrast, clinical genomes from GenBank had resistance genes, in mobile/mobilizable genetic elements in the chromosome, except for the Mexican genomes that carried them mostly in plasmids. This was related to the presence of CRISPR-Cas and anti-CRISPR; however, Mexican strains only had plasmids and CRISPR-Cas. blaOXA-488 (a variant of blaOXA50) with higher activity against carbapenems was more prevalent in sputum genomes. The virulome analysis showed that exoS was most prevalent in the genomes of urinary samples and exoU and pldA in sputum samples. This study provides evidence regarding the genetic variability among P. aeruginosa isolated from different niches.

SUMMARY: Cryptotaenia japonica, a traditional medicinal and edible vegetable crops, is well‐known for its attractive flavors and health care functions. As a member of the Apiaceae family, the evolutionary trajectory and biological properties of C. japonica are not clearly understood. Here, we first reported a high‐quality genome of C. japonica with a total length of 427 Mb and N50 length 50.76 Mb, was anchored into 10 chromosomes, which confirmed by chromosome (cytogenetic) analysis. Comparative genomic analysis revealed C. japonica exhibited low genetic redundancy, contained a higher percentage of single‐cope gene families. The homoeologous blocks, Ks, and collinearity were analyzed among Apiaceae species contributed to the evidence that C. japonica lacked recent species‐specific WGD. Through comparative genomic and transcriptomic analyses of Apiaceae species, we revealed the genetic basis of the production of anthocyanins. Several structural genes encoding enzymes and transcription factor genes of the anthocyanin biosynthesis pathway in different species were also identified. The CjANSa, CjDFRb, and CjF3H gene might be the target of Cjaponica_2.2062 (bHLH) and Cjaponica_1.3743 (MYB). Our findings provided a high‐quality reference genome of C. japonica and offered new insights into Apiaceae evolution and biology. Significance Statement: Our results indicated how the genome of C. japonica provided a useful model for studying evolutionary trajectory and biological properties in Apiaceae species. Our findings are helpful for enriching genome research of Apiaceae family. [ABSTRACT FROM AUTHOR]

Molecular studies about cyanide biodegradation have been mainly focused on the hydrolytic pathways catalyzed by the cyanide dihydratase CynD or the nitrilase NitC. In some Pseudomonas strains, the assimilation of cyanide has been linked to NitC, such as the cyanotrophic model strain Pseudomonas pseudoalcaligenes CECT 5344, which has been recently reclassified as Pseudomonas oleovorans CECT 5344. In this work, a phylogenomic approach established a more precise taxonomic position of the strain CECT 5344 within the species P. oleovorans. Furthermore, a pan-genomic analysis of P. oleovorans and other species with cyanotrophic strains, such as P. fluorescens and P. monteilii, allowed for the comparison and identification of the cioAB and mqoAB genes involved in cyanide resistance, and the nitC and cynS genes required for the assimilation of cyanide or cyanate, respectively. While cyanide resistance genes presented a high frequency among the analyzed genomes, genes responsible for cyanide or cyanate assimilation were identified in a considerably lower proportion. According to the results obtained in this work, an in silico approach based on a comparative genomic approach can be considered as an agile strategy for the bioprospection of putative cyanotrophic bacteria and for the identification of new genes putatively involved in cyanide biodegradation. [ABSTRACT FROM AUTHOR]

Key message: This study provides novel insights into the evolution, diversification, and functions of melatonin biosynthesis genes in Prunus species, highlighting their potential role in regulating bud dormancy and abiotic stresses. The biosynthesis of melatonin (MEL) in plants is primarily governed by enzymatic reactions involving key enzymes such as serotonin N-acetyltransferase (SNAT), tryptamine 5-hydroxylase (T5H), N-acetylserotonin methyltransferase (ASMT) and tryptophan decarboxylase (TDC). In this study, we analyzed Melatonin genes in four Prunus species such as Prunus avium (Pavi), Prunus pusilliflora (Ppus), Prunus serulata (Pser), and Prunus persica (Pper) based on comparative genomics approach. Among the four Prunus species, a total of 29 TDCs, 998 T5Hs, 16 SNATs, and 115 ASMTs within the genome of four Prunus genomes. A thorough investigation of melatonin-related genes was carried out using systematic biological methods and comparative genomics. Through phylogenetic analysis, orthologous clusters, Go enrichment, syntenic relationship, and gene duplication analysis, we discovered both similarities and variations in Melatonin genes among these Prunus species. Additionally, our study revealed the existence of unique subgroup members in the Melatonin genes of these species, which were distinct from those found in Arabidopsis genes. Furthermore, the transcriptomic expression analysis revealed the potential significance of melatonin genes in bud dormancy regulation and abiotic stresses. Our extensive results offer valuable perspectives on the evolutionary patterns, intricate expansion, and functions of PavMEL genes. Given their promising attributes, PavTDCs, PavT5H, PavNAT, and three PavASMT genes warrant in-depth exploration as prime candidates for manipulating dormancy in sweet cherry. This was done to lay the foundation for future explorations into the structural and functional aspects of these factors in Prunus species. This study offers significant insights into the functions of ASMT, SNAT, T5H, and TDC genes and sheds light on their roles in Prunus avium. Moreover, it established a robust foundation for further exploration functional characterization of melatonin genes in fruit species. [ABSTRACT FROM AUTHOR]

Simple Summary: Cervidae represents a substantial family within the Artiodactyla, yet their phylogenetic relationship has not been fully clarified due to limited data available. With the increasing availability of genomic data, there is now an opportunity to further explore their phylogenetic relationship. In our study, we employed a comparative genomics approach focusing on the chromosome-level genomes of eight Cervidae species to explore their phylogenetic relationship and chromosomal evolutionary events. Furthermore, we conducted an analysis of gene families to identify those potentially involved in adaptive evolution. Cervidae represents a family that is not only rich in species diversity but also exhibits a wide range of karyotypes. The controversies regarding the phylogeny and classification of Cervidae still persist. The flourishing development of the genomic era has made it possible to address these issues at the genomic level. Here, the genomes of nine species were used to explore the phylogeny and chromosomal evolutionary events of Cervidae. By conducting whole-genome comparisons, we identified single-copy orthologous genes across the nine species and constructed a phylogenetic tree based on the single-copy orthologous genes sequences, providing new insights into the phylogeny of Cervidae, particularly the phylogenetic relationship among sika deer, red deer, wapiti and Tarim red deer. Gene family analysis revealed contractions in the olfactory receptor gene family and expansions in the histone gene family across eight Cervidae species. Furthermore, synteny analysis was used to explore the chromosomal evolutionary events of Cervidae species, revealing six chromosomal fissions during the evolutionary process from Bovidae to Cervidae. Notably, specific chromosomal fusion events were found in four species of Cervus, and a unique chromosomal fusion event was identified in Muntiacus reevesi. Our study further completed the phylogenetic relationship within the Cervidae and demonstrated the feasibility of inferring species phylogeny at the whole-genome level. Additionally, our findings on gene family evolution and the chromosomal evolutionary events in eight Cervidae species lay a foundation for comprehensive research of the evolution of Cervidae. [ABSTRACT FROM AUTHOR]

Cryobacterium spp. are Gram-positive bacteria that inhabit diverse geographical locations, particularly extremely cold environments like the Polar Regions. However, strategies that enable them to survive in harsh Antarctic environments are not fully understood. In this study, we conducted a comparative genomic analysis of the Antarctic Cryobacterium sp. SO2 as well as other members of the Cryobacterium genus. Phylogenetic analysis revealed that strain SO2 formed a distinct cluster with the validly described species: C. adonitolivorans, C. lactosi, C. soli, C. arcticum, and C. zongtaii. Comparative analysis based on ANI and AAI indicated that strain SO2 is a novel species. Relative Synonymous Codon Usage (RSCU) of Cryobacterium species exhibits a bias towards codon ending with G/C. The genomes of all strains harbored numerous genes associated with environmental-associated stress responses, including oxidative stress response, general stress response, heat-stress response, cold-stress response, cell envelope alteration, and osmotic stress response. Strain SO2 and related strains possess genes involved in breaking down and utilization of both plant and animal carbohydrate-containing materials. KEGG annotation indicated that strain SO2 and related species shared almost the same genes for the metabolism of trehalose (TreS, partial TPS/TPP, and TreY-TreZ pathway) and glycogen (classical and non-classical pathway). The results from this work helped us to better understand the genomic characteristics of Cryobacterium spp. in terms of genomic diversity and adaptation strategies, which may have significant implications for biotechnology and climate change research. [ABSTRACT FROM AUTHOR]

ABSTRACTCysteiniphilum is a newly discovered genus in 2017 and is phylogenetically closely related to highly pathogenic Francisella tularensis. Recently, it has become an emerging pathogen in humans. However, the complete genome sequence of genus Cysteiniphilum is lacking, and the genomic characteristics of genetic diversity, evolutionary dynamics, and pathogenicity have not been characterized. In this study, the complete genome of the first reported clinical isolate QT6929 of genus Cysteiniphilum was sequenced, and comparative genomics analyses to Francisella genus were conducted to unveil the genomic landscape and diversity of the genus Cysteiniphilum. Our results showed that the complete genome of QT6929 consists of one 2.61 Mb chromosome and a 76,819 bp plasmid. The calculated average nucleotide identity and DNA–DNA hybridization values revealed that two clinical isolates QT6929 and JM-1 should be reclassified as two novel species in genus Cysteiniphilum. Pan-genome analysis revealed genomic diversity within the genus Cysteiniphilum and an open pan-genome state. Genomic plasticity analysis exhibited abundant mobile genetic elements including genome islands, insertion sequences, prophages, and plasmids on Cysteiniphilum genomes, which facilitated the broad exchange of genetic material between Cysteiniphilum and other genera like Francisella and Legionella. Several potential virulence genes associated with lipopolysaccharide/lipooligosaccharide, capsule, and haem biosynthesis specific to clinical isolates were predicted and might contribute to their pathogenicity in humans. Incomplete Francisella pathogenicity island was identified in most Cysteiniphilum genomes. Overall, our study provides an updated phylogenomic relationship of members of the genus Cysteiniphilum and comprehensive genomic insights into this rare emerging pathogen.

A Whole Genome Duplication (WGD) event occurred several Ma in a Rosaceae ancestor, giving rise to the Maloideae subfamily which includes today many pome fruits such as pear (Pyrus communis) and apple (Malus domestica). This complete and well-conserved genome duplication makes the apple an organism of choice to study the early evolutionary events occurring to ohnologous chromosome fragments. In this study, we investigated gene sequence evolution and expression, transposable elements (TE) density, and DNA methylation level. Overall, we identified 16,779 ohnologous gene pairs in the apple genome, confirming the relatively recent WGD. We identified several imbalances in QTL localization among duplicated chromosomal fragments and characterized various biases in genome fractionation, gene transcription, TE densities, and DNA methylation. Our results suggest a particular chromosome dominance in this autopolyploid species, a phenomenon that displays similarities with subgenome dominance that has only been described so far in allopolyploids. [ABSTRACT FROM AUTHOR]

Molecular studies about cyanide biodegradation have been mainly focused on the hydrolytic pathways catalyzed by the cyanide dihydratase CynD or the nitrilase NitC. In some Pseudomonas strains, the assimilation of cyanide has been linked to NitC, such as the cyanotrophic model strain Pseudomonas pseudoalcaligenes CECT 5344, which has been recently reclassified as Pseudomonas oleovorans CECT 5344. In this work, a phylogenomic approach established a more precise taxonomic position of the strain CECT 5344 within the species P. oleovorans. Furthermore, a pan-genomic analysis of P. oleovorans and other species with cyanotrophic strains, such as P. fluorescens and P. monteilii, allowed for the comparison and identification of the cioAB and mqoAB genes involved in cyanide resistance, and the nitC and cynS genes required for the assimilation of cyanide or cyanate, respectively. While cyanide resistance genes presented a high frequency among the analyzed genomes, genes responsible for cyanide or cyanate assimilation were identified in a considerably lower proportion. According to the results obtained in this work, an in silico approach based on a comparative genomic approach can be considered as an agile strategy for the bioprospection of putative cyanotrophic bacteria and for the identification of new genes putatively involved in cyanide biodegradation.

Cervidae represents a family that is not only rich in species diversity but also exhibits a wide range of karyotypes. The controversies regarding the phylogeny and classification of Cervidae still persist. The flourishing development of the genomic era has made it possible to address these issues at the genomic level. Here, the genomes of nine species were used to explore the phylogeny and chromosomal evolutionary events of Cervidae. By conducting whole-genome comparisons, we identified single-copy orthologous genes across the nine species and constructed a phylogenetic tree based on the single-copy orthologous genes sequences, providing new insights into the phylogeny of Cervidae, particularly the phylogenetic relationship among sika deer, red deer, wapiti and Tarim red deer. Gene family analysis revealed contractions in the olfactory receptor gene family and expansions in the histone gene family across eight Cervidae species. Furthermore, synteny analysis was used to explore the chromosomal evolutionary events of Cervidae species, revealing six chromosomal fissions during the evolutionary process from Bovidae to Cervidae. Notably, specific chromosomal fusion events were found in four species of Cervus, and a unique chromosomal fusion event was identified in Muntiacus reevesi. Our study further completed the phylogenetic relationship within the Cervidae and demonstrated the feasibility of inferring species phylogeny at the whole-genome level. Additionally, our findings on gene family evolution and the chromosomal evolutionary events in eight Cervidae species lay a foundation for comprehensive research of the evolution of Cervidae.

The metabolic versatility of Levilactobacillus brevis, a heterofermentative lactic acid bacterium, could benefit environmentally compatible and low salt cucumber fermentation. The biodiversity of Lvb. brevis autochthonous to cucumber fermentation was studied using genotypic and phenotypic analyses to identify unique adjunct cultures. A group of 131 isolates autochthonous to industrial fermentations was screened using rep-PCR-(GTG)5 and a fermentation ability assay under varied combinations of salt (0 or 6%), initial pH (4.0 or 5.2), and temperature (15 or 30◦C). No apparent similarities were observed among the seven and nine clusters in the genotypic and phenotypic dendrograms, respectively. A total of 14 isolates representing the observed biodiversity were subjected to comparative genome analysis. The autochthonous Lvb. brevis clustered apart from allochthonous isolates, as their genomes lack templates for citrate lyase, several putative hypothetical proteins, and some plasmid- and phage-associated proteins. Four and two representative autochthonous and allochthonous Lvb. brevis, respectively, were subjected to phenotype microarray analysis using an Omnilog. Growth of all Lvb. brevis strains was supported to various levels by glucose, fructose, gentiobiose, 1,2-propanediol, and propionic acid, whereas the allochthonous isolate ATCC14890 was unique in utilizing citric acid. All the Lvb. brevis genomes encode for 1,2-propanediol utilization microcompartments. This study identified a unique Lvb. brevis strain, autochthonous to cucumber, as a potential functional adjunct culture for commercial fermentation that is distinct in metabolic activities from allochthonous isolates of the same species. [ABSTRACT FROM AUTHOR]

Inonotus hispidus mainly growing in broad-leaved trees, including Morus alba, Fraxinus mandshurica, and Ulmus macrocarpa etc. The fruiting body of I. hispidus growing in M. alba (hereafter as MA) is used as a traditional Chinese medicine "Sanghuang". However, differences between the genetic material basis of I. hispidus growing in other tree species have not been reported. Therefore, in this paper, the genomic comparison between MA and I. hispidus growing in F. mandshurica (hereafter as FM) were studied. The whole genome of MA monokaryon was sequenced by Illumina combined with Pac Bio platform. Next, genome assembly, genome component prediction and genome functional annotation were performed. Comparative genomics analysis was performed between FM monokaryon and MA monokaryon, using MA as the reference. The results showed that, MA had 24 contigs with a N50 length of 2.6 Mb. Specifically, 5,342, 6,564, 1,595, 383 and 123 genes were annotated from GO, KEGG, KOG, CAZymes and CYP450, respectively. Moreover, comparative genomics showed that, the coding genes and total number of genes annotated in different databases of FM were higher than that of MA. This study provides a foundation for the medicinal application of FM as MA from the perspective of genetic composition. [ABSTRACT FROM AUTHOR]

Precise classification of foodborne pathogen Listeria monocytogenes is a necessity in efficient foodborne disease surveillance, outbreak detection, and source tracking throughout the food chain. In this study, a total of 150 L. monocytogenes isolates from various food products, food processing environments, and clinical sources were investigated for variations in virulence, biofilm formation, and the presence of antimicrobial resistance genes based on their Whole-Genome Sequences. Clonal complex (CC) determination based on Multi-Locus Sequence Typing (MLST) revealed twenty-eight CC-types including eight isolates representing novel CC-types. The eight isolates comprising the novel CC-types share the majority of the known (cold and acid) stress tolerance genes and are all genetic lineage II, serogroup 1/2a-3a. Pan-genome-wide association analysis by Scoary using Fisher's exact test identified eleven genes specifically associated with clinical isolates. Screening for the presence of antimicrobial and virulence genes using the ABRicate tool uncovered variations in the presence of Listeria Pathogenicity Islands (LIPIs) and other known virulence genes. Specifically, the distributions of actA, ecbA, inlF, inlJ, lapB, LIPI-3, and vip genes across isolates were found to be significantly CC-dependent while the presence of ami, inlF, inlJ, and LIPI-3 was associated with clinical isolates specifically. In addition, Roary-derived phylogenetic grouping based on Antimicrobial-Resistant Genes (AMRs) revealed that the thiol transferase (FosX) gene was present in all lineage I isolates, and the presence of the lincomycin resistance ABC-F-type ribosomal protection protein (lmo0919_fam) was also genetic-lineage-dependent. More importantly, the genes found to be specific to CC-type were consistent when a validation analysis was performed with fully assembled, high-quality complete L. monocytogenes genome sequences (n = 247) extracted from the National Centre for Biotechnology Information (NCBI) microbial genomes database. This work highlights the usefulness of MLST-based CC typing using the Whole-Genome Sequence as a tool in classifying isolates. [ABSTRACT FROM AUTHOR]

Blepharoglossum is a rare orchid genus of the Malaxidinae primarily distributed in tropical Pacific islands, with several species occurring in the Taiwan and Hainan Islands of China. Currently, the monophyletic status of Blepharoglossum has been challenged, and the phylogenetic relationships among its allied groups have remained unresolved with traditional DNA markers. In this study, we initially sequenced and annotated the chloroplast (cp) genomes of two Blepharoglossum species, Blepharoglossum elegans (Lindl.) L. Li and Blepharoglossum grossum (Rchb.f.) L. Li. These cp genomes of Blepharoglossum share the typical quadripartite and circular structure. Each of the genomes encodes a total of 133 functional genes, including 87 protein-coding genes (CDS), 38 tRNA genes and 8 rRNA genes. By comparing the sequence differences between these two cp genomes, it was found that they are relatively conserved in terms of overall gene content and gene arrangement. However, a total of 684 SNPs and 2664 indels were still identified, with ycf1, clpP, and trnK-UUU protein-coding genes having the highest number of SNPs and indels. In further comparative analyses among the six cp genomes in Malaxidinae, significant sequence divergences were identified in the intergenic regions, namely rps16–trnQ-UUG, trnS-GCU–trnG-GCC, rpoB–trnC-GCA, trnE-UUC–trnT-GGU, trnF-GAA–trnV-UAC, atpB–rbcL, petA–psbJ, psbE–petL, psbB–psbT, trnN-GUU–rpl32, trnV-GAC–rps7, and rps7–trnL-CAA, and five coding regions, including matK, and rpoC2, ycf1, and two ycf2 genes. Phylogenetic analysis indicated that Blepharoglossum and Oberonia form a highly supported sister group relationship. Our results are consistent with previous studies and present increased resolution among major clades. [ABSTRACT FROM AUTHOR]

Polar regions tend to support simple food webs, which are vulnerable to phage-induced gene transfer or microbial death. To further investigate phage-host interactions in polar regions and the potential linkage of phage communities between the two poles, we induced the release of a lysogenic phage, vB_PaeM-G11, from Pseudomonas sp. D3 isolated from the Antarctic, which formed clear phage plaques on the lawn of Pseudomonas sp. G11 isolated from the Arctic. From permafrost metagenomic data of the Arctic tundra, we found the genome with high-similarity to that of vB_PaeM-G11, demonstrating that vB_PaeM-G11 may have a distribution in both the Antarctic and Arctic. Phylogenetic analysis indicated that vB_PaeM-G11 is homologous to five uncultured viruses, and that they may represent a new genus in the Autographiviridae family, named Fildesvirus here. vB_PaeM-G11 was stable in a temperature range (4–40 °C) and pH (4–11), with latent and rise periods of about 40 and 10 min, respectively. This study is the first isolation and characterization study of a Pseudomonas phage distributed in both the Antarctic and Arctic, identifying its lysogenic host and lysis host, and thus provides essential information for further understanding the interaction between polar phages and their hosts and the ecological functions of phages in polar regions. [ABSTRACT FROM AUTHOR]

The metabolic versatility of Levilactobacillus brevis, a heterofermentative lactic acid bacterium, could benefit environmentally compatible and low salt cucumber fermentation. The biodiversity of Lvb. brevis autochthonous to cucumber fermentation was studied using genotypic and phenotypic analyses to identify unique adjunct cultures. A group of 131 isolates autochthonous to industrial fermentations was screened using rep-PCR-(GTG)5 and a fermentation ability assay under varied combinations of salt (0 or 6%), initial pH (4.0 or 5.2), and temperature (15 or 30°C). No apparent similarities were observed among the seven and nine clusters in the genotypic and phenotypic dendrograms, respectively. A total of 14 isolates representing the observed biodiversity were subjected to comparative genome analysis. The autochthonous Lvb. brevis clustered apart from allochthonous isolates, as their genomes lack templates for citrate lyase, several putative hypothetical proteins, and some plasmid- and phage-associated proteins. Four and two representative autochthonous and allochthonous Lvb. brevis, respectively, were subjected to phenotype microarray analysis using an Omnilog. Growth of all Lvb. brevis strains was supported to various levels by glucose, fructose, gentiobiose, 1,2-propanediol, and propionic acid, whereas the allochthonous isolate ATCC14890 was unique in utilizing citric acid. All the Lvb. brevis genomes encode for 1,2-propanediol utilization microcompartments. This study identified a unique Lvb. brevis strain, autochthonous to cucumber, as a potential functional adjunct culture for commercial fermentation that is distinct in metabolic activities from allochthonous isolates of the same species.

Brassica oleracea displays remarkable morphological variations. It intrigued researchers to study the underlying cause of the enormous diversification of this organism. However, genomic variations in complex heading traits are less known in B. oleracea. Herein, we performed a comparative population genomics analysis to explore structural variations (SVs) responsible for heading trait formation in B. oleracea. Synteny analysis showed that chromosomes C1 and C2 of B. oleracea (CC) shared strong collinearity with A01 and A02 of B. rapa (AA), respectively. Two historical events, whole genome triplication (WGT) of Brassica species and differentiation time between AA and CC genomes, were observed clearly by phylogenetic and Ks analysis. By comparing heading and non-heading populations of B. oleracea genomes, we found extensive SVs during the diversification of the B. oleracea genome. We identified 1205 SVs that have an impact on 545 genes and might be associated with the heading trait of cabbage. Overlapping the genes affected by SVs and the differentially expressed genes identified by RNA-seq analysis, we identified six vital candidate genes that may be related to heading trait formation in cabbage. Further, qRT-PCR experiments also verified that six genes were differentially expressed between heading leaves and non-heading leaves, respectively. Collectively, we used available genomes to conduct a comparison population genome analysis and identify candidate genes for the heading trait of cabbage, which provides insight into the underlying reason for heading trait formation in B. oleracea. [ABSTRACT FROM AUTHOR]

Horseshoe crabs are famous for their blood lysate that is extensively used for the detection of bacterial endotoxin contamination in injectable drugs and medical equipment. However, their existence is now threatened because of overexploitation for bleeding. Synthetic antimicrobial peptides or proteins created by bioengineering may be effective in solving the present predicament. Factor D (FD) is a bioactive substance that shows significant sensitivity to gram-negative bacteria. However, little is known about the expansion information of FD orthologs. In the present study, a total of nine FD orthologs were detected in horseshoe crabs according to the reference genomes. The composition of the FD orthologs in different species was highly conserved, although the common ancestor of the extant horseshoe crabs dates back to the Silurian period. These data suggested that the composition of FD orthologs in horseshoe crabs was formed before the speciation of these species. Considering that three rounds of whole-genome duplication (WGD) events may expanded the homologs in horseshoe crabs, while only one pair of FD orthologs showed significant collinearity according to the intraspecies comparative analysis. Unexpectedly, tandem duplication events that occurred before speciation also expanded the FD orthologs. In addition, several separately distributed FD orthologs also showed high conservation with each other. These data revealed that transposon-mediated duplication may have expanded the FD orthologs in horseshoe crabs. Intriguingly, the C-terminus of the FD orthologs is extremely conserved, although the expansion occurred more than 400 million years ago. In summary, our research provides evidence for the duplication of FD orthologs in horseshoe crabs. Additionally, by demonstrating the conservation of the segments in the C-terminus of these duplicated orthologs, our results also contributed to understanding the functional differentiation mechanism of the diversified FD orthologs. [ABSTRACT FROM AUTHOR]

Simple Summary: In this study, we conducted a comparative genomics approach to explore the convergent evolution of high-altitude adaptation mechanisms in six independently evolved mammals belonging to four orders. The results showed that the convergent evolution of the six species was mainly reflected at the level of rapidly evolving genes, and the functions of these rapidly evolving genes were mainly related to hypoxia response and DNA damage repair. In addition, we found that the convergence of the gene family contraction of high-altitude species is much greater than that of expansion, revealing a possible pattern of species in adapting to high-altitude. Furthermore, we detected a positive selection signature in four genes related to hypoxia response and ultraviolet radiation damage in these six species (FYCO1, ERBIN, SCAMP1 and CXCL10). In general, our study reveals that hypoxia response and UV-radiation might play an important role in the adaptation of independently evolved species to a high-altitude environment, providing a basic perspective for further exploring the high-altitude adaptation mechanism of different related species in the future. The species living in the Qinghai-Tibet Plateau provide an excellent model system for studying the relationship between molecular convergent evolution and adaptation. Distant species experiencing the same selection pressure (i.e., hypoxia, low temperature and strong ultraviolet radiation) are likely to evolve similar genetic adaptations independently. Here, we performed comparative genomics studies on six independently evolved high-altitude species. The results also showed that the convergent evolution of the six species was mainly reflected at the level of rapidly evolving genes, and the functions of these rapidly evolving genes were mainly related to hypoxia response and DNA damage repair. In addition, we found that high-altitude species had more gene family changes than their low-altitude relatives, except for the order Lagomorpha. The results also show that the convergence of the gene family contraction of high-altitude species is much greater than that of expansion, revealing a possible pattern of species in adapting to high-altitude. Furthermore, we detected a positive selection signature in four genes related to hypoxia response and ultraviolet radiation damage in these six species (FYCO1, ERBIN, SCAMP1 and CXCL10). Our study reveals that hypoxia response might play an important role in the adaptation of independently evolved species to a high-altitude environment, providing a basic perspective for further exploring the high-altitude adaptation mechanism of different related species in the future. [ABSTRACT FROM AUTHOR]

Sugarcane (Saccharum sp.) is potential as a biofuel and biomaterial source for its high cellulose content. Cellulose is the main constituent of the plant cell wall, as a linear chain arranged in a polysaccharide bundle, called cellulose microfibril. A gene named COBRA has been revealed to play role in the orientation of microfibril and cellulose crystallization. The COBRA gene in the Saccharum spp is under-explored. Therefore, the in silico study was conducted to explore the COBRA gene in Saccharum sp. By comparative genomics methods, the COBRA genes from Arabidopsis sp. (AtCOBLs) were compared to the Saccharum sp. (SoCOBLs). The conserved domain was then identified and the cluster system was constructed under a phylogenetic tree. Furthermore, each SoCOBLs protein was modelled to analyze its structure. According to the analysis, eleven of Saccharum sp. genomic scaffolds were successfully identified. Moreover, conserved domain identification resulted in nine SoCOBLs proteins. The phylogenetic tree showed two main clusters: I and II, differentiating those COBLs families based on the protein sequence, domain motif and amino acid properties. It leads to the variation of SoCOBLs protein structure as the results of the amino acid properties. Overall, the COBRA gene has been identified genomically in Saccharum sp. Yet, the function and tissue-specific expression are still unclear. It was predicted to act as the regulator of microfibril orientation and the cellulose synthesis process. Hence, further analyses by in vitro and in vivo are indispensable.

Fungal-plant interactions have persisted for 460 million years, and almost all terrestrial plants on Earth have endophytic fungi. However, the mechanism of symbiosis between endophytic fungi and host plants has been inconclusive. In this dissertation, we used a strain of endophytic Fusarium lateritium (Fl617), which was found in the previous stage to promote disease resistance in tomato, and selected the pathogenic Fusarium oxysporum Fo4287 and endophytic Fusarium oxysporum Fo47, which are in the same host and the closest relatives of Fl617, to carry out a comparative genomics analysis of the three systems and to provide a new perspective for the elucidation of the special lifestyle of the fungal endophytes. We found that endophytic F. lateritium has a smaller genome, fewer clusters and genes associated with pathogenicity, and fewer plant cell wall degrading enzymes (PCWDEs). There were also relatively fewer secondary metabolisms and typical Fusarium spp. toxins, and a lack of the key Fusarium spp. pathogenicity factor, secreted in xylem (SIX), but the endophytic fungi may be more sophisticated in their regulation of the colonization process. It is hypothesized that the endophytic fungi may have maintained their symbiosis with plants due to the relatively homogeneous microenvironment in plants for a long period of time, considering only plant interactions and discarding the relevant pathogenicity factors, and that their endophytic evolutionary tendency may tend to be genome streamlining and to enhance the fineness of the regulation of plant interactions, thus maintaining their symbiotic status with plants. • Genome of Fusarium lateritium Fl617 was sequenced and analyzed. • The Fl617 genome contained less virulence and pathogenesis related genes. • Comparative genomic analysis provides new insights for dissecting the molecular mechanisms of Fl617 endocytosis in plants. [ABSTRACT FROM AUTHOR]

Abstract Background Mobile colistin resistance like gene (mcr-like gene) is a new type of polymyxin resistance gene that can be horizontally transferred in the Enterobacteriaceae. This has brought great challenges to the treatment of multidrug-resistant Escherichia coli and K. pneumoniae. Results K. pneumoniae 16BU137 and E. coli 17MR471 were isolated from the bus and subway handrails in Guangzhou, China. K. pneumoniae 19PDR22 and KP20191015 were isolated from patients with urinary tract infection and severe pneumonia in Anhui, China. Sequence analysis indicated that the mcr-1.1 gene was present on the chromosome of E. coli 17MR471, and the gene was in the gene cassette containing pap2 and two copies of ISApl1.The mcr-1.1 was found in the putative IncX4 type plasmid p16BU137_mcr-1.1 of K. pneumoniae 16BU137, but ISApl1 was not found in its flanking sequence. Mcr-8 variants were found in the putative IncFIB/ IncFII plasmid pKP20191015_mcr-8 of K. pneumoniae KP20191015 and flanked by ISEcl1 and ISKpn26. Conclusion This study provides timely information on Enterobacteriaceae bacteria carrying mcr-like genes, and provides a reference for studying the spread of mcr-1 in China and globally.

Oceanobacter-related bacteria (ORB) are a group of oligotrophic marine bacteria play an underappreciated role in carbon cycling. They have been frequently described as one of the dominant bacterial groups with a wide distribution in coastal and deep seawater of global oceans. To clarify their taxonomic affiliation in relation to alkane utilization, phylogenomic and comparative genomics analyses were performed based on currently available genomes from GenBank and four newly isolated strains, in addition to phenotypic and chemotaxonomic characteristics. Consistently, phylogenomic analysis robustly separated them into two groups, which are accordingly hydrocarbon-degrading (HD, Thalassolituus and Oleibacter) and non-HD (NHD, Oceanobacter). In addition, the two groups can also be readily distinguished by several polyphasic taxonomic characteristics. Furthermore, both AAI and POCP genomic indices within the HD group support the conclusion that the members of the genus Oleibacter should be transferred into the genus Thalassolituus. Moreover, HD and NHD bacteria differed significantly in terms of genome size, G + C content and genes involved in alkane utilization. All HD bacteria contain the key gene alkB encoding an alkane monooxygenase, which can be used as a marker gene to distinguish the members of closely related genera Oceanobacter and Thalassolituus. Pangenome analysis revealed that the larger accessory genome may endow Thalassolituus with the flexibility to cope with the dynamics of marine environments and thrive therein, although they possess smaller pan, core- and unique-genomes than Oceanobacter. Within the HD group, twelve species were clearly distinguished from each other by both dDDH and ANI genomic indices, including two novel species represented by the newly isolated strains alknpb1M-1T and 59MF3M-4T, for which the names Thalassolituus hydrocarbonoclasticus sp. nov. and Thalassolituus pacificus sp. nov. are proposed. Collectively, these findings build a phylogenetic framework for the ORB and contribute to understanding of their role in marine carbon cycling.

Variovorax represents a widespread and ecologically significant genus of soil bacteria. Despite the ecological importance of these bacteria, our knowledge about the viruses infecting Variovorax spp. is quite poor. This study describes the isolation and characterization of the mitomycin-induced phage, named VarioGold. To the best of our knowledge, VarioGold represents the first characterized virus for this genus. Comparative genomic analyses suggested that VarioGold is distinct from currently known bacteriophages at both the nucleotide and protein levels; thus, it could be considered a new virus genus. In addition, another 37 prophages were distinguished in silico within the complete genomic sequences of Variovorax spp. that are available in public databases. The similarity networking analysis highlighted their general high diversity, which, despite clustering with previously described phages, shows their unique genetic load. Therefore, the novelty of Variovorax phages warrants the great enrichment of databases, which could, in turn, improve bioinformatic strategies for finding (pro)phages. [ABSTRACT FROM AUTHOR]

Simple Summary: The methanogenesis pathway via methanogens dates back to the Hadean or Archaean Earth. These methanogens are considered to have a thermophilic origin and are presently ubiquitously distributed across anaerobic environments. The class Methanobacteria comprises methanogens that are found extensively in geothermal environments, such as hot springs and hydrothermal vents, and their evolutionary history and how they adapted to different temperatures remain unclear. In this study, we isolated a novel species of the class Methanobacteria from a natural hot spring in Tengchong, China. This species can produce methane, utilizing hydrogen and carbon dioxide, at 65 °C. In addition, we found that members of the class Methanobacteria originated in a geothermal niche and then evolved to adapt to ambient temperatures; during this process, thermal adaptation genes were lost and a wide range of metabolic genes were acquired. This research on methanogen evolution will help us understand how life originated in geothermal environments and then spread extensively across present-day Earth. Methanogens can produce methane in anaerobic environments via the methanogenesis pathway, and are regarded as one of the most ancient life forms on Earth. They are ubiquitously distributed across distinct ecosystems and are considered to have a thermophilic origin. In this study, we isolated, pure cultured, and completely sequenced a single methanogen strain DL9LZB001, from a hot spring at Tengchong in Southwest China. DL9LZB001 is a thermophilic and hydrogenotrophic methanogen with an optimum growth temperature of 65 °C. It is a putative novel species, which has been named Methanothermobacter tengchongensis—a Class I methanogen belonging to the class Methanobacteria. Comparative genomic and ancestral analyses indicate that the class Methanobacteria originated in a hyperthermal environment and then evolved to adapt to ambient temperatures. This study extends the understanding of methanogens living in geothermal niches, as well as the origin and evolutionary history of these organisms in ecosystems with different temperatures. [ABSTRACT FROM AUTHOR]

Casuarina equisetifolia is crucial in protecting coastal regions of China against typhoon attacks but has faced a substantial challenge due to wilt disease caused by pathogens of the Ralstonia solanacearum species complex (RSSC). Although the initial outbreak of Casuarina varieties, the disease has recently re-emerged in coastal regions of Guangdong. In this study, we report the isolation, characterization, and comparative genomic analysis of 11 RSSC strains from diseased C. equisetifolia varieties, the disease has recently re-emerged in coastal regions of Guangdong. In this study, we report the isolation, characterization, and comparative genomic analysis of 11 RSSC strains from diseased C. equisetifolia at various locations along the coast of Guangdong. Phylogenomic analysis showed that the strains were closely related and clustered with phylotype I strains previously isolated from peanuts. Single-gene-based analysis further suggested these strains could be derived from strains present in Guangdong since the 1980s, indicating a historical context to their current pathogenicity. Casuarina and peanuts than the representative RSSC strains GMI1000 and EP1, suggesting host-specific adaptations that possibly contributed to the recent outbreak. Comparative genomic analysis among RSSC strains revealed a largely conserved genome structure and high levels of conservation in gene clusters encoding extracellular polysaccharide biosynthesis, secretion systems, and quorum sensing regulatory systems. However, we also found a number of unique genes in the C. equisetifolia and peanuts than the representative RSSC strains GMI1000 and EP1, suggesting host-specific adaptations that possibly contributed to the recent outbreak. Comparative genomic analysis among RSSC strains revealed a largely conserved genome structure and high levels of conservation in gene clusters encoding extracellular polysaccharide biosynthesis, secretion systems, and quorum sensing regulatory systems. However, we also found a number of unique genes in the Casuarina -isolated strains that were absent in GMI1000 and EP1, and vice versa, pointing to potential genetic factors underpinning their differential virulence. These unique genes offer promising targets for future functional studies. Overall, our findings provide crucial insights into the RSSC pathogens causing Casuarina wilt in Guangdong, guiding future efforts in disease control and prevention., Competing Interests: The author(s) declare no conflict of interest.

Abstract The Bacillus velezensis strain PG12, belonging to the Bacillus amyloliquefaciens group, is an endophytic bacterium known for its antimicrobial activities against crop pathogens. However, our knowledge of the molecular basis underlying its biocontrol activity and the relatedness of different strains in the Bacillus amyloliquefaciens group is limited. Here, we sequenced and analyzed the genome of PG12 to test its taxonomic affiliation and identified genes involved in the biocontrol activity. The phylogenomic analysis results indicate that PG12 belongs to B. velezensis, a subgroup of the B. amyloliquefaciens group. By comparing the genomes of 22 strains in this group, we confirmed that it comprises three different phylogenetic lineages: B. amyloliquefaciens, B. velezensis and B. siamensis. Three secondary metabolism gene clusters related to the production of lipopeptides, namely fengycin, iturin and surfactin, were identified in the genomes of the B. amyloliquefaciens group. The core genome of B. velezensis is enriched in secondary metabolism genes compared with B. siamensis and B. amyloliquefaciens. Three of the five genes pertaining to the gene cluster responsible for fengycin biosynthesis (fenBCD) were found in B. velezensis and B. siamensis, but not in B. amyloliquefaciens. Phenotypic analysis showed that the ∆fenA mutant of PG12 displayed significantly decreased biofilm formation and swarming motility, which indicates that fengycin contributes to the colonization and pathogen control abilities of PG12. Our results also suggest that B. siamensis and B. velezensis have acquired the fenBCD genes from Paenibacillus spp. by horizontal gene transfer (HGT). Taken together, the results provide insights into the evolutionary pattern of the B. amyloliquefaciens group strains and will promote further researches on their taxonomy and functional genomics.

Precise classification of foodborne pathogen Listeria monocytogenes is a necessity in efficient foodborne disease surveillance, outbreak detection, and source tracking throughout the food chain. In this study, a total of 150 L. monocytogenes isolates from various food products, food processing environments, and clinical sources were investigated for variations in virulence, biofilm formation, and the presence of antimicrobial resistance genes based on their Whole-Genome Sequences. Clonal complex (CC) determination based on Multi-Locus Sequence Typing (MLST) revealed twenty-eight CC-types including eight isolates representing novel CC-types. The eight isolates comprising the novel CC-types share the majority of the known (cold and acid) stress tolerance genes and are all genetic lineage II, serogroup 1/2a-3a. Pan-genome-wide association analysis by Scoary using Fisher’s exact test identified eleven genes specifically associated with clinical isolates. Screening for the presence of antimicrobial and virulence genes using the ABRicate tool uncovered variations in the presence of Listeria Pathogenicity Islands (LIPIs) and other known virulence genes. Specifically, the distributions of actA, ecbA, inlF, inlJ, lapB, LIPI-3, and vip genes across isolates were found to be significantly CC-dependent while the presence of ami, inlF, inlJ, and LIPI-3 was associated with clinical isolates specifically. In addition, Roary-derived phylogenetic grouping based on Antimicrobial-Resistant Genes (AMRs) revealed that the thiol transferase (FosX) gene was present in all lineage I isolates, and the presence of the lincomycin resistance ABC-F-type ribosomal protection protein (lmo0919_fam) was also genetic-lineage-dependent. More importantly, the genes found to be specific to CC-type were consistent when a validation analysis was performed with fully assembled, high-quality complete L. monocytogenes genome sequences (n = 247) extracted from the National Centre for Biotechnology Information (NCBI) microbial genomes database. This work highlights the usefulness of MLST-based CC typing using the Whole-Genome Sequence as a tool in classifying isolates.

Halomonas bacteria are ubiquitous in global marine environments, however, their sulfur-oxidizing abilities and survival adaptations in hydrothermal environments are not well understood. In this study, we characterized the sulfur oxidation ability and metabolic mechanisms of Halomonas titanicae SOB56, which was isolated from the sediment of the Tangyin hydrothermal field in the Southern Okinawa Trough. Physiological characterizations showed that it is a heterotrophic sulfur-oxidizing bacterium that can oxidize thiosulfate to tetrathionate, with the Na2S2O3 degradation reaching 94.86%. Two potential thiosulfate dehydrogenase-related genes, tsdA and tsdB , were identified as encoding key catalytic enzymes, and their expression levels in strain SOB56 were significantly upregulated. Nine of fifteen examined Halomonas genomes possess TsdA- and TsdB-homologous proteins, whose amino acid sequences have two typical Cys-X2-Cys-His heme-binding regions. Moreover, the thiosulfate oxidation process in H. titanicae SOB56 might be regulated by quorum sensing, and autoinducer-2 synthesis protein LuxS was identified in its genome. Regarding the mechanisms underlying adaptation to hydrothermal environment, strain SOB56 was capable of forming biofilms and producing EPS. In addition, genes related to complete flagellum assembly system, various signal transduction histidine kinases, heavy metal transporters, anaerobic respiration, and variable osmotic stress regulation were also identified. Our results shed light on the potential functions of heterotrophic Halomonas bacteria in hydrothermal sulfur cycle and revealed possible adaptations for living at deep-sea hydrothermal fields by H. titanicae SOB56. [ABSTRACT FROM AUTHOR]

Halomonas bacteria are ubiquitous in global marine environments, however, their sulfur-oxidizing abilities and survival adaptations in hydrothermal environments are not well understood. In this study, we characterized the sulfur oxidation ability and metabolic mechanisms of Halomonas titanicae SOB56, which was isolated from the sediment of the Tangyin hydrothermal field in the Southern Okinawa Trough. Physiological characterizations showed that it is a heterotrophic sulfur-oxidizing bacterium that can oxidize thiosulfate to tetrathionate, with the Na2S2O3 degradation reaching 94.86%. Two potential thiosulfate dehydrogenase-related genes, tsdA and tsdB, were identified as encoding key catalytic enzymes, and their expression levels in strain SOB56 were significantly upregulated. Nine of fifteen examined Halomonas genomes possess TsdA- and TsdB-homologous proteins, whose amino acid sequences have two typical Cys-X2-Cys-His heme-binding regions. Moreover, the thiosulfate oxidation process in H. titanicae SOB56 might be regulated by quorum sensing, and autoinducer-2 synthesis protein LuxS was identified in its genome. Regarding the mechanisms underlying adaptation to hydrothermal environment, strain SOB56 was capable of forming biofilms and producing EPS. In addition, genes related to complete flagellum assembly system, various signal transduction histidine kinases, heavy metal transporters, anaerobic respiration, and variable osmotic stress regulation were also identified. Our results shed light on the potential functions of heterotrophic Halomonas bacteria in hydrothermal sulfur cycle and revealed possible adaptations for living at deep-sea hydrothermal fields by H. titanicae SOB56.

The Pseudomonas aeruginosa genome can change to adapt to different ecological niches. We compared four genomes from a Mexican hospital and 59 genomes from GenBank from different niches, such as urine, sputum, and environmental. The ST analysis showed that high-risk STs (ST235, ST773, and ST27) were present in the genomes of the three niches from GenBank, and the STs of Mexican genomes (ST167, ST2731, and ST549) differed from the GenBank genomes. Phylogenetic analysis showed that the genomes were clustering according to their ST and not their niche. When analyzing the genomic content, we observed that environmental genomes had genes involved in adapting to the environment not found in the clinics and that their mechanisms of resistance were mutations in antibiotic resistance-related genes. In contrast, clinical genomes from GenBank had resistance genes, in mobile/mobilizable genetic elements in the chromosome, except for the Mexican genomes that carried them mostly in plasmids. This was related to the presence of CRISPR-Cas and anti-CRISPR; however, Mexican strains only had plasmids and CRISPR-Cas. blaOXA-488 (a variant of blaOXA50) with higher activity against carbapenems was more prevalent in sputum genomes. The virulome analysis showed that exoS was most prevalent in the genomes of urinary samples and exoU and pldA in sputum samples. This study provides evidence regarding the genetic variability among P. aeruginosa isolated from different niches.

Polar regions tend to support simple food webs, which are vulnerable to phage-induced gene transfer or microbial death. To further investigate phage-host interactions in polar regions and the potential linkage of phage communities between the two poles, we induced the release of a lysogenic phage, vB_PaeM-G11, from Pseudomonas sp. D3 isolated from the Antarctic, which formed clear phage plaques on the lawn of Pseudomonas sp. G11 isolated from the Arctic. From permafrost metagenomic data of the Arctic tundra, we found the genome with high-similarity to that of vB_PaeM-G11, demonstrating that vB_PaeM-G11 may have a distribution in both the Antarctic and Arctic. Phylogenetic analysis indicated that vB_PaeM-G11 is homologous to five uncultured viruses, and that they may represent a new genus in the Autographiviridae family, named Fildesvirus here. vB_PaeM-G11 was stable in a temperature range (4–40 °C) and pH (4–11), with latent and rise periods of about 40 and 10 min, respectively. This study is the first isolation and characterization study of a Pseudomonas phage distributed in both the Antarctic and Arctic, identifying its lysogenic host and lysis host, and thus provides essential information for further understanding the interaction between polar phages and their hosts and the ecological functions of phages in polar regions.

Planktonic cells of the luminous marine bacterium Vibrio fischeri establish themselves in the light-emitting organ of each generation of newly hatched Euprymna scolopes bobtail squid. A symbiont population is maintained within the 6 separated crypts of the organ for the ∼9-month life of the host. In the wild, the initial colonization step is typically accomplished by a handful of planktonic V. fischeri cells, leading to a species-specific, but often multi-strain, symbiont population. Within a few hours, the inoculating cells proliferate within the organ's individual crypts, after which there is evidently no supernumerary colonization. Nevertheless, every day at dawn, the majority of the symbionts is expelled, and the regrowth of the remaining ∼5% of cells provides a daily opportunity for the population to evolve and diverge, thereby increasing its genomic diversity. To begin to understand the extent of this diversification, we characterized the light-organ population of an adult animal. First, we used 16S sequencing to determine that species in the V. fischeri clade were essentially the only ones detectable within a field-caught E. scolopes. Efforts to colonize the host with a minor species that appeared to be identified, V. litoralis , revealed that, although some cells could be imaged within the organ, they were <0.1% of the typical V. fischeri population, and did not persist. Next, we determined the genome sequences of seventy-two isolates from one side of the organ. While all these isolates were associated with one of three clusters of V. fischeri strains, there was considerable genomic diversity within this natural symbiotic population. Comparative analyses revealed a significant difference in both the number and the presence/absence of genes within each cluster; in contrast, there was little accumulation of single-nucleotide polymorphisms. These data suggest that, in nature, the light organ is colonized by a small number of V. fischeri strains that can undergo significant genetic diversification, including by horizontal-gene transfer, over the course of ∼1500 generations of growth in the organ. When the resulting population of symbionts is expelled into seawater, its genomic mix provides the genetic basis for selection during the subsequent environmental dispersal, and transmission to the next host. [ABSTRACT FROM AUTHOR]

Planktonic cells of the luminous marine bacterium Vibrio fischeri establish themselves in the light-emitting organ of each generation of newly hatched Euprymna scolopes bobtail squid. A symbiont population is maintained within the 6 separated crypts of the organ for the ∼9-month life of the host. In the wild, the initial colonization step is typically accomplished by a handful of planktonic V. fischeri cells, leading to a species-specific, but often multi-strain, symbiont population. Within a few hours, the inoculating cells proliferate within the organ’s individual crypts, after which there is evidently no supernumerary colonization. Nevertheless, every day at dawn, the majority of the symbionts is expelled, and the regrowth of the remaining ∼5% of cells provides a daily opportunity for the population to evolve and diverge, thereby increasing its genomic diversity. To begin to understand the extent of this diversification, we characterized the light-organ population of an adult animal. First, we used 16S sequencing to determine that species in the V. fischeri clade were essentially the only ones detectable within a field-caught E. scolopes. Efforts to colonize the host with a minor species that appeared to be identified, V. litoralis, revealed that, although some cells could be imaged within the organ, they were

Persistent infections caused by Staphylococcus aureus remain a clinical challenge. Adaptational mechanisms of the pathogen influencing infection persistence, treatment success, and clinical outcome in these types of infections by S. aureus have not been fully elucidated so far. We applied a whole-genome sequencing approach on fifteen isolates retrieved from a persistent S. aureus infection to determine their genetic relatedness, virulome, and resistome. The analysis of the genomic data indicates that all isolates shared a common clonal origin but displayed a heterogenous composition of virulence factors and antimicrobial resistance. This heterogeneity was reflected by different mutations in the rpoB gene that were related to the phenotypic antimicrobial resistance towards rifampicin and different minimal inhibitory concentrations of oxacillin. In addition, one group of isolates had acquired the genes encoding for staphylokinase (sak) and staphylococcal complement inhibitor (scn), leading to the truncation of the hemolysin b (hlb) gene. These features are characteristic for temperate phages of S. aureus that carry genes of the immune evasion cluster and confer triple conversion by integration into the hlb gene. Modulation of immune evasion mechanisms was demonstrated by significant differences in biofilm formation capacity, while invasion and intracellular survival in neutrophils were not uniformly altered by the presence of the immune evasion cluster. Virulence factors carried by temperate phages of S. aureus may contribute to the course of infection at different stages and affect immune evasion and pathogen persistence. In conclusion, the application of comparative genomic demonstrated clonal heterogeneity in persistent S. aureus infection. [ABSTRACT FROM AUTHOR]

Background: Mobile colistin resistance like gene (mcr-like gene) is a new type of polymyxin resistance gene that can be horizontally transferred in the Enterobacteriaceae. This has brought great challenges to the treatment of multidrug-resistant Escherichia coli and K. pneumoniae. Results: K. pneumoniae 16BU137 and E. coli 17MR471 were isolated from the bus and subway handrails in Guangzhou, China. K. pneumoniae 19PDR22 and KP20191015 were isolated from patients with urinary tract infection and severe pneumonia in Anhui, China. Sequence analysis indicated that the mcr-1.1 gene was present on the chromosome of E. coli 17MR471, and the gene was in the gene cassette containing pap2 and two copies of ISApl1.The mcr-1.1 was found in the putative IncX4 type plasmid p16BU137_mcr-1.1 of K. pneumoniae 16BU137, but ISApl1 was not found in its flanking sequence. Mcr-8 variants were found in the putative IncFIB/ IncFII plasmid pKP20191015_mcr-8 of K. pneumoniae KP20191015 and flanked by ISEcl1 and ISKpn26. Conclusion: This study provides timely information on Enterobacteriaceae bacteria carrying mcr-like genes, and provides a reference for studying the spread of mcr-1 in China and globally. [ABSTRACT FROM AUTHOR]

Abstract Background Sporobolomyces pararoseus is regarded as an oleaginous red yeast, which synthesizes numerous valuable compounds with wide industrial usages. This species hold biotechnological interests in biodiesel, food and cosmetics industries. Moreover, the ballistospores-shooting promotes the colonizing of S. pararoseus in most terrestrial and marine ecosystems. However, very little is known about the basic genomic features of S. pararoseus. To assess the biotechnological potential and ballistospores-shooting mechanism of S. pararoseus on genome-scale, the whole genome sequencing was performed by next-generation sequencing technology. Results Here, we used Illumina Hiseq platform to firstly assemble S. pararoseus genome into 20.9 Mb containing 54 scaffolds and 5963 predicted genes with a N50 length of 2,038,020 bp and GC content of 47.59%. Genome completeness (BUSCO alignment: 95.4%) and RNA-seq analysis (expressed genes: 98.68%) indicated the high-quality features of the current genome. Through the annotation information of the genome, we screened many key genes involved in carotenoids, lipids, carbohydrate metabolism and signal transduction pathways. A phylogenetic assessment suggested that the evolutionary trajectory of the order Sporidiobolales species was evolved from genus Sporobolomyces to Rhodotorula through the mediator Rhodosporidiobolus. Compared to the lacking ballistospores Rhodotorula toruloides and Saccharomyces cerevisiae, we found genes enriched for spore germination and sugar metabolism. These genes might be responsible for the ballistospores-shooting in S. pararoseus NGR. Conclusion These results greatly advance our understanding of S. pararoseus NGR in biotechnological potential and ballistospores-shooting, which help further research of genetic manipulation, metabolic engineering as well as its evolutionary direction.

Persistent infections caused by Staphylococcus aureus remain a clinical challenge. Adaptational mechanisms of the pathogen influencing infection persistence, treatment success, and clinical outcome in these types of infections by S. aureus have not been fully elucidated so far. We applied a whole-genome sequencing approach on fifteen isolates retrieved from a persistent S. aureus infection to determine their genetic relatedness, virulome, and resistome. The analysis of the genomic data indicates that all isolates shared a common clonal origin but displayed a heterogenous composition of virulence factors and antimicrobial resistance. This heterogeneity was reflected by different mutations in the rpoB gene that were related to the phenotypic antimicrobial resistance towards rifampicin and different minimal inhibitory concentrations of oxacillin. In addition, one group of isolates had acquired the genes encoding for staphylokinase (sak) and staphylococcal complement inhibitor (scn), leading to the truncation of the hemolysin b (hlb) gene. These features are characteristic for temperate phages of S. aureus that carry genes of the immune evasion cluster and confer triple conversion by integration into the hlb gene. Modulation of immune evasion mechanisms was demonstrated by significant differences in biofilm formation capacity, while invasion and intracellular survival in neutrophils were not uniformly altered by the presence of the immune evasion cluster. Virulence factors carried by temperate phages of S. aureus may contribute to the course of infection at different stages and affect immune evasion and pathogen persistence. In conclusion, the application of comparative genomic demonstrated clonal heterogeneity in persistent S. aureus infection.

Brassica oleracea displays remarkable morphological variations. It intrigued researchers to study the underlying cause of the enormous diversification of this organism. However, genomic variations in complex heading traits are less known in B. oleracea. Herein, we performed a comparative population genomics analysis to explore structural variations (SVs) responsible for heading trait formation in B. oleracea. Synteny analysis showed that chromosomes C1 and C2 of B. oleracea (CC) shared strong collinearity with A01 and A02 of B. rapa (AA), respectively. Two historical events, whole genome triplication (WGT) of Brassica species and differentiation time between AA and CC genomes, were observed clearly by phylogenetic and Ks analysis. By comparing heading and non-heading populations of B. oleracea genomes, we found extensive SVs during the diversification of the B. oleracea genome. We identified 1205 SVs that have an impact on 545 genes and might be associated with the heading trait of cabbage. Overlapping the genes affected by SVs and the differentially expressed genes identified by RNA-seq analysis, we identified six vital candidate genes that may be related to heading trait formation in cabbage. Further, qRT-PCR experiments also verified that six genes were differentially expressed between heading leaves and non-heading leaves, respectively. Collectively, we used available genomes to conduct a comparison population genome analysis and identify candidate genes for the heading trait of cabbage, which provides insight into the underlying reason for heading trait formation in B. oleracea.

The species living in the Qinghai-Tibet Plateau provide an excellent model system for studying the relationship between molecular convergent evolution and adaptation. Distant species experiencing the same selection pressure (i.e., hypoxia, low temperature and strong ultraviolet radiation) are likely to evolve similar genetic adaptations independently. Here, we performed comparative genomics studies on six independently evolved high-altitude species. The results also showed that the convergent evolution of the six species was mainly reflected at the level of rapidly evolving genes, and the functions of these rapidly evolving genes were mainly related to hypoxia response and DNA damage repair. In addition, we found that high-altitude species had more gene family changes than their low-altitude relatives, except for the order Lagomorpha. The results also show that the convergence of the gene family contraction of high-altitude species is much greater than that of expansion, revealing a possible pattern of species in adapting to high-altitude. Furthermore, we detected a positive selection signature in four genes related to hypoxia response and ultraviolet radiation damage in these six species (FYCO1, ERBIN, SCAMP1 and CXCL10). Our study reveals that hypoxia response might play an important role in the adaptation of independently evolved species to a high-altitude environment, providing a basic perspective for further exploring the high-altitude adaptation mechanism of different related species in the future.

Coagulase-negative Staphylococcus (CoNS) is the most common pathogen causing traumatic endophthalmitis. Among which, Staphylococcus epidermidis is the most common species that colonizes human skin, eye surfaces, and nasal cavity. It is also the main cause of nosocomial infection, specially foreign body-related bloodstream infections (FBR-BSIs). Although some studies have reported the genome characteristics of S. epidermidis , the genome of ocular trauma-sourced S. epidermidis strain and a comprehensive understanding of its pathogenicity are still lacking. Our study sequenced, analyzed, and reported the whole genomes of 11 ocular trauma-sourced samples of S. epidermidis that caused traumatic endophthalmitis. By integrating publicly available genomes, we obtained a total of 187 S. epidermidis samples from healthy and diseased eyes, skin, respiratory tract, and blood. Combined with pan-genome, phylogenetic, and comparative genomic analyses, our study showed that S. epidermidis , regardless of niche source, exhibits two founder lineages with different pathogenicity. Moreover, we identified several potential biomarkers associated with the virulence of S. epidermidis , including essD , uhpt , sdrF , sdrG , fbe , and icaABCDR. EssD and uhpt have high homology with esaD and hpt in Staphylococcus aureus , showing that the genomes of S. epidermidis and S. aureus may have communicated during evolution. SdrF , sdrG , fbe , and icaABCDR are related to biofilm formation. Compared to S. epidermidis from blood sources, ocular-sourced strains causing intraocular infection had no direct relationship with biofilm formation. In conclusion, this study provided additional data resources for studies on S. epidermidis and improved our understanding of the evolution and pathogenicity among strains of different sources. [ABSTRACT FROM AUTHOR]

A 26-year-old girl with a longstanding colonization by Pandoraea nosoerga underwent liver-lung transplantation for cystic fibrosis (CF) in 2018. Her brother also suffering from CF was also colonized by P. nosoerga. Despite appropriate perioperative antibiotic therapy, she had post-transplant bacteremic pneumonia caused by extensively drug-resistant P. nosoerga. Drug repurposing was used to optimize treatment options. The cause of post-transplant contamination was studied by comparative whole-genome sequencing including pre- and post-transplant strains and her brother's strains. Post-transplant contamination appeared to be due to her own pre-transplant strain, emphasizing the urgent need to study and implement effective decontamination protocols before transplantation. [ABSTRACT FROM AUTHOR]