Genomes of the “Candidatus Actinomarinales” Order: Highly Streamlined Marine Epipelagic Actinobacteria

ABSTRACT“Candidatus Actinomarinales” was defined as a subclass of exclusively marine Actinobacteria with small cells and genomes. We have collected all the available genomes in databases to assess the diversity included in this group and analyzed it by comparative genomics. We have found the equivalent of five genera and 18 genomospecies. They have genome reduction parameters equal to those of freshwater actinobacterial “Candidatus Nanopelagicales” or marine alphaproteobacterial Pelagibacterales. Genome recruitment shows that they are found only in the photic zone and mainly in surface waters, with only one genus that is found preferentially at or below the deep chlorophyll maximum. “Ca. Actinomarinales” show a highly conserved core genome (80% of the gene families conserved for the whole order) with a saturation of genomic diversity of the flexible genome at the genomospecies level. We found only a flexible genomic island preserved throughout the order; it is related to the sugar decoration of the envelope and uses several tRNAs as hot spots to increase its genomic diversity. Populations had a discrete level of sequence diversity similar to other marine microbes but drastically different from the much higher levels found for Pelagibacterales. Genomic analysis suggests that they are all aerobic photoheterotrophs with one type 1 rhodopsin and a heliorhodopsin. Like other actinobacteria, they possess the F420 coenzyme biosynthesis pathway, and its lower reduction potential could provide access to an increased range of redox chemical transformations. Last, sequence analysis revealed the first “Ca. Actinomarinales” phages, including a prophage, with metaviromic islands related to sialic acid cleavage.IMPORTANCE Microbiology is in a new age in which sequence databases are primary sources of information about many microbes. However, in-depth analysis of environmental genomes thus retrieved is essential to substantiate the new knowledge. Here, we study 182 genomes belonging to the only known exclusively marine pelagic group of the phylum Actinobacteria. The aquatic branch of this phylum is largely known from environmental sequencing studies (single-amplified genomes [SAGs] and metagenome-assembled genomes [MAGs]), and we have collected and analyzed the available information present in databases about the “Ca. Actinomarinales.” They are among the most streamlined microbes to live in the epipelagic zone of the ocean, and their study is critical to obtain a proper view of the diversity of Actinobacteria and their role in aquatic ecosystems.

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Annotation and analysis of yellow genes in Diaphorina citri, vector for the Huanglongbing disease

10.1101/2020.12.22.422960 ◽

2020 ◽

Author(s):

Crissy Massimino ◽

Chad Vosburg ◽

Teresa Shippy ◽

Prashant S. Hosmani ◽

Mirella Flores-Gonzalez ◽

...

Keyword(s):

Phylogenetic Trees ◽

Life Stage ◽

Genomic Analysis ◽

Gene Families ◽

Manual Annotation ◽

Diaphorina Citri ◽

In Planta ◽

Specific Expression ◽

Molecular Control ◽

Depth Analysis

ABSTRACTHuanglongbing (HLB), also known as citrus greening disease, is caused by the bacterium Candidatus Liberibacter asiaticus (CLas) and represents a serious threat to global citrus production. This bacteria is transmitted by the Asian citrus psyllid, Diaphorina citri (Hemiptera) and there are no effective in-planta treatments for CLas. Therefore, one strategy is to manage the psyllid population. Manual annotation of the D. citri genome can identify and characterize gene families that could serve as novel targets for psyllid control. The yellow gene family represents an excellent target as yellow genes are linked to development and immunity due to their roles in melanization. Combined analysis of the genome with RNA-seq datasets, sequence homology, and phylogenetic trees were used to identify and annotate nine yellow genes for the D. citri genome. Phylogenetic analysis shows a unique duplication of yellow-y in D. citri, with life stage specific expression for these two genes. Genomic analysis also indicated the loss of a gene vital to the process of melanization, yellow-f, and the gain of a gene which seems to be unique to hemipterans, yellow 9. We suggest that yellow 9 or the gene yellow 8 (c), which consistently groups closely to yellow-f, may take on this role. Manual curation of genes in D. citri has provided an in-depth analysis of the yellow family among hemipteran insects and provides new targets for molecular control of this psyllid pest. Manual annotation was done as part of a collaborative community annotation project (https://citrusgreening.org/annotation/index).

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Chromosome-scale genome assembly of Cucumis hystrix—a wild species interspecifically cross-compatible with cultivated cucumber

Horticulture Research ◽

10.1038/s41438-021-00475-5 ◽

2021 ◽

Vol 8 (1) ◽

Author(s):

Xiaodong Qin ◽

Zhonghua Zhang ◽

Qunfeng Lou ◽

Lei Xia ◽

Ji Li ◽

...

Keyword(s):

Disease Resistance ◽

Wild Species ◽

Genomic Analysis ◽

Gene Families ◽

Comparative Genomic ◽

Disease Resistance Gene ◽

Introgression Breeding ◽

Interspecific Introgression ◽

Cucumber Genome ◽

Cucumis Hystrix

AbstractCucumis hystrix Chakr. (2n = 2x = 24) is a wild species that can hybridize with cultivated cucumber (C. sativus L., 2n = 2x = 14), a globally important vegetable crop. However, cucumber breeding is hindered by its narrow genetic base. Therefore, introgression from C. hystrix has been anticipated to bring a breakthrough in cucumber improvement. Here, we report the chromosome-scale assembly of C. hystrix genome (289 Mb). Scaffold N50 reached 14.1 Mb. Over 90% of the sequences were anchored onto 12 chromosomes. A total of 23,864 genes were annotated using a hybrid method. Further, we conducted a comprehensive comparative genomic analysis of cucumber, C. hystrix, and melon (C. melo L., 2n = 2x = 24). Whole-genome comparisons revealed that C. hystrix is phylogenetically closer to cucumber than to melon, providing a molecular basis for the success of its hybridization with cucumber. Moreover, expanded gene families of C. hystrix were significantly enriched in “defense response,” and C. hystrix harbored 104 nucleotide-binding site–encoding disease resistance gene analogs. Furthermore, 121 genes were positively selected, and 12 (9.9%) of these were involved in responses to biotic stimuli, which might explain the high disease resistance of C. hystrix. The alignment of whole C. hystrix genome with cucumber genome and self-alignment revealed 45,417 chromosome-specific sequences evenly distributed on C. hystrix chromosomes. Finally, we developed four cucumber–C. hystrix alien addition lines and identified the exact introgressed chromosome using molecular and cytological methods. The assembled C. hystrix genome can serve as a valuable resource for studies on Cucumis evolution and interspecific introgression breeding of cucumber.

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Ecophysiology of Freshwater Verrucomicrobia Inferred from Metagenome-Assembled Genomes

mSphere ◽

10.1128/msphere.00277-17 ◽

2017 ◽

Vol 2 (5) ◽

Cited By ~ 33

Author(s):

Shaomei He ◽

Sarah L. R. Stevens ◽

Leong-Keat Chan ◽

Stefan Bertilsson ◽

Tijana Glavina del Rio ◽

...

Keyword(s):

Electron Transfer ◽

Potential Role ◽

Carbon Sources ◽

Genomic Analysis ◽

Distribution Patterns ◽

Eutrophic Lake ◽

Genomic Diversity ◽

Extracellular Electron Transfer ◽

Different Origins ◽

Encoding Genes

ABSTRACT Freshwater Verrucomicrobia spp. are cosmopolitan in lakes and rivers, and yet their roles and ecophysiology are not well understood, as cultured freshwater Verrucomicrobia spp. are restricted to one subdivision of this phylum. Here, we greatly expanded the known genomic diversity of this freshwater lineage by recovering 19 Verrucomicrobia draft genomes from 184 metagenomes collected from a eutrophic lake and a humic bog across multiple years. Most of these genomes represent the first freshwater representatives of several Verrucomicrobia subdivisions. Genomic analysis revealed Verrucomicrobia to be potential (poly)saccharide degraders and suggested their adaptation to carbon sources of different origins in the two contrasting ecosystems. We identified putative extracellular electron transfer genes and so-called “Planctomycete-specific” cytochrome c-encoding genes and identified their distinct distribution patterns between the lakes/layers. Overall, our analysis greatly advances the understanding of the function, ecophysiology, and distribution of freshwater Verrucomicrobia, while highlighting their potential role in freshwater carbon cycling. Microbes are critical in carbon and nutrient cycling in freshwater ecosystems. Members of the Verrucomicrobia are ubiquitous in such systems, and yet their roles and ecophysiology are not well understood. In this study, we recovered 19 Verrucomicrobia draft genomes by sequencing 184 time-series metagenomes from a eutrophic lake and a humic bog that differ in carbon source and nutrient availabilities. These genomes span four of the seven previously defined Verrucomicrobia subdivisions and greatly expand knowledge of the genomic diversity of freshwater Verrucomicrobia. Genome analysis revealed their potential role as (poly)saccharide degraders in freshwater, uncovered interesting genomic features for this lifestyle, and suggested their adaptation to nutrient availabilities in their environments. Verrucomicrobia populations differ significantly between the two lakes in glycoside hydrolase gene abundance and functional profiles, reflecting the autochthonous and terrestrially derived allochthonous carbon sources of the two ecosystems, respectively. Interestingly, a number of genomes recovered from the bog contained gene clusters that potentially encode a novel porin-multiheme cytochrome c complex and might be involved in extracellular electron transfer in the anoxic humus-rich environment. Notably, most epilimnion genomes have large numbers of so-called “Planctomycete-specific” cytochrome c-encoding genes, which exhibited distribution patterns nearly opposite to those seen with glycoside hydrolase genes, probably associated with the different levels of environmental oxygen availability and carbohydrate complexity between lakes/layers. Overall, the recovered genomes represent a major step toward understanding the role, ecophysiology, and distribution of Verrucomicrobia in freshwater. IMPORTANCE Freshwater Verrucomicrobia spp. are cosmopolitan in lakes and rivers, and yet their roles and ecophysiology are not well understood, as cultured freshwater Verrucomicrobia spp. are restricted to one subdivision of this phylum. Here, we greatly expanded the known genomic diversity of this freshwater lineage by recovering 19 Verrucomicrobia draft genomes from 184 metagenomes collected from a eutrophic lake and a humic bog across multiple years. Most of these genomes represent the first freshwater representatives of several Verrucomicrobia subdivisions. Genomic analysis revealed Verrucomicrobia to be potential (poly)saccharide degraders and suggested their adaptation to carbon sources of different origins in the two contrasting ecosystems. We identified putative extracellular electron transfer genes and so-called “Planctomycete-specific” cytochrome c-encoding genes and identified their distinct distribution patterns between the lakes/layers. Overall, our analysis greatly advances the understanding of the function, ecophysiology, and distribution of freshwater Verrucomicrobia, while highlighting their potential role in freshwater carbon cycling.

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Characterization, Pathogenicity, Phylogeny, and Comparative Genomic Analysis of Pseudomonas tolaasii Strains Isolated from Various Mushrooms in China

Phytopathology ◽

10.1094/phyto-12-20-0550-r ◽

2021 ◽

Author(s):

Zhenghui Liu ◽

Yitong Zhao ◽

Frederick Leo Sossah ◽

Benjamin Azu Okorley ◽

Daniel G. Amoako ◽

...

Keyword(s):

Antibiotic Resistance ◽

Genomic Analysis ◽

Gene Families ◽

Effective Control ◽

Economic Losses ◽

Comparative Genomic ◽

Bacterial Strains ◽

Secretion Systems ◽

Pseudomonas Tolaasii ◽

Antimicrobial Resistance Genes

Since 2016, devastating bacterial blotch affecting the fruiting bodies of Agaricus bisporus, Cordyceps militaris, Flammulina filiformis, and Pleurotus ostreatus in China has caused severe economic losses. We isolated 102 bacterial strains and characterized them polyphasically. We identified the causal agent as Pseudomonas tolaasii and confirmed the pathogenicity of the strains. A host range test further confirmed the pathogen’s ability to infect multiple hosts. This is the first report in China of bacterial blotch in C. militaris caused by P. tolaasii. Whole-genome sequences were generated for three strains: Pt11 (6.48 Mb), Pt51 (6.63 Mb), and Pt53 (6.80 Mb), and pangenome analysis was performed with 13 other publicly accessible P. tolaasii genomes to determine their genetic diversity, virulence, antibiotic resistance, and mobile genetic elements. The pangenome of P. tolaasii is open, and many more gene families are likely to emerge with further genome sequencing. Multilocus sequence analysis using the sequences of four common housekeeping genes (glns, gyrB, rpoB, and rpoD) showed high genetic variability among the P. tolaasii strains, with 115 strains clustered into a monophyletic group. The P. tolaasii strains possess various genes for secretion systems, virulence factors, carbohydrate-active enzymes, toxins, secondary metabolites, and antimicrobial resistance genes that are associated with pathogenesis and adapted to different environments. The myriad of insertion sequences, integrons, prophages, and genome islands encoded in the strains may contribute to genome plasticity, virulence, and antibiotic resistance. These findings advance understanding of the determinants of virulence, which can be targeted for the effective control of bacterial blotch disease.

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Whole genome sequencing reveals the genomic diversity, taxonomic classification, and evolutionary relationships of the genus Nocardia

PLoS Neglected Tropical Diseases ◽

10.1371/journal.pntd.0009665 ◽

2021 ◽

Vol 15 (8) ◽

pp. e0009665

Author(s):

Shuai Xu ◽

Zhenpeng Li ◽

Yuanming Huang ◽

Lichao Han ◽

Yanlin Che ◽

...

Keyword(s):

Genetic Diversity ◽

Phylogenetic Trees ◽

Gene Families ◽

Single Copy ◽

Taxonomic Classification ◽

Genomic Diversity ◽

Evolutionary Relationships ◽

Taxonomic Structure ◽

Pan Genome ◽

Dipeptidyl Aminopeptidase

Nocardia is a complex and diverse genus of aerobic actinomycetes that cause complex clinical presentations, which are difficult to diagnose due to being misunderstood. To date, the genetic diversity, evolution, and taxonomic structure of the genus Nocardia are still unclear. In this study, we investigated the pan-genome of 86 Nocardia type strains to clarify their genetic diversity. Our study revealed an open pan-genome for Nocardia containing 265,836 gene families, with about 99.7% of the pan-genome being variable. Horizontal gene transfer appears to have been an important evolutionary driver of genetic diversity shaping the Nocardia genome and may have caused historical taxonomic confusion from other taxa (primarily Rhodococcus, Skermania, Aldersonia, and Mycobacterium). Based on single-copy gene families, we established a high-accuracy phylogenomic approach for Nocardia using 229 genome sequences. Furthermore, we found 28 potentially new species and reclassified 16 strains. Finally, by comparing the topology between a phylogenomic tree and 384 phylogenetic trees (from 384 single-copy genes from the core genome), we identified a novel locus for inferring the phylogeny of this genus. The dapb1 gene, which encodes dipeptidyl aminopeptidase BI, was far superior to commonly used markers for Nocardia and yielded a topology almost identical to that of genome-based phylogeny. In conclusion, the present study provides insights into the genetic diversity, contributes a robust framework for the taxonomic classification, and elucidates the evolutionary relationships of Nocardia. This framework should facilitate the development of rapid tests for the species identification of highly variable species and has given new insight into the behavior of this genus.

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Roseomonas oleicola sp. nov., isolated from an oil production mixture in Yumen Oilfield, and emended description of Roseomonas frigidaquae

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY ◽

10.1099/ijsem.0.005064 ◽

2021 ◽

Vol 71 (10) ◽

Author(s):

Danni Wu ◽

Hongcan Liu ◽

Yuguang Zhou ◽

Xiaolei Wu ◽

Yong Nie ◽

...

Keyword(s):

Type Species ◽

Genomic Analysis ◽

Oil Production ◽

Gene Families ◽

Specific Gene ◽

Rrna Gene ◽

Strictly Aerobic ◽

Content Type ◽

Link Type ◽

Type Strains

A pink, ovoid-shaped, Gram-stain-negative, strictly aerobic and motile bacterial strain, designated ROY-5-3T, was isolated from an oil production mixture from Yumen Oilfield in PR China. The strain grew at 4–42 °C (optimum, 30 °C), at pH 5–10 (optimum, 7) and with 0–5 % (w/v) NaCl (optimum, 0%). The results of phylogenetic analysis based on 16S rRNA gene sequences indicated that ROY-5-3T belongs to the genus Roseomonas and shared the highest pairwise similarities with Roseomonas frigidaquae CW67T (98.1%), Roseomonas selenitidurans BU-1T (97.8%), Roseomonas tokyonensis K-20T (97.7%) and Roseomonas stagni HS-69T (97.3%). The average nucleotide identity and digital DNA–DNA hybridization values between ROY-5-3T and other related type strains of Roseomonas species were less than 84.08 and 28.60 %, respectively, both below the species delineation threshold. Pan-genomic analysis showed that the novel isolate ROY-5-3T shared 3265 core gene families with the four closely related type strains in Roseomonas , and the number of strain-specific gene families was 513. The major fatty acids were identified as summed feature 8 (C18 : 1 ω6c/C18 : 1 ω7c), summed feature 3 (C16 : 1 ω6c/C16 : 1 ω7c) and C16 : 0. Strain ROY-5-3T contained Q-10 as the main ubiquinone and the genomic DNA G+C content was 69.8 mol%. The major polar lipids were diphosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine and phosphatidylglycerol. Based on the phylogenetic, morphological, physiological, chemotaxonomic and genome analyses, strain ROY-5-3T represents a novel species of the genus Roseomonas for which the name Roseomonas oleicola sp. nov. is proposed. The type strain is ROY-5-3T (=CGMCC 1.13459T =KCTC 82484T).

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Clonal diversity of Haemophilus influenzae carriage isolated from under the age of 6 years children

BMC Research Notes ◽

10.1186/s13104-019-4603-7 ◽

2019 ◽

Vol 12 (1) ◽

Author(s):

Fahimeh Shooraj ◽

Bahman Mirzaei ◽

Seyed Fazlollah Mousavi ◽

Farzaneh Hosseini

Keyword(s):

Genetic Diversity ◽

Gel Electrophoresis ◽

Genomic Analysis ◽

Clonal Diversity ◽

Invasive Disease ◽

Pulsed Field Gel Electrophoresis ◽

Genomic Diversity ◽

Biochemical Tests ◽

Genetic Origin ◽

Susceptibility Tests

Abstract Objectives Pharyngeal carriers such as H. influenzae seem to constitute the only reservoir and probably the only transmission vehicle of the invasive disease. The aims of this study were to estimate the prevalence of H. influenzae carriage, to characterize antibiotic susceptibility, and to explore genetic diversity of H. influenzae isolates. Sampling was carried out as nasopharynx swabs among children less than 6 years old volunteers. After traditional biochemical tests, isolates were confirmed by targeting omp6 sequence. Following the susceptibility tests, genomic diversity of strains was analyzed by Pulsed-Field Gel Electrophoresis procedure. Results Out of 328 nasopharynx swabs, 73 strains were identified as H. influenzae. Among H. influenzae isolates, resistance to chloramphenicol (42%) and ampicillin (43%) was observed. Levofloxacin is the most effective antibiotic and the least effect belonged to tetracycline. By genomic analysis of selected H. influenza, 28 PFGE patterns were achieved among which 11 patterns included at least 2 strains. All strains clustered into 25 different clones. The dendrogram analysis of the isolated H. influenzae strains showed that some of these strains had a clonal relationship and common genetic origin. According to our results, antibiotic resistance didn’t show any significant correlation with the clonality of strains.

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Candidate gene mapping identifies genomic variations in the fire blight susceptibility genes HIPM and DIPM across the Malus germplasm

Scientific Reports ◽

10.1038/s41598-020-73284-w ◽

2020 ◽

Vol 10 (1) ◽

Author(s):

Richard Tegtmeier ◽

Valerio Pompili ◽

Jugpreet Singh ◽

Diego Micheletti ◽

Katchen Julliany Pereira Silva ◽

...

Keyword(s):

Candidate Gene ◽

Fire Blight ◽

Gene Families ◽

Genomic Diversity ◽

Bacterial Disease ◽

Nucleotide Polymorphisms ◽

Germplasm Collections ◽

Apple Cultivars ◽

Candidate Gene Mapping ◽

In Fire

Abstract Development of apple (Malus domestica) cultivars resistant to fire blight, a devastating bacterial disease caused by Erwinia amylovora, is a priority for apple breeding programs. Towards this goal, the inactivation of members of the HIPM and DIPM gene families with a role in fire blight susceptibility (S genes) can help achieve sustainable tolerance. We have investigated the genomic diversity of HIPM and DIPM genes in Malus germplasm collections and used a candidate gene-based association mapping approach to identify SNPs (single nucleotide polymorphisms) with significant associations to fire blight susceptibility. A total of 87 unique SNP variants were identified in HIPM and DIPM genes across 93 Malus accessions. Thirty SNPs showed significant associations (p < 0.05) with fire blight susceptibility traits, while two of these SNPs showed highly significant (p < 0.001) associations across two different years. This research has provided knowledge about genetic diversity in fire blight S genes in diverse apple accessions and identified candidate HIPM and DIPM alleles that could be used to develop apple cultivars with decreased fire blight susceptibility via marker-assisted breeding or biotechnological approaches.

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Combined Transcriptomic Analysis Revealed AKR1B10 Played an Important Role in Psoriasis through the Dysregulated Lipid Pathway and Overproliferation of Keratinocyte

BioMed Research International ◽

10.1155/2017/8717369 ◽

2017 ◽

Vol 2017 ◽

pp. 1-10 ◽

Cited By ~ 5

Author(s):

Yunlu Gao ◽

Xuemei Yi ◽

Yangfeng Ding

Keyword(s):

Lipid Metabolism ◽

Gene Families ◽

Keratinocyte Differentiation ◽

Receptor Interaction ◽

Rna Seq ◽

Keratinocyte Proliferation ◽

Therapeutic Uses ◽

Depth Analysis ◽

Transcriptomic Level ◽

New Biomarkers

RNA-seq has enabled in-depth analysis of the pathogenesis of psoriasis on the transcriptomic level, and many biomarkers have been discovered to be related to the immune response, lipid metabolism, and keratinocyte proliferation. However, few studies have combined analysis from various datasets. In this study, we integrated different psoriasis RNA-seq datasets to reveal the pathogenesis of psoriasis through the analysis of differentially expressed genes (DEGs), pathway analysis, and functional annotation. The revealed biomarkers were further validated through proliferation phenotypes. The results showed that DEGs were functionally related to lipid metabolism and keratinocyte differentiation dysregulation. The results also showed new biomarkers, such as AKR1B10 and PLA2G gene families, as well as pathways that include the PPAR signaling pathway, cytokine-cytokine receptor interaction, alpha-linoleic acid metabolism, and glycosphingolipid biosynthesis. Using siRNA knockdown assays, we further validated the role that the AKR1B10 gene plays in proliferation. Our study demonstrated not only the dysfunction of the AKR1B10 gene in lipid metabolizing but also its important role in the overproliferation and migration of keratinocyte, which provided evidence for further therapeutic uses for psoriasis.

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Manifestations of expert power in gatekeeping: a conceptual study

Journal of Documentation ◽

10.1108/jd-01-2020-0010 ◽

2020 ◽

Vol 76 (6) ◽

pp. 1215-1232

Author(s):

Reijo Savolainen

Keyword(s):

Social Power ◽

Research Literature ◽

Power Relationships ◽

Access To Information ◽

Sources Of Information ◽

Specific Domain ◽

Content Type ◽

Referent Power ◽

Expert Power ◽

Depth Analysis

PurposeThis study aims to elaborate the picture of the relationships between information and power by examining how expert power appears in the characterizations of gatekeeping presented in the research literature.Design/methodology/approachThis study uses conceptual analysis for examining how expert power is constitutive of the construct of gatekeeper and how people subject to the influence of gatekeeping trust or challenge the expert power attributed to gatekeepers. The study draws on the analysis of 40 key studies on the above issues.FindingsResearchers have mainly constructed the gatekeepers' expert power in terms of superior knowledge and skills applicable to a specific domain, coupled with an ability to control or facilitate access to information. The gatekeeper's expert power has been approached as a contextual factor that facilitates rather than controls access to information. The power relationships between the gatekeepers and those subject to gatekeeping vary contextually, depending on the extent to which the latter have access to alternative sources of information. The findings highlight the need to elaborate the construct of gatekeeping by rethinking its relevance in the networked information environments where the traditional picture of gatekeepers controlling access to information sources is eroding.Research limitations/implicationsAs the study focuses on how expert power figures in gatekeeping, no attention is devoted to the role of social power of other types, for example, reward power and referent power.Originality/valueThe study pioneers by providing an in-depth analysis of the nature of expert power as a constituent of gatekeeping.

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