Chaenomeles (family Rosaceae) is a genus of five diploid species of deciduous spiny shrubs that are native to Central Asia and Japan. It is an important horticultural crop (commonly known as ...flowering quinces) in Europe and Asia for its high yield in fruits that are rich in juice, aroma, and dietary fiber. Therefore, the development of effective genetic markers of Chaenomeles species is advantageous for crop improvement through breeding and selection. In this study, we successfully assembled and analyzed the chloroplast genome of five Chaenomeles species. The chloroplast genomes of the five Chaenomeles species were very similar with no structural or content rearrangements among them. The chloroplast genomes ranged from 159,436 to 160,040 bp in length and contained a total of 112 unique genes, including 78 protein-coding genes, 30 tRNAs, and 4 rRNAs. Three highly variable regions, including trnR-atpA, trnL-F, and rpl32-ccsA, were identified. Phylogenetic analysis based on the complete chloroplast genome showed that Chaenomeles forms a monophyletic clade and had a close relationship with the genera Docynia and Malus. Analyses for phylogenetic relationships and the development of available genetic markers in future could provide valuable information regarding genetics and breeding mechanisms of the Chaenomeles species.
Anaerobic ammonium oxidation (anammox) combined with partial-denitrification (NO3 – → NO2 –) is an innovative process for the simultaneous removal of ammonia and nitrate from wastewaters. An ...efficient method for the selection of partial denitrifying community, which relies on increasing influent salinity, is described. Using this method, a denitratating community was enriched, which showed a nitrite accumulation efficiency higher than 75% as well as a high nitrate conversion efficiency. Community analysis using 16S rDNA indicated that Halomonas became the dominant genus as salinity increased. Metagenomic analysis revealed that there was not a significant difference in reads mapping to downstream denitrification genes in a comparison of samples from cultures with 5% salinity to those without salinity. The majority of the reads mapping to the genes encoding dissimilatory nitrate and nitrite reductases nar and nirS came from Halomonas under high salinity conditions. Two metagenome-assembled genomes taxonomically assigned to Halomonas were obtained, one of which accounted for ∼35% of the reads under high salinity conditions. Both genomes harbored the genes for the complete denitrification pathway. These results indicate progressive onset denitrifiers, a phenotype where nitrite reduction only occurs after nitrate exhaustion, could be successfully enriched with increasing salinity. Progressive onset denitrifiers may be more widespread in natural and artificial habitats than anticipated and are shown here to be valuable for nitrogen mitigating processes.
•A transcriptome of Populus tomentosa during cold stress has been analyzed.•This work identified numerous cold-related genes involved in sugar metabolisms, antioxidant defense system, hormone signal ...transduction and photosynthesis.•Our study provides valuable information for further studies on cold response mechanisms and genetic improvement of cold tolerance in Populus tomentosa.
Low temperature affects the growth, development, and even survival in plants. Populus tomentosa is a major industrial tree species used for timber and pulp manufacturing in northern China. Low temperature is an important stress factor for this species, and restricts its extensive cultivation and distribution. To face this problem, an understanding of the molecular mechanism underlying responses to cold stress in this species is necessary for molecular breeding. In this study, Illumina RNA-sequencing was employed to comprehensively investigate the gene expression profiles of P. tomentosa in response to cold stress. Two cDNA libraries from cold-treated and control samples were constructed and sequenced, generating a total of 94,226 unigenes. Of these, 1978 were differentially expressed, with 1468 upregulated and 510 downregulated. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes enrichment analyses identified the relevant biological functions and metabolic pathways of these differentially expressed genes. Based on enrichment results, a diverse range of cold response candidate genes were obtained and mainly involved in sugar metabolism, antioxidant defense system, hormone signal transduction, and photosynthesis, such as genes encoding sucrose synthase, superoxide dismutase, brassinosteroid-signaling kinase, and ferredoxin. Various transcription factors with divergent expression patterns were identified. Finally, RNA-seq data were validated using real-time quantitative polymerase chain reaction analyses. This study provides valuable information for further studies on cold response mechanisms and genetic improvement of cold tolerance in P. tomentosa.
Meiosis, although essential for reproduction, is also variable and error-prone: rates of chromosome crossover vary among gametes, between the sexes, and among humans of the same sex, and chromosome ...missegregation leads to abnormal chromosome numbers (aneuploidy)
. To study diverse meiotic outcomes and how they covary across chromosomes, gametes and humans, we developed Sperm-seq, a way of simultaneously analysing the genomes of thousands of individual sperm. Here we analyse the genomes of 31,228 human gametes from 20 sperm donors, identifying 813,122 crossovers and 787 aneuploid chromosomes. Sperm donors had aneuploidy rates ranging from 0.01 to 0.05 aneuploidies per gamete; crossovers partially protected chromosomes from nondisjunction at the meiosis I cell division. Some chromosomes and donors underwent more-frequent nondisjunction during meiosis I, and others showed more meiosis II segregation failures. Sperm genomes also manifested many genomic anomalies that could not be explained by simple nondisjunction. Diverse recombination phenotypes-from crossover rates to crossover location and separation, a measure of crossover interference-covaried strongly across individuals and cells. Our results can be incorporated with earlier observations into a unified model in which a core mechanism, the variable physical compaction of meiotic chromosomes, generates interindividual and cell-to-cell variation in diverse meiotic phenotypes.
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•A novel aerobic selenite reductase CsrF of Alishewanella sp. WH16-1 was identified.•The reduction of selenite and chromate formed Se(0) and Cr(III) nanoparticles.•The bacterial ...strain and enzyme have a great potential for bioremediation of heavy metals.
Alishewanella sp. WH16-1 is a facultative anaerobic bacterium isolated from mining soil. Under aerobic conditions, this bacterium efficiently reduces selenite and chromate. A flavoprotein showing 37% amino acid identity to E. coli chromate reductase ChrR was identified from the genome (named CsrF). Gene mutation and complementation along with heterologous expression revealed the ability of CsrF to reduce selenite and chromate in vivo. The purified CsrF was yellow and showed an absorption spectra similar to that of FMN. The molecular weight of CsrF was 23,906 for the monomer and 47,960 for the dimer. In vitro, CsrF catalyzes the reduction of Se(IV) and Cr(VI) using NAD(P)H as cofactors with optimal condition of pH 7.0 and temperature of 30–37°C. This enzyme also catalyze the reduction of sulfate and ferric iron but not arsenate and nitrate. Using NADPH as its electron donor, the Km for the reduction of Se(IV) and Cr(VI) was 204.1±27.91 and 250.6±23.46μmol/L, respectively. Site-directed mutagenesis showed that Arg13 and Gly113 were essential for the reduction of Se(IV) and Cr(VI). The products of the reduction of Se(IV) and Cr(VI) were Se(0)- and Cr(III)-nanoparticles, respectively. To our knowledge, CsrF is a novel and well-characterized bacterial aerobic selenite reductase.
Whole genome sequencing (WGS) of important foodborne pathogens is a technology under development, but is already employed in routine surveillance by public health agencies and is being increasingly ...exploited in tracing transmission routes and identifying contamination events (source tracking) that take place in the farm-to-fork continuum. Furthermore, data generated from WGS, complemented by other –omics data, have the potential to be integrated into and strengthen microbiological risk assessment. In this paper, we discuss the contribution of WGS in diverse areas important to food safety and public health. Additionally, an outlook of future WGS applications, which should contribute to our understanding of the ecology and physiology of foodborne microorganisms, is presented.
•Applications of whole genome sequencing (WGS) in surveillance are presented.•Suitability of WGS as a typing method for source tracking is discussed.•Potential of WGS data integration into risk assessment is evaluated.
•236 genome bins were extracted from metagenomic assembly in biogas reactors.•Existence of a core essential microbial group in biogas production system.•Expansion of the biogas microbiome database ...with 157 new genomes.•Comparison of metagenomes unveiled differences in phylogenetic distribution.
This research aimed to better characterize the biogas microbiome by means of high throughput metagenomic sequencing and to elucidate the core microbial consortium existing in biogas reactors independently from the operational conditions. Assembly of shotgun reads followed by an established binning strategy resulted in the highest, up to now, extraction of microbial genomes involved in biogas producing systems. From the 236 extracted genome bins, it was remarkably found that the vast majority of them could only be characterized at high taxonomic levels. This result confirms that the biogas microbiome is comprised by a consortium of unknown species. A comparative analysis between the genome bins of the current study and those extracted from a previous metagenomic assembly demonstrated a similar phylogenetic distribution of the main taxa. Finally, this analysis led to the identification of a subset of common microbes that could be considered as the core essential group in biogas production.
Theobroma cacao is one of the most economically important tropical trees, being the source of chocolate. As part of an ongoing study to understand the diversity of the badnavirus complex, responsible ...for the cacao swollen shoot virus disease in West Africa, evidence was found recently of virus-like sequences in asymptomatic cacao plants. The present study exploited the wealth of genomic resources in this crop, and combined bioinformatic, molecular, and genetic approaches to report for the first time the presence of integrated badnaviral sequences in most of the cacao genetic groups. These sequences, which we propose to name eTcBV for endogenous T. cacao bacilliform virus, varied in type with each predominating in a specific genetic group. A diagnostic multiplex PCR method was developed to identify the homozygous or hemizygous condition of one specific insert, which was inherited as a single Mendelian trait. These data suggest that these integration events occurred before or during the species diversification in Central and South America, and prior to its cultivation in other regions. Such evidence of integrated sequences is relevant to the management of cacao quarantine facilities and may also aid novel methods to reduce the impact of such viruses in this crop.
Klebsiella variicola is considered an emerging pathogen in humans and has been described in different environments. K. variicola belongs to Klebsiella pneumoniae complex, which has expanded the ...taxonomic classification and hindered epidemiological and evolutionary studies. The present work describes the molecular epidemiology of K. variicola based on MultiLocus Sequence Typing (MLST) developed for this purpose. In total, 226 genomes obtained from public data bases and 28 isolates were evaluated, which were mainly obtained from humans, followed by plants, various animals, the environment and insects. A total 166 distinct sequence types (STs) were identified, with 39 STs comprising at least two isolates. The molecular epidemiology of K. variicola showed a global distribution for some STs was observed, and in some cases, isolates obtained from different sources belong to the same ST. Several examples of isolates corresponding to kingdom-crossing bacteria from plants to humans were identified, establishing this as a possible route of transmission. goeBURST analysis identified Clonal Complex 1 (CC1) as the clone with the greatest distribution. Whole-genome sequencing of K. variicola isolates revealed extended-spectrum β-lactamase- and carbapenemase-producing strains with an increase in pathogenicity. MLST of K. variicola is a strong molecular epidemiological tool that allows following the evolution of this bacterial species obtained from different environments.
APOBEC3 family members are cytidine deaminases with roles in intrinsic responses to infection by retroviruses and retrotransposons, and in the control of other DNA viruses, such as herpesviruses, ...parvoviruses and hepatitis B virus. Although effects of APOBEC3 members on viral DNA have been demonstrated, it is not known whether they edit RNA genomes through cytidine deamination. Here, we investigated APOBEC3-mediated restriction of Coronaviridae. In experiments in vitro, three human APOBEC3 proteins (A3C, A3F and A3H) inhibited HCoV-NL63 infection and limited production of progeny virus, but did not cause hypermutation of the coronaviral genome. APOBEC3-mediated restriction was partially dependent on enzyme activity, and was reduced by the use of enzymatically inactive APOBEC3. Moreover, APOBEC3 proteins bound to the coronaviral nucleoprotein, and this interaction also affected viral replication. Although the precise molecular mechanism of deaminase-dependent inhibition of coronavirus replication remains elusive, our results further our understanding of APOBEC-mediated restriction of RNA virus infections.
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