scholarly journals Genome Analysis of Phytophthora nicotianae JM01 Provides Insights into Its Pathogenicity Mechanisms

Plants ◽  
2021 ◽  
Vol 10 (8) ◽  
pp. 1620
Author(s):  
Xiao-Long Yuan ◽  
Cheng-Sheng Zhang ◽  
Fan-Yu Kong ◽  
Zhong-Feng Zhang ◽  
Feng-Long Wang
Keyword(s):  
Genome Analysis ◽  
Plant Pathogen ◽  
Gc Content ◽  
Gene Families ◽  
Phytophthora Nicotianae ◽  
Glycoside Hydrolases ◽  
Economic Losses ◽  
Whole Genome ◽  
Pathogenic Mechanisms ◽  
A Genome

Phytophthora nicotianae is a widely distributed plant pathogen that can cause serious disease and cause significant economic losses to various crops, including tomatoes, tobacco, onions, and strawberries. To understand its pathogenic mechanisms and explore strategies for controlling diseases caused by this pathogen, we sequenced and analyzed the whole genome of Ph. nicotianae JM01. The Ph. nicotianae JM01 genome was assembled using a combination of approaches including shotgun sequencing, single-molecule sequencing, and the Hi-C technique. The assembled Ph. nicotianae JM01 genome is about 95.32 Mb, with contig and scaffold N50 54.23 kb and 113.15 kb, respectively. The average GC content of the whole-genome is about 49.02%, encoding 23,275 genes. In addition, we identified 19.15% of interspersed elements and 0.95% of tandem elements in the whole genome. A genome-wide phylogenetic tree indicated that Phytophthora diverged from Pythium approximately 156.32 Ma. Meanwhile, we found that 252 and 285 gene families showed expansion and contraction in Phytophthora when compared to gene families in Pythium. To determine the pathogenic mechanisms Ph. nicotianae JM01, we analyzed a suite of proteins involved in plant–pathogen interactions. The results revealed that gene duplication contributed to the expansion of Cell Wall Degrading Enzymes (CWDEs) such as glycoside hydrolases, and effectors such as Arg-Xaa-Leu-Arg (RXLR) effectors. In addition, transient expression was performed on Nicotiana benthamiana by infiltrating with Agrobacterium tumefaciens cells containing a cysteine-rich (SCR) protein. The results indicated that SCR can cause symptoms of hypersensitive response. Moreover, we also conducted comparative genome analysis among four Ph. nicotianae genomes. The completion of the Ph. nicotianae JM01 genome can not only help us understand its genomic characteristics, but also help us discover genes involved in infection and then help us understand its pathogenic mechanisms.

scholarly journals Efficient and accurate determination of genome-wide DNA methylation patterns in Arabidopsis thaliana with enzymatic methyl sequencing

2020 ◽  
Vol 13 (1) ◽  
Author(s):  
Suhua Feng ◽  
Zhenhui Zhong ◽  
Ming Wang ◽  
Steven E. Jacobsen
Keyword(s):  
Dna Methylation ◽  
Bisulfite Sequencing ◽  
Accurate Determination ◽  
Gc Content ◽  
Epigenetic Mark ◽  
Whole Genome ◽  
Whole Genome Bisulfite Sequencing ◽  
Genome Wide ◽  
A Genome ◽  
Genome Bisulfite Sequencing

Abstract Background 5′ methylation of cytosines in DNA molecules is an important epigenetic mark in eukaryotes. Bisulfite sequencing is the gold standard of DNA methylation detection, and whole-genome bisulfite sequencing (WGBS) has been widely used to detect methylation at single-nucleotide resolution on a genome-wide scale. However, sodium bisulfite is known to severely degrade DNA, which, in combination with biases introduced during PCR amplification, leads to unbalanced base representation in the final sequencing libraries. Enzymatic conversion of unmethylated cytosines to uracils can achieve the same end product for sequencing as does bisulfite treatment and does not affect the integrity of the DNA; enzymatic methylation sequencing may, thus, provide advantages over bisulfite sequencing. Results Using an enzymatic methyl-seq (EM-seq) technique to selectively deaminate unmethylated cytosines to uracils, we generated and sequenced libraries based on different amounts of Arabidopsis input DNA and different numbers of PCR cycles, and compared these data to results from traditional whole-genome bisulfite sequencing. We found that EM-seq libraries were more consistent between replicates and had higher mapping and lower duplication rates, lower background noise, higher average coverage, and higher coverage of total cytosines. Differential methylation region (DMR) analysis showed that WGBS tended to over-estimate methylation levels especially in CHG and CHH contexts, whereas EM-seq detected higher CG methylation levels in certain highly methylated areas. These phenomena can be mostly explained by a correlation of WGBS methylation estimation with GC content and methylated cytosine density. We used EM-seq to compare methylation between leaves and flowers, and found that CHG methylation level is greatly elevated in flowers, especially in pericentromeric regions. Conclusion We suggest that EM-seq is a more accurate and reliable approach than WGBS to detect methylation. Compared to WGBS, the results of EM-seq are less affected by differences in library preparation conditions or by the skewed base composition in the converted DNA. It may therefore be more desirable to use EM-seq in methylation studies.

scholarly journals Whole-Genome Analysis of Porcine Circovirus Type 2 in Russia

Pathogens ◽  
2021 ◽  
Vol 10 (12) ◽  
pp. 1631
Author(s):  
Sergei Raev ◽  
Anton Yuzhakov ◽  
Taras Aliper
Keyword(s):  
Genetic Diversity ◽  
Genome Analysis ◽  
Porcine Circovirus Type ◽  
Porcine Circovirus Type 2 ◽  
Porcine Circovirus ◽  
Economic Losses ◽  
Whole Genome ◽  
Whole Genome Analysis ◽  
Reading Frame

Porcine circovirus type 2 (PCV2) is the causative agent of porcine circovirus-associated diseases (PCVAD) that bring about significant economic losses in the pig industry all over the world. The aim of this study was to investigate the genetic diversity of PCV2 in Russia and characterize the available complete genome sequences. PCV2 DNA was detected at all investigated farms located in different regions of Russia. Whole-genome analysis demonstrated that the majority of PCV2 strains belonged to genotype PCV2d (12 out of 14), while PCV2a and PCV2b were only detected at 2 farms (one at each). Further analysis revealed that all antibody recognition sites in Russian PCV2 strains were different from the corresponding epitopes in a PCV2a vaccine strain, suggesting that PCV2a-based vaccines may only provide limited protection against these strains. PCV2d strains could be grouped into 3 distinct lines which shared 98.7–100% identity within open reading frame 2 (ORF2). It is the first study reporting the genetic diversity of PCV2 strains in Russia. Our data indicated that, similarly to China, Europe, and USA, PCV2a and PCV2b have largely been replaced by PCV2d.

scholarly journals Improved whole genome sequence of Phytophthora capsici generated by long-read sequencing

2021 ◽  
Author(s):  
Jinxia Shi ◽  
Wenwu Ye ◽  
Dongfang Ma ◽  
Junliang Yin ◽  
Zhichao Zhang ◽  
...  
Keyword(s):  
Genome Sequence ◽  
De Novo ◽  
Phytophthora Capsici ◽  
Management Strategies ◽  
Gc Content ◽  
Whole Genome Sequence ◽  
Economic Losses ◽  
Whole Genome ◽  
Vegetable Crops ◽  
Long Read

The soil-borne oomycete Phytophthora capsici is the most destructive pathogen of vegetable crops and is responsible for substantial economic losses worldwide. Here, we present an improved genome assembly of P. capsici generated by Oxford Nanopore long-read sequencing (for de novo assembly) and Illumina short-read sequencing (for polishing). The genome of P. capsici is 100.5 Mb in length (GC content = 50.8%) and contains 26,069 predicted protein-coding genes. The whole genome of P. capsici is assembled into 194 scaffolds, 90% of which are larger than 300 kb. The N50 scaffold length and maximum scaffold length are 1.0 and 4.1 Mb, respectively. The whole genome sequence of P. capsici will broaden our knowledge of this pathogen and enhance our understanding of the molecular basis of its pathogenicity, which will facilitate the development of effective management strategies.

Biological characteristics and whole-genome analysis of the Enterococcus faecalis phage PEf771

2020 ◽  
Vol 66 (9) ◽  
pp. 505-520 ◽  
Author(s):  
Yingying Xiang ◽  
Wenyu Li ◽  
Fei Song ◽  
Xianghong Yang ◽  
Jing Zhou ◽  
...  
Keyword(s):  
Enterococcus Faecalis ◽  
Burst Size ◽  
Gc Content ◽  
Lytic Cycle ◽  
Proteinase K ◽  
Host Bacterium ◽  
Whole Genome ◽  
Strain Specificity ◽  
Whole Genome Analysis ◽  
A Genome

Enterococcus faecalis is a common pathogen causing refractory periapical periodontitis and secondary intraradicular infections. In this study, E. faecalis YN771 isolated from a re-treated root canal at a stomatology department was used as the host bacterium and was co-cultured with wastewater from the same department and patient samples to isolate a phage that lyses E. faecalis. We studied the biological and genomic characteristics of this phage. Transmission electron microscopy showed that this phage’s head is icosahedral in structure, with a head diameter of around 98.4 nm, and a contractile tail of around 228.5 nm in length and a diameter of 17.3 nm. The phage was identified as a member of the Myoviridae family and named PEf771. It is sensitive to proteinase K but resistant to chloroform and Triton X-100. Its lytic cycle is 45 min, burst size is 78, optimal multiplicity of infection is 0.1, lysis spectrum is narrow, and host strain specificity is strong. Its optimal growth temperature is 37 °C, most suitable pH is 6.0, and is sensitive to ultraviolet radiation. Whole-genome sequencing of PEf771 indicated it has a genome size of 151 052 bp, with a GC content of 36.97%, and encodes 197 proteins plus 26 tRNAs. PEf771 is most closely related to E. faecalis phage EFDG1. Phage PEf771 has strong host specificity and lytic ability, so it is important to further characterize this phage and its interaction with E. faecalis.

scholarly journals A chromosome‐level genome assembly of Brachymystax lenok tsinlingensis provides new insights into salmonids evolution

2021 ◽  
Author(s):  
Wenbo Zhu ◽  
Zhongkai Wang ◽  
Haorong Li ◽  
Hui Xiang ◽  
Ping Li ◽  
...  
Keyword(s):  
Genome Assembly ◽  
Whole Genome Duplication ◽  
Genome Duplication ◽  
Gc Content ◽  
Gene Families ◽  
Whole Genome ◽  
Genome Duplication Event ◽  
Brachymystax Lenok Tsinlingensis ◽  
Brachymystax Lenok ◽  
Chromosome Level

The salmonid-specific fourth vertebrate whole-genome duplication (Ss4R) occurred ~80 million years ago in the ancestor of all salmonids and provides a unique opportunity to study the evolutionary history of the duplicated genome. Study of the genome of Brachymystax lenok tsinlingensis might be particularly insightful given that this is the only Brachymystax species with a published salmonid genome. Here, we present a high-quality chromosome-level genome assembly for B. l. tsinlingensis and found that the salmonids have a unique GC content and codon usage, have undergone a whole-genome duplication event and a burst of transposon-mediated repeat expansion, have a slower evolutionary rate, and possess specific expanded gene families and unique positively selected genes. Generally, the B. l. tsinlingensis genome could provide a valuable reference for the study of other salmonids as well as aid the conservation of this endangered species.

scholarly journals STARRPeaker: Uniform processing and accurate identification of STARR-seq active regions

2019 ◽  
Author(s):  
Donghoon Lee ◽  
Manman Shi ◽  
Jennifer Moran ◽  
Martha Wall ◽  
Jing Zhang ◽  
...  
Keyword(s):  
Negative Binomial ◽  
Accurate Determination ◽  
Regulatory Region ◽  
Gc Content ◽  
Active Regions ◽  
Clear Correlation ◽  
Whole Genome ◽  
Accurate Identification ◽  
Genomic Libraries ◽  
A Genome

AbstractBackgroundHigh-throughput reporter assays, such as self-transcribing active regulatory region sequencing (STARR-seq), allow for unbiased and quantitative assessment of enhancers at a genome-wide scale. Recent advances in STARR-seq technology have employed progressively more complex genomic libraries and increased sequencing depths, to assay larger sized regions, up to the entire human genome. These advances necessitate a reliable processing pipeline and peak-calling algorithm.ResultsMost STARR-seq studies have relied on chromatin immunoprecipitation sequencing (ChIP-seq) processing pipelines. However, there are key differences in STARR-seq versus ChIP-seq. First, STARR-seq uses transcribed RNA to measure the activity of an enhancer, making an accurate determination of the basal transcription rate important. Second, STARR-seq coverage is highly non-uniform, overdispersed, and often confounded by sequencing biases, such as GC content and mappability. Lastly, here, we observed a clear correlation between RNA thermodynamic stability and STARR-seq readout, suggesting that STARR-seq may be sensitive to RNA secondary structure and stability. Considering these findings, we developed a negative-binomial regression framework for uniformly processing STARR-seq data, called STARRPeaker. In support of this, we generated whole-genome STARR-seq data from the HepG2 and K562 human cell lines and applied STARRPeaker to call enhancers.ConclusionsWe show STARRPeaker can unbiasedly detect active enhancers from both captured and whole-genome STARR-seq data. Specifically, we report ∼33,000 and ∼20,000 candidate enhancers from HepG2 and K562, respectively. Moreover, we show that STARRPeaker outperforms other peak callers in terms of identifying known enhancers with fewer false positives. Overall, we demonstrate an optimized processing framework for STARR-seq experiments can identify putative enhancers while addressing potential confounders.

scholarly journals Efficient and Accurate Determination of Genome-Wide DNA Methylation Patterns in Arabidopsis with Enzymatic Methyl Sequencing.

2020 ◽  
Author(s):  
Suhua Feng ◽  
Zhenhui Zhong ◽  
Ming Wang ◽  
Steven E. Jacobsen
Keyword(s):  
Dna Methylation ◽  
Bisulfite Sequencing ◽  
Accurate Determination ◽  
Gc Content ◽  
Epigenetic Mark ◽  
Whole Genome ◽  
Whole Genome Bisulfite Sequencing ◽  
Genome Wide ◽  
A Genome ◽  
Genome Bisulfite Sequencing

Abstract Background: 5’ methylation of cytosines in DNA molecules is an important epigenetic mark in eukaryotes. Bisulfite sequencing is the gold standard of DNA methylation detection, and whole-genome bisulfite sequencing (WGBS) has been widely used to detect methylation at single-nucleotide resolution on a genome-wide scale. However, sodium bisulfite is known to severely degrade DNA, which, in combination with biases introduced during PCR amplification, leads to unbalanced base representation in the final sequencing libraries. Enzymatic conversion of unmethylated cytosines to uracils can achieve the same end product for sequencing as does bisulfite treatment and does not affect the integrity of the DNA; enzymatic methylation sequencing may thus provide advantages over bisulfite sequencing.Results: Using an enzymatic methyl-seq (EM-seq) technique to selectively deaminate unmethylated cytosines to uracils, we generated and sequenced libraries based on different amounts of Arabidopsis input DNA and different numbers of PCR cycles, and compared these data to results from traditional whole genome bisulfite sequencing. We found that EM-seq libraries were more consistent between replicates and had higher mapping and lower duplication rates, lower background noise, higher average coverage, and higher coverage of total cytosines. Differential methylation region (DMR) analysis showed that WGBS tended to over-estimate methylation levels especially in CHG and CHH contexts, whereas EM-seq detected higher CG methylation levels in certain highly methylated areas. These phenomena can be mostly explained by a correlation of WGBS methylation estimation with GC content and methylated cytosine density. We used EM-seq to compare methylation between leaves and flowers, and found that CHG methylation level is greatly elevated in flowers, especially in pericentromeric regions. Conclusion: We suggest that EM-seq is a more accurate and reliable approach than WGBS to detect methylation. Compared to WGBS, the results of EM-seq are less affected by differences in library preparation conditions or by the skewed base composition in the converted DNA. It may therefore be more desirable to use EM-seq in methylation studies.

scholarly journals Hemicellulosic biomass conversion by Moroccan hot spring Bacillus paralicheniformis CCMM B940 evidenced by glycoside hydrolase activities and whole genome sequencing

3 Biotech ◽  
2021 ◽  
Vol 11 (8) ◽  
Author(s):  
Soufiane Maski ◽  
Serigne Inssa Ngom ◽  
Bahia Rached ◽  
Taha Chouati ◽  
Mohamed Benabdelkhalek ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Plant Cell Wall ◽  
Hot Spring ◽  
Thermophilic Bacteria ◽  
Draft Genome ◽  
Glycoside Hydrolases ◽  
Whole Genome ◽  
A Genome ◽  
Bacillus Paralicheniformis

AbstractThermophilic bacteria, especially from the genus Bacillus, constitute a huge potential source of novel enzymes that could be relevant for biotechnological applications. In this work, we described the cellulose and hemicellulose-related enzymatic activities of the hot spring Bacillus aerius CCMM B940 from the Moroccan Coordinated Collections of Microorganisms (CCMM), and revealed its potential for hemicellulosic biomass utilization. Indeed, B940 was able to degrade complex polysaccharides such as xylan and lichenan and exhibited activity towards carboxymethylcellulose. The strain was also able to grow on agriculture waste such as orange and apple peels as the sole carbon source. Whole-genome sequencing allowed the reclassification of CCMM B940 previously known as B. aerius into Bacillus paralicheniformis since the former species name has been rejected. The draft genome reported here is composed of 38 contigs resulting in a genome of 4,315,004 bp and an average G + C content of 45.87%, and is an important resource for illuminating the molecular mechanisms of carbohydrate metabolism. The annotated genomic sequences evidenced more than 52 genes encoding glycoside hydrolases and pectate lyases belonging to 27 different families of CAZymes that are involved in the degradation of plant cell wall carbohydrates. Genomic predictions in addition to in vitro experiments have revealed broad hydrolytic capabilities of the strain, thus reinforcing its relevance for biotechnology applications.

scholarly journals GAAP: A Genome Assembly + Annotation Pipeline

2019 ◽  
Vol 2019 ◽  
pp. 1-12 ◽  
Author(s):  
Jinhwa Kong ◽  
Sun Huh ◽  
Jung-Im Won ◽  
Jeehee Yoon ◽  
Baeksop Kim ◽  
...  
Keyword(s):  
Genome Analysis ◽  
De Novo ◽  
Transcriptome Assembly ◽  
Genomic Analysis ◽  
Whole Genome ◽  
High Throughput Analysis ◽  
Whole Genome Analysis ◽  
A Genome ◽  
Base Sequences ◽  
Wide Range

Genomic analysis begins with de novo assembly of short-read fragments in order to reconstruct full-length base sequences without exploiting a reference genome sequence. Then, in the annotation step, gene locations are identified within the base sequences, and the structures and functions of these genes are determined. Recently, a wide range of powerful tools have been developed and published for whole-genome analysis, enabling even individual researchers in small laboratories to perform whole-genome analyses on their objects of interest. However, these analytical tools are generally complex and use diverse algorithms, parameter setting methods, and input formats; thus, it remains difficult for individual researchers to select, utilize, and combine these tools to obtain their final results. To resolve these issues, we have developed a genome analysis pipeline (GAAP) for semiautomated, iterative, and high-throughput analysis of whole-genome data. This pipeline is designed to perform read correction, de novo genome (transcriptome) assembly, gene prediction, and functional annotation using a range of proven tools and databases. We aim to assist non-IT researchers by describing each stage of analysis in detail and discussing current approaches. We also provide practical advice on how to access and use the bioinformatics tools and databases and how to implement the provided suggestions. Whole-genome analysis of Toxocara canis is used as case study to show intermediate results at each stage, demonstrating the practicality of the proposed method.

scholarly journals Whole-Genome Sequencing of Micrococcus luteus MT1691313, Isolated from the Mariana Trench

2021 ◽  
Vol 10 (23) ◽  
Author(s):  
Zhen Wang ◽  
Ji-xing Feng ◽  
Xue-peng Li ◽  
Jian Zhang
Keyword(s):  
Genome Sequencing ◽  
Deep Sea ◽  
Micrococcus Luteus ◽  
Gc Content ◽  
Whole Genome ◽  
Positive Bacterium ◽  
Mariana Trench ◽  
Content Type ◽  
Deep Sea Sediment ◽  
A Genome

Micrococcus luteus MT1691313 is a Gram-positive bacterium isolated from the deep-sea sediment located at a −4,448-m depth in the Mariana Trench. Here, we report the complete genome sequence of this strain, which has a genome size of 2.32 Mb with a GC content of 72.04%.

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