scholarly journals Comparing the cariogenic species Streptococcus sobrinus and S. mutans on whole genome level

2014 ◽  
Vol 6 (1) ◽  
pp. 26189 ◽  
Author(s):  
Georg Conrads ◽  
Johannes J. de Soet ◽  
Lifu Song ◽  
Karsten Henne ◽  
Helena Sztajer ◽  
...  
Keyword(s):  
Whole Genome ◽  
Streptococcus Sobrinus ◽  
Genome Level

On the Identification of Clinically Relevant Bacterial Amino Acid Changes at the Whole Genome Level Using Auto-PSS-Genome

2021 ◽  
Author(s):  
Hugo López-Fernández ◽  
Cristina P. Vieira ◽  
Pedro Ferreira ◽  
Paula Gouveia ◽  
Florentino Fdez-Riverola ◽  
...  
Keyword(s):  
Amino Acid ◽  
Whole Genome ◽  
Genome Level

148 Multiple Dysregulated Novel Pathways and Genes in Aleutian Mink Disease Revealed by Selection Signatures and Gene Network Analyses Using Whole-genome Sequence Data

2021 ◽  
Vol 99 (Supplement_3) ◽  
pp. 76-76
Author(s):  
Seyed Milad Vahedi ◽  
Karim Karimi ◽  
Siavash Salek Ardestani ◽  
Younes Miar
Keyword(s):  
Sequence Data ◽  
American Mink ◽  
Enrichment Analysis ◽  
Whole Genome Sequence ◽  
Fixation Index ◽  
Pathway Enrichment Analysis ◽  
Whole Genome ◽  
Nucleotide Polymorphisms ◽  
Network Analyses ◽  
Genome Level

Abstract Aleutian disease (AD) is a chronic persistent infection in domestic mink caused by Aleutian mink disease virus (AMDV). Female mink’s fertility and pelt quality depression are the main reasons for the AD’s negative economic impacts on the mink industry. A total number of 79 American mink from the Canadian Center for Fur Animal Research at Dalhousie University (Truro, NS, Canada) were classified based on the results of counter immunoelectrophoresis (CIEP) tests into two groups of positive (n = 48) and negative (n = 31). Whole-genome sequences comprising 4,176 scaffolds and 8,039,737 single nucleotide polymorphisms (SNPs) were used to trace the selection footprints for response to AMDV infection at the genome level. Window-based fixation index (Fst) and nucleotide diversity (θπ) statistics were estimated to compare positive and negative animals’ genomes. The overlapped top 1% genomic windows between two statistics were considered as potential regions underlying selection pressures. A total of 98 genomic regions harboring 33 candidate genes were detected as selective signals. Most of the identified genes were involved in the development and functions of immune system (PPP3CA, SMAP2, TNFRSF21, SKIL, and AKIRIN2), musculoskeletal system (COL9A2, PPP1R9A, ANK2, AKAP9, and STRIT1), nervous system (ASCL1, ZFP69B, SLC25A27, MCF2, and SLC7A14), reproductive system (CAMK2D, GJB7, SSMEM1, C6orf163), liver (PAH and DPYD), and lung (SLC35A1). Gene-expression network analysis showed the interactions among 27 identified genes. Moreover, pathway enrichment analysis of the constructed genes network revealed significant oxytocin (KEGG: hsa04921) and GnRH signaling (KEGG: hsa04912) pathways, which are likely to be impaired by AMDV leading to dams’ fecundity reduction. These results provided a perspective to the genetic architecture of response to AD in American mink and novel insight into the pathogenesis of AMDV.

scholarly journals Characterization and analysis ofCCRandCADgene families at the whole-genome level for lignin synthesis of stone cells in pear (Pyrus bretschneideri) fruit

Biology Open ◽  
2017 ◽  
Vol 6 (11) ◽  
pp. 1602-1613 ◽  
Author(s):  
Xi Cheng ◽  
Manli Li ◽  
Dahui Li ◽  
Jinyun Zhang ◽  
Qing Jin ◽  
...  
Keyword(s):  
Whole Genome ◽  
Lignin Synthesis ◽  
Genome Level

scholarly journals Systematic Identification of Pathogenic Streptomyces sp. AMCC400023 That Causes Common Scab and Genomic Analysis of Its Pathogenicity Island

2019 ◽  
Vol 109 (7) ◽  
pp. 1115-1128 ◽  
Author(s):  
Feiyang Liang ◽  
Rongshan Lin ◽  
Yaqian Yao ◽  
Yunli Xiao ◽  
Mingshuo Zhang ◽  
...  
Keyword(s):  
Common Scab ◽  
Taxonomic Status ◽  
Pathogenicity Island ◽  
Economic Losses ◽  
Whole Genome ◽  
Streptomyces Species ◽  
Streptomyces Sp ◽  
Soilborne Disease ◽  
Thaxtomin A ◽  
Genome Level

Potato scab, a serious soilborne disease caused by Streptomyces spp., occurs in potato-growing areas worldwide and results in severe economic losses. In this paper, the pathogenicity of Streptomyces strain AMCC400023, isolated from potato scabs in Hebei Province, China, was verified systematically by the radish seedling test, the potato tuber slice assay, the potted back experiment, and the detection of phytotoxin thaxtomin A. Morphological, physiological, and biochemical characteristics were determined, and the 16S ribosomal RNA analyses of Streptomyces sp. AMCC400023 were carried out. To obtain the accurate taxonomic status of the pathogen strain, the whole genome was sequenced, and the phylogenetic tree among 31 Streptomyces genomes was formed. The average nucleotide identity (ANI) and in silico DNA-DNA hybridization (isDDH) were analyzed, and at the same time, the toxicity-related genes between Streptomyces sp. AMCC400023 and Streptomyces scabiei were compared, all based on the whole-genome level. All of the data supported that, instead of a member of S. scabiei, test strain Streptomyces sp. AMCC400023 was a distinct phytopathogen of potato common scab, which had a relatively close relationship with S. scabiei while separating clearly from S. scabiei at least in the species level of taxonomic status. The complete pathogenicity island (PAI) composition of Streptomyces sp. AMCC400023 was identified, which contained a toxin region and a colonization region. It was conjectured that the PAI of Streptomyces sp. AMCC400023 might be directly or indirectly acquired from S. scabiei 87-22 by horizontal gene transfer, or at the very least, there was a very close homologous relationship between the two pathogens as indicated by a series of analyses, such as phylogenetic relationships among 31 Streptomyces species, ANI and isDDH analyses, PAI structure mapping, thaxtomin A synthetic gene cluster tree construction, and most important, the collinearity analysis at the genome level.

scholarly journals Whole genome sequence analysis of rice genotypes with contrasting response to salinity stress

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Prasanta K. Subudhi ◽  
Rama Shankar ◽  
Mukesh Jain
Keyword(s):  
Salt Tolerance ◽  
Dna Polymorphisms ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
Salt Tolerant ◽  
Tolerance Mechanisms ◽  
Rice Varieties ◽  
Genome Wide ◽  
Rice Genotypes ◽  
Genome Level

AbstractSalinity is a major abiotic constraint for rice farming. Abundant natural variability exists in rice germplasm for salt tolerance traits. Since few studies focused on the genome level variation in rice genotypes with contrasting response to salt stress, genomic resequencing in diverse genetic materials is needed to elucidate the molecular basis of salt tolerance mechanisms. The whole genome sequences of two salt tolerant (Pokkali and Nona Bokra) and three salt sensitive (Bengal, Cocodrie, and IR64) rice genotypes were analyzed. A total of 413 million reads were generated with a mean genome coverage of 93% and mean sequencing depth of 18X. Analysis of the DNA polymorphisms revealed that 2347 nonsynonymous SNPs and 51 frameshift mutations could differentiate the salt tolerant from the salt sensitive genotypes. The integration of genome-wide polymorphism information with the QTL mapping and expression profiling data led to identification of 396 differentially expressed genes with large effect variants in the coding regions. These genes were involved in multiple salt tolerance mechanisms, such as ion transport, oxidative stress tolerance, signal transduction, and transcriptional regulation. The genome-wide DNA polymorphisms and the promising candidate genes identified in this study represent a valuable resource for molecular breeding of salt tolerant rice varieties.

Grafting-responsive miRNAs in cucumber and pumpkin seedlings identified by high-throughput sequencing at whole genome level

2013 ◽  
Vol 151 (4) ◽  
pp. 406-422 ◽  
Author(s):  
Chaohan Li ◽  
Yansu Li ◽  
Longqiang Bai ◽  
Tieyao Zhang ◽  
Chaoxing He ◽  
...  
Keyword(s):  
High Throughput ◽  
High Throughput Sequencing ◽  
Whole Genome ◽  
Genome Level

scholarly journals Prevalence and Genetic Diversity of Listeria monocytogenes Isolated From Retail Pork in Wuhan, China

2021 ◽  
Vol 12 ◽  
Author(s):  
Yiqian Wang ◽  
Qiang Ji ◽  
Shaowen Li ◽  
Mei Liu
Keyword(s):  
Listeria Monocytogenes ◽  
Whole Genome ◽  
Whole Genome Analysis ◽  
Supply Source ◽  
Antibiotic Resistant ◽  
Resistant Genes ◽  
Genetic Makeup ◽  
Genome Level ◽  
Pork Samples ◽  
Cas Proteins

Listeria monocytogenes is a ubiquitous bacteria and causative agent of zoonotic listeriosis with high mortality. The consumption of contaminated animal-derived foods has been linked with both epidemic and sporadic listeriosis. In this work, a total of 64 L. monocytogenes isolates from 259 pork samples sold in 11 supermarket chains were identified and characterized by comparative whole-genome analysis. All isolates were delineated into eight clonal complexes (CCs), namely CC2, CC8, CC9, CC11, CC155, CC121, CC204, and CC619, spanning two lineages (I and II) and carrying 3–5 antibiotic-resistant genes (fosX, lnu, mprF, tetM, and dhfR). It is noted that Listeria pathogenicity island (LIPI)-1, LIPI-3, and LIPI-4 were distributed in all ST619 isolates from two supermarket chains that were closely related with clinical isolates (<40 SNP). Some of the isolates from different supermarket chains with 0 SNP difference indicated a common pork supply source. Notably, 57.81% of the strains carried types IB, IIA, or IIIB CRISPR-Cas system, CC121 isolates carried both types IB and IIA CRISPR-Cas systems, Cas proteins of CC155 isolates located between two CRISPR loci, each CC has unique organization of Cas proteins as well as CRISPR loci. CRISPR-Cas system-based subtyping improved discrimination of pork-derived L. monocytogenes isolates. Comparisons at the genome level contributed to understand the genetic diversities and variations among the isolates and provided insights into the genetic makeup and relatedness of these pathogens.

scholarly journals Conversion of Genomic DNA to Proxy Constructs Suitable for Accurate Nanopore Sequencing

2015 ◽  
Author(s):  
Dimitra Tsavachidou
Keyword(s):  
Dna Sequence ◽  
Genomic Dna ◽  
Average Length ◽  
Consensus Sequence ◽  
Whole Genome ◽  
Nanopore Sequencing ◽  
Ion Torrent ◽  
Dna Molecules ◽  
Dna Fragment ◽  
Genome Level

AbstractNanopore sequencing at single-base resolution is challenging. There are developing technologies to convert DNA molecules to expanded constructs. Such constructs can be sequenced by nanopores in place of the original DNA molecules. We present a novel method for converting genomic DNA to expanded constructs (“proxies”) with 99.67% accuracy. Our method “reads” each base in each DNA fragment and appends an oligonucleotide to the DNA fragment after each base “reading”. Each appended oligonucleotide represents a specific base type, so that the proxy construct consisting of all the appended oligonucleotides faithfully represents the original DNA sequence. We generated proxies for genomic DNA and confirmed the identities of both the proxies and their corresponding original DNA sequences by performing sequencing using Ion Torrent sequencer.Conversion to proxies had only 0.33% raw error rate. Errors were: 93.96% deletions, 5.29% insertions, and 0.74% substitutions. The longest sequenced proxy was 170 bases, corresponding to a 17-base original DNA sequence. The short length of the detected proxies reflected restrictions imposed by Ion Torrent’s short reads and was not caused by limitations of our method. The consensus sequence built by using proxies alone (average length: 120 bases; corresponding to original sequences with average length 12 bases) covered 55% of the reference genome with 100% accuracy, and outperformed the Ion Torrent sequencing of the corresponding original DNA fragments in terms of accuracy, coverage and number of aligned sequences. Data and other materials can be found at http://www.vastogen.com/data.html. This proof-of-concept experiment demonstrates highly accurate proxy construction at the whole genome level. To our knowledge, this is the first demonstrated construction of expanded versions of DNA at the whole genome level.

scholarly journals Pangolin homology associated with 2019-nCoV

2020 ◽  
Author(s):  
Tao Zhang ◽  
Qunfu Wu ◽  
Zhigang Zhang
Keyword(s):  
Amino Acid ◽  
Intermediate Host ◽  
Common Ancestor ◽  
Whole Genome ◽  
Amino Acid Residues ◽  
Pathogenic Potential ◽  
Lowest Common Ancestor ◽  
Amino Acid Mutations ◽  
Genome Level ◽  
Novel Coronavirus

AbstractTo explore potential intermediate host of a novel coronavirus is vital to rapidly control continuous COVID-19 spread. We found genomic and evolutionary evidences of the occurrence of 2019-nCoV-like coronavirus (named as Pangolin-CoV) from dead Malayan Pangolins. Pangolin-CoV is 91.02% and 90.55% identical at the whole genome level to 2019-nCoV and BatCoV RaTG13, respectively. Pangolin-CoV is the lowest common ancestor of 2019-nCoV and RaTG13. The S1 protein of Pangolin-CoV is much more closely related to 2019-nCoV than RaTG13. Five key amino-acid residues involved in the interaction with human ACE2 are completely consistent between Pangolin-CoV and 2019-nCoV but four amino-acid mutations occur in RaTG13. It indicates Pangolin-CoV has similar pathogenic potential to 2019-nCoV, and would be helpful to trace the origin and probable intermediate host of 2019-nCoV.

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