scholarly journals Repertoire of SSRs in the Castor Bean Genome and Their Utilization in Genetic Diversity Analysis inJatropha curcas

2011 ◽  
Vol 2011 ◽  
pp. 1-9 ◽  
Author(s):  
Arti Sharma ◽  
Rajinder Singh Chauhan
Keyword(s):  
Linkage Mapping ◽  
Castor Bean ◽  
Seed Oil ◽  
Polymorphic Information Content ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
Dinucleotide Repeats ◽  
Whole Genome Analysis ◽  
Diversity Studies ◽  
Germplasm Analysis

Castor bean andJatrophacontain seed oil of industrial importance, share taxonomical and biochemical similarities, which can be explored for identifying SSRs in the whole genome sequence of castor bean and utilized inJatropha curcas. Whole genome analysis of castor bean identified 5,80,986 SSRs with a frequency of 1 per 680 bp. Genomic distribution of SSRs revealed that 27% were present in the non-genic region whereas 73% were also present in the putative genic regions with 26% in 5′UTRs, 25% in introns, 16% in 3′UTRs and 6% in the exons. Dinucleotide repeats were more frequent in introns, 5′UTRs and 3′UTRs whereas trinucleotide repeats were predominant in the exons. The transferability of randomly selected 302 SSRs, from castor bean to 49J. curcasgenotypes and 8Jatrophaspecies other thanJ. curcas, showed that 211 (~70%) amplified onJatrophaout of which 7.58% showed polymorphisms inJ. curcasgenotypes and 12.32% inJatrophaspecies. The higher rate of transferability of SSR markers from castor bean toJatrophacoupled with a good level of PIC (polymorphic information content) value (0.2 inJ. curcasgenotypes and 0.6 inJatrophaspecies) suggested that SSRs would be useful in germplasm analysis, linkage mapping, diversity studies and phylogenetic relationships, and so forth, inJ. curcasas well as otherJatrophaspecies.

Whole-genome analysis of Pandoraea species strains from cystic fibrosis patients

2019 ◽  
Vol 14 (16) ◽  
pp. 1357-1367
Author(s):  
Jumamurat R Bayjanov ◽  
Miquel B Ekkelenkamp ◽  
Malbert RC Rogers ◽  
Rafael Cantón ◽  
Barry J Benaissa-Trouw ◽  
...  
Keyword(s):  
Cystic Fibrosis ◽  
Core Genome ◽  
Genetic Characterization ◽  
Novel Species ◽  
Antibiotic Resistance Genes ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
Whole Genome Analysis ◽  
Acquired Antibiotic Resistance

Aim: Genetic characterization of Pandoraea strains recovered from cystic fibrosis patients. Materials & methods: The whole-genome sequence of 12 Pandoraea strains was determined using Illumina technology. The position of the strains within the genus Pandoraea was analyzed using selected partial gene sequences, core genome multi-locus sequence typing and average nucleotide identity analysis. Furthermore, the sequences were annotated. Results: The results show that some strains previously identified as Pandoraea pnomenusa, Pandoraea sputorum, Pandoraea oxalativorans and Pandoraea pulmonicola belong to novel species. The strains did not harbor acquired antibiotic resistance genes but encoded an OXA-type ß-lactamase. Conclusion: The taxonomy of the genus Pandoraea needs to be revised.

scholarly journals Whole-Genome Analysis of a Shiga Toxin-Producing Escherichia coli O103:H2 Strain Isolated from Cattle Feces

2020 ◽  
Vol 9 (45) ◽  
Author(s):  
Yujie Zhang ◽  
Yen-Te Liao ◽  
Vivian C. H. Wu
Keyword(s):  
Escherichia Coli ◽  
Shiga Toxin ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
Whole Genome Analysis ◽  
Content Type ◽  
Cattle Feces ◽  
Beef Products ◽  
Foodborne Outbreaks ◽  
Enterocyte Effacement

ABSTRACT Shiga toxin-producing Escherichia coli (STEC) serotype O103 is one of the primary pathogenic contaminants of beef products, contributing to several foodborne outbreaks in recent years. Here, we report the whole-genome sequence of a STEC O103:H2 strain isolated from cattle feces that contains a locus of enterocyte effacement (LEE) pathogenicity island.

scholarly journals Whole-genome analysis of Malawian Plasmodium falciparum isolates identifies potential targets of allele-specific immunity to clinical malaria

2020 ◽  
Author(s):  
Zalak Shah ◽  
Myo T Naung ◽  
Kara A Moser ◽  
Matthew Adams ◽  
Andrea G Buchwald ◽  
...  
Keyword(s):  
Plasmodium Falciparum ◽  
Sequence Data ◽  
Clinical Malaria ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
Whole Genome Analysis ◽  
Multiple Alleles ◽  
Vaccine Candidates ◽  
Genome Wide ◽  
Allele Specific

Individuals acquire immunity to clinical malaria after repeated Plasmodium falciparum infections. This immunity to disease is thought to reflect the acquisition of a repertoire of responses to multiple alleles in diverse parasite antigens. In previous studies, we identified polymorphic sites within individual antigens that are associated with parasite immune evasion by examining antigen allele dynamics in individuals followed longitudinally. Here we expand this approach by analyzing genome-wide polymorphisms using whole genome sequence data from 140 parasite isolates representing malaria cases from a longitudinal study in Malawi and identify 25 genes that encode likely targets of naturally acquired immunity and that should be further characterized for their potential as vaccine candidates.

scholarly journals Phylogenomic analysis of Pseudomonas nitroreducens strains FY43 and FY47

2022 ◽  
pp. 1-11
Author(s):  
Xue Li Tan ◽  
Wei Yee Wee ◽  
Boon Chin Tan ◽  
Chee How Teo
Keyword(s):  
Genome Analysis ◽  
Phylogenomic Analysis ◽  
Whole Genome ◽  
The Novel ◽  
Species Classification ◽  
Whole Genome Analysis ◽  
Pseudomonas Nitroreducens ◽  
High Level ◽  
Next Generation Sequencing Ngs ◽  
Diversity Studies

Proper identification of strain is essential in understanding the ecology of a bacteria species. The classification of Pseudomonas nitroreducens is still being questioned and revised until now. The novel P. nitroreducens strains FY43 and FY47 used in this study have been reported to show a high level of tolerance to glyphosate. In this study, next-generation sequencing (NGS) and whole genome analysis were used to clarify the delineation of the species. Whole genome analysis showed that P. nitroreducens strains FY43 and FY47 shared high homology to five reference genomes of P. nitroreducens: strain B, Aramco J, NBRC 12694, DF05, and TX01. Phylogenomic and phylogenetic analysis (average nucleotide identity based on BLAST (ANIb), genome-to-genome distance (GGDC) analysis) showed that both P. nitroreducens strains FY43 and FY47 are Pseudomonas nitroreducens members. However, strains DF05 and TX01 were not correctly assigned at the species level for all the analyses. The P. nitroreducens strain DF05 and TX01 should be further investigated for their classification as the correct species classification is the prerequisite for future diversity studies.

scholarly journals SARS-CoV-2 whole-genome classification analysis, protein homology modelling and elucidation of associated protein functions

2020 ◽  
Author(s):  
Deepanshu Sharma ◽  
Anamika Saini ◽  
Desh Deepak Singh
Keyword(s):  
Vaccine Development ◽  
Homology Modelling ◽  
Protein Structures ◽  
Whole Genome Sequence ◽  
Reference Sequence ◽  
Sequence Length ◽  
Whole Genome ◽  
Protein Homology ◽  
Whole Genome Analysis ◽  
Multiple Sequence

The most recent whole-genome sequence of SARS-CoV-2 was published on NCBI on 13th March 2020, with accession no. NC_045512. The protein products, genetic features, sequence length, NCBI reference sequence, protein structures (published/ homology modelling) and functions are discussed and analysed in this paper. Multiple sequence alignment is performed and Phylogenic tree is prepared for the 4 closely related coronavirus species. This study provides the whole genome analysis with protein homology structures and elucidates functions of structurally similar proteins for further exploration and contributes to the search for anti-SARS-CoV-2 drugs. The application of this data in new vaccine development techniques such as Rapid-Response Platform and a possibility of a recombinant SARS-CoV-2 are discussed in this paper.

scholarly journals Whole-Genome Sequencing in Microbial Forensic Analysis of Gamma-Irradiated Microbial Materials

2015 ◽  
Vol 82 (2) ◽  
pp. 596-607 ◽  
Author(s):  
Stacey M. Broomall ◽  
Mohamed Ait Ichou ◽  
Michael D. Krepps ◽  
Lauren A. Johnsky ◽  
Mark A. Karavis ◽  
...  
Keyword(s):  
Sequence Data ◽  
454 Sequencing ◽  
Forensic Analysis ◽  
Whole Genome Sequence ◽  
High Dose ◽  
Whole Genome ◽  
Whole Genome Analysis ◽  
Potential Sources ◽  
Gamma Irradiated ◽  
Sequencing Platforms

ABSTRACTEffective microbial forensic analysis of materials used in a potential biological attack requires robust methods of morphological and genetic characterization of the attack materials in order to enable the attribution of the materials to potential sources and to exclude other potential sources. The genetic homogeneity and potential intersample variability of many of the category A to C bioterrorism agents offer a particular challenge to the generation of attributive signatures, potentially requiring whole-genome or proteomic approaches to be utilized. Currently, irradiation of mail is standard practice at several government facilities judged to be at particularly high risk. Thus, initial forensic signatures would need to be recovered from inactivated (nonviable) material. In the study described in this report, we determined the effects of high-dose gamma irradiation on forensic markers of bacterial biothreat agent surrogate organisms with a particular emphasis on the suitability of genomic DNA (gDNA) recovered from such sources as a template for whole-genome analysis. While irradiation of spores and vegetative cells affected the retention of Gram and spore stains and sheared gDNA into small fragments, we found that irradiated material could be utilized to generate accurate whole-genome sequence data on the Illumina and Roche 454 sequencing platforms.

scholarly journals Whole Genome Sequence Analysis of Porcine Astroviruses Reveals Novel Genetically Diverse Strains Circulating in East African Smallholder Pig Farms

Viruses ◽  
2020 ◽  
Vol 12 (11) ◽  
pp. 1262
Author(s):  
Joshua O. Amimo ◽  
Eunice M. Machuka ◽  
Edward O. Abworo ◽  
Anastasia N. Vlasova ◽  
Roger Pelle
Keyword(s):  
Genetic Diversity ◽  
Nucleotide Sequence ◽  
Epitope Prediction ◽  
Whole Genome Sequence ◽  
Diagnostic Tools ◽  
Whole Genome ◽  
Potential Candidate ◽  
Whole Genome Analysis ◽  
Porcine Astrovirus ◽  
Sequence Identities

Astroviruses (AstVs) are widely distributed and are associated with gastroenteritis in human and animals. The knowledge of the genetic diversity and epidemiology of AstVs in Africa is limited. This study aimed to characterize astroviruses in asymptomatic smallholder piglets in Kenya and Uganda. Twenty-four samples were randomly selected from a total of 446 piglets aged below 6 months that were initially collected for rotavirus study and sequenced for whole genome analysis. Thirteen (13/24) samples had contigs with high identity to genus Mamastrovirus. Analysis of seven strains with complete (or near complete) AstV genome revealed variable nucleotide and amino acid sequence identities with known porcine astrovirus (PoAstV) strains. The U083 and K321 strains had nucleotide sequence identities ranging from 66.4 to 75.4% with the known PoAstV2 strains; U460 strain had nucleotide sequence identities of 57.0 to 65.1% regarding the known PoAstV3; and K062, K366, K451, and K456 strains had nucleotide sequence identities of 63.5 to 80% with the known PoAstV4 strains. The low sequence identities (<90%) indicate that novel genotypes of PoAstVs are circulating in the study area. Recombination analysis using whole genomes revealed evidence of multiple recombination events in PoAstV4, suggesting that recombination might have contributed to the observed genetic diversity. Linear antigen epitope prediction and a comparative analysis of capsid protein of our field strains identified potential candidate epitopes that could help in the design of immuno-diagnostic tools and a subunit vaccine. These findings provide new insights into the molecular epidemiology of porcine astroviruses in East Africa.

scholarly journals Phenotypic, Genotypic, and Antimicrobial Characteristics of Streptococcus halichoeri Isolates from Humans, Proposal To Rename Streptococcus halichoeri as Streptococcus halichoeri subsp. halichoeri, and Description of Streptococcus halichoeri subsp. hominis subsp. nov., a Bacterium Associated with Human Clinical Infections

2016 ◽  
Vol 54 (3) ◽  
pp. 739-744 ◽  
Author(s):  
P. L. Shewmaker ◽  
A. M. Whitney ◽  
B. W. Humrighouse
Keyword(s):  
16S Rrna ◽  
Type Strain ◽  
Sequence Similarity ◽  
Clinical Isolates ◽  
Whole Genome Sequence ◽  
Rrna Gene ◽  
Whole Genome ◽  
Sequencing Analysis ◽  
Whole Genome Analysis ◽  
Content Type

Phenotypic, genotypic, and antimicrobial characteristics of six phenotypically distinct human clinical isolates that most closely resembled the type strain ofStreptococcus halichoeriisolated from a seal are presented. Sequencing of the 16S rRNA,rpoB,sodA, andrecNgenes; comparative whole-genome analysis; conventional biochemical and Rapid ID 32 Strep identification methods; and antimicrobial susceptibility testing were performed on the human isolates, the type strain ofS.halichoeri, and type strains of closely related species. The six human clinical isolates were biochemically indistinguishable from each other and showed 100% 16S rRNA,rpoB,sodA, andrecNgene sequence similarity. Comparative 16S rRNA gene sequencing analysis revealed 98.6% similarity toS. halichoeriCCUG 48324T, 97.9% similarity toS. canisATCC 43496T, and 97.8% similarity toS. ictaluriATCC BAA-1300T. A 3,530-bp fragment of therpoBgene was 98.8% similar to theS. halichoeritype strain, 84.6% to theS. canistype strain, and 83.8% to theS.ictaluritype strain. TheS. halichoeritype strain and the human clinical isolates were susceptible to the antimicrobials tested based on CLSI guidelines forStreptococcusspecies viridans group with the exception of tetracycline and erythromycin. The human isolates were phenotypically distinct from the type strain isolated from a seal; comparative whole-genome sequence analysis confirmed that the human isolates wereS. halichoeri. On the basis of these results, a novel subspecies,Streptococcushalichoerisubsp.hominis, is proposed for the human isolates andStreptococcus halichoerisubsp.halichoeriis proposed for the gray seal isolates. The type strain of the novel subspecies is SS1844T= CCUG 67100T= LMG 28801T.

scholarly journals Genome-Wide Investigation of the NF-X1 Gene Family in Populus trichocarpa Expression Profiles during Development and Stress

2021 ◽  
Vol 22 (9) ◽  
pp. 4664
Author(s):  
Fang He ◽  
Yu-Jie Shi ◽  
Jia-Xuan Mi ◽  
Kuang-Ji Zhao ◽  
Xing-Lei Cui ◽  
...  
Keyword(s):  
Expression Profiles ◽  
Populus Trichocarpa ◽  
Expression Patterns ◽  
Molecular Genetic ◽  
Mechanical Damage ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
Genetic Progress ◽  
Whole Genome Analysis ◽  
Element Analysis

Poplar are planted extensively in reforestation and afforestation. However, their successful establishment largely depends on the environmental conditions of the newly established plantation and their resistance to abiotic as well as biotic stresses. NF-X1, a widespread transcription factor in plants, plays an irreplaceable role in plant growth, development, and stress tolerance. Although the whole genome sequence of Populus trichocarpa has been published for a long time, little is known about the NF-X1 genes in poplar, especially those related to drought stress, mechanical damage, insect feeding, and hormone response at the whole genome level. In this study, whole genome analysis of the poplar NF-X1 family was performed, and 4 PtrNF-X1 genes were identified. Then, bioinformatics analysis and qRT-PCR were applied to analyze the gene structure, phylogeny, chromosomal localization, gene replication, Cis-elements, and expression patterns of PtrNF-X1genes. Sequence analysis revealed that one-quarter of the PtrNF-X1 genes did not contain introns. Phylogenetic analysis revealed that all NF-X1 genes were split into three subfamilies. The number of two pairs of segmented replication genes were detected in poplars. Cis-acting element analysis identified a large number of elements of growth and development and stress-related elements on the promoters of different NF-X1 members. In addition, some PtrNF-X1 could be significantly induced by polyethylene glycol (PEG) and abscisic acid (ABA), thus revealing their potential role in regulating stress response. Comprehensive analysis is helpful in selecting candidate NF-X1 genes for the follow-up study of the biological function, and molecular genetic progress of stress resistance in forest trees provides genetic resources.

scholarly journals Soybean Haplotype Map (GmHapMap): A Universal Resource for Soybean Translational and Functional Genomics

2019 ◽  
Author(s):  
Davoud Torkamaneh ◽  
Jérôme Laroche ◽  
Babu Valliyodan ◽  
Louise O’Donoughue ◽  
Elroy Cober ◽  
...  
Keyword(s):  
Glycine Max ◽  
Gene Function ◽  
Oil Content ◽  
Seed Oil ◽  
Sequence Data ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
Loss Of Function ◽  
Seed Oil Content ◽  
Extensive Coverage

AbstractHere we describe the first worldwide haplotype map for soybean (GmHapMap) constructed using whole-genome sequence data for 1,007 Glycine max accessions and yielding 15 million variants. The number of unique haplotypes plateaued within this collection (4.3 million tag SNPs) suggesting extensive coverage of diversity within the cultivated germplasm. We imputed GmHapMap variants onto 21,618 previously genotyped (50K array/210K GBS) accessions with up to 96% success for common alleles. A GWAS performed with imputed data enabled us to identify a causal SNP residing in the NPC1 gene and to demonstrate its role in controlling seed oil content. We identified 405,101 haplotypes for the 55,589 genes and show that such haplotypes can help define alleles. Finally, we predicted 18,031 putative loss-of-function (LOF) mutations in 10,662 genes and illustrate how such a resource can be used to explore gene function. The GmHapMap provides a unique worldwide resource for soybean genomics and breeding.

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