Identification and characterization of SNPs in released, landrace and wild accessions of mungbean (Vigna radiata (L.) Wilczek) using whole genome re-sequencing

ABSTRACT Lactococcus lactis phage mutants that are insensitive to the recently characterized abortive infection mechanism AbiV were isolated and analyzed in an effort to elucidate factors involved in the sensitivity to AbiV. Whole-genome sequencing of the phage mutants p2.1 and p2.2 revealed mutations in an orf that is transcribed early, indicating that this orf was responsible for AbiV sensitivity. Sequencing of the homologous regions in the genomes of other AbiV-insensitive mutants derived from p2 and six other lactococcal wild-type phages revealed point mutations in the homologous orf sequences. The orf was named sav (for sensitivity to AbiV), and the encoded polypeptide was named SaV. The purification of a His-tagged SaV polypeptide by gel filtration suggested that the polypeptide formed a dimer in its native form. The overexpression of SaV in L. lactis and Escherichia coli led to a rapid toxic effect. Conserved, evolutionarily related regions in SaV polypeptides of different phage groups are likely to be responsible for the AbiV-sensitive phenotype and the toxicity.

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Identification and Characterization of Mycobacterium tuberculosis Beijing Genotype Strain SBH163, Isolated in Sabah, Malaysia

Microbiology Resource Announcements ◽

10.1128/mra.01322-19 ◽

2020 ◽

Vol 9 (2) ◽

Author(s):

Jaeyres Jani ◽

Siti Fatimah Abu Bakar ◽

Zainal Arifin Mustapha ◽

Chin Kai Ling ◽

Roddy Teo ◽

...

Keyword(s):

Mycobacterium Tuberculosis ◽

Whole Genome Sequence ◽

Beijing Genotype ◽

Molecular Characteristics ◽

Whole Genome ◽

Content Type ◽

Identification And Characterization ◽

Insight Into ◽

Malaysian Borneo

This is a report on the whole-genome sequence of Mycobacterium tuberculosis strain SBH163, which was isolated from a patient in the Malaysian Borneo state of Sabah. This report provides insight into the molecular characteristics of an M. tuberculosis Beijing genotype strain related to strains from Russia and South Africa.

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Insight on Rosaceae Family with Genome Sequencing and Functional Genomics Perspective

BioMed Research International ◽

10.1155/2019/7519687 ◽

2019 ◽

Vol 2019 ◽

pp. 1-12

Author(s):

Prabhakaran Soundararajan ◽

So Youn Won ◽

Jung Sun Kim

Keyword(s):

Functional Genomics ◽

Genome Sequencing ◽

Developmental Process ◽

Abiotic Stress Tolerance ◽

Whole Genome ◽

Rosaceae Family ◽

Genome Information ◽

Aesthetic Values ◽

Identification And Characterization

Rosaceae is one of the important families possessing a variety of diversified plant species. It includes many economically valuable crops that provide nutritional and health benefits for the human. Whole genome sequences of valuable crop plants were released in recent years. Understanding of genomics helps to decipher the plant physiology and developmental process. With the information of cultivating species and its wild relative genomes, genome sequence-based molecular markers and mapping loci for economically important traits can be used to accelerate the genome assisted breeding. Identification and characterization of disease resistant capacities and abiotic stress tolerance related genes are feasible to study across species with genome information. Further breeding studies based on the identification of gene loci for aesthetic values, flowering molecular circuit controls, fruit firmness, nonacid fruits, etc. is required for producing new cultivars with valuable traits. This review discusses the whole genome sequencing reports of Malus, Pyrus, Fragaria, Prunus, and Rosa and status of functional genomics of representative traits in individual crops.

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Publisher Correction: Identification and characterization of the novel colonization factor CS30 based on whole genome sequencing in enterotoxigenic Escherichia coli (ETEC)

Scientific Reports ◽

10.1038/s41598-018-23723-6 ◽

2018 ◽

Vol 8 (1) ◽

Author(s):

Astrid von Mentzer ◽

Joshua Tobias ◽

Gudrun Wiklund ◽

Stefan Nordqvist ◽

Martin Aslett ◽

...

Keyword(s):

Escherichia Coli ◽

Whole Genome Sequencing ◽

Genome Sequencing ◽

Enterotoxigenic Escherichia Coli ◽

Whole Genome ◽

The Novel ◽

Colonization Factor ◽

Identification And Characterization

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36. Identification and characterization of complete and partial MEF2C gene deletions in 3 individuals with developmental delay by whole genome microarray analysis

Cancer Genetics ◽

10.1016/j.cancergen.2018.04.039 ◽

2018 ◽

Vol 224-225 ◽

pp. 64

Author(s):

Frank Bartel ◽

Timothy Fee ◽

Barbara DuPont

Keyword(s):

Developmental Delay ◽

Microarray Analysis ◽

Whole Genome ◽

Gene Deletions ◽

Whole Genome Microarray ◽

Identification And Characterization

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Ornithobacterium rhinotracheale: MALDI-TOF MS and Whole Genome Sequencing Confirm That Serotypes K, L and M Deviate from Well-Known Reference Strains and Numerous Field Isolates

Microorganisms ◽

10.3390/microorganisms9051006 ◽

2021 ◽

Vol 9 (5) ◽

pp. 1006

Author(s):

Merima Alispahic ◽

Lukas Endler ◽

Michael Hess ◽

Claudia Hess

Keyword(s):

Whole Genome Sequencing ◽

Genome Sequencing ◽

Whole Genome ◽

Maldi Tof Ms ◽

Maldi Tof ◽

Identification And Characterization ◽

Reference Strains ◽

Ornithobacterium Rhinotracheale ◽

Tof Ms

Ornithobacterium rhinotracheale is one of the most important bacterial agents of respiratory diseases in poultry. For correct identification and characterization of this fastidious bacterium, reliable diagnostic tools are essential. Still, phenotypic tests are used to identify O. rhinotracheale and serotyping is the most common method for characterization, despite known drawbacks and disadvantages such as divergent results, cross-reactivity between strains, or the non-typeability of strains. The intention of the present study was to evaluate MALDI-TOF MS and whole genome sequencing for the identification and characterization of O. rhinotracheale. For this purpose, a selection of 59 well-defined reference strains and 47 field strains derived from outbreaks on Austrian turkey farms were investigated by MALDI-TOF MS. The field strains originated from different geographical areas in Austria with some of the isolates derived from multiple outbreaks on farms within a year, or recurrent outbreaks over several years. MALDI-TOF MS proved a suitable method for identification of O. rhinotracheale to genus or species level except for 3 strains representing serotypes M, K and F. Phylogenetic analysis showed that most strains grouped within one cluster even though they were comprised of different serotypes, while serotypes F, K, and M clearly formed a different cluster. All field isolates from turkey farms clustered together, independent of the origin of the isolates, e.g., geographical area, multiple outbreaks within a year or recurrent outbreaks over several years. Whole genome sequencing of serotype M, K and F strains confirmed the extraordinary status and deviation from known fully-sequenced strains due to a lack of sequence similarity. This was further confirmed by alignments of single genes (16S-RNA and rpoB) and multilocus sequence typing although the demarcation was less obvious. Altogether, the results indicate that these three serotypes belong to a different species than O. rhinotracheale, and might even be members of multiple new species.

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Identification and Characterization of SNPs in released, landrace and wild accessions of Mungbean (Vigna radiata (L.) Wilczek) using whole genome re-sequencing

10.21203/rs.2.13417/v1 ◽

2019 ◽

Author(s):

Pooja Bangar ◽

Neetu Tyagi ◽

Bhavana Tiwari ◽

Sanjay Kumar ◽

Paramananda Barman ◽

...

Keyword(s):

Vigna Radiata ◽

Agronomic Traits ◽

Genetic Relationships ◽

Genetic Research ◽

Grain Legume ◽

Whole Genome ◽

Nucleotide Polymorphisms ◽

Ion Torrent Pgm ◽

Wild Accessions ◽

Landrace Accessions

Abstract Mungbean [Vigna radiata (L.) R. Wilczek var. radiata] is vital grain legume having nutritional and socio-economic importance, especially in the developing countries. We performed whole genome re-sequencing of three accessions representing the wild progenitor species, released and landrace of mungbean to identify SNPs with relevance to genetic relationships analyses. Approximately 9.3 million raw reads were obtained by using Ion Torrent PGM™ platform and more than 92% of the reads were mapped to the reference mungbean genome. We identified a total of 233,799 single nucleotide polymorphisms in relation to the reference genome (SNPs: 103,341 in wild, 93,078 in released and 37,380 in landrace accessions) and 9,544 insertions and deletions (InDels: 4,742 in wild, 3,608 in released and 1,194 in landrace accessions) in the coding and non-coding regions. In all accessions, genomic variants were unevenly distributed within and across the mungbean chromosomes. Among these 5,339; 4,739 and 1,795 SNPs were non-synonymous in 815, 790 and 317 genes of wild, released and landrace accessions, respectively. These polymorphisms might contribute to the variation in important pathways of genes for abiotic and biotic stress tolerance and important agronomic traits such as seed dormancy, flowering time and seed size in mungbean. Among the randomly selected SNPs, a selected subset was validated using Sanger sequencing technique. The genomic variations among mungbean wild, released and landrace accessions constitute a powerful tool to support genetic research and molecular breeding of mungbean.

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