Molecular characterization of a Bacillus thuringiensis strain from Argentina, toxic against Lepidoptera and Coleoptera, based on its whole-genome and Cry protein analysis

AbstractHuanglongbing (HLB) is a worldwide deadly citrus disease caused by the phloem-limited bacteria ‘Candidatus Liberibacter asiaticus’ (CLas) vectored by Asian citrus psyllids. In order to effectively manage this disease, it is crucial to understand the relationship among the bacterial isolates from different geographical locations. Whole genome sequencing approaches will provide more precise molecular characterization of the diversity among populations. Due to the lack of in vitro culture, obtaining the whole genome sequence of CLas is still a challenge, especially for medium to low titer samples. Hundreds of millions of sequencing reads are needed to get good coverage of CLas from an HLB positive citrus sample. In order to overcome this limitation, we present here a new method, Agilent SureSelect XT HS target enrichment, which can specifically enrich CLas from a metagenomic sample while greatly reducing cost and increasing whole genome coverage of the pathogen. In this study, the CLas genome was successfully sequenced with 99.3% genome coverage and over 72X sequencing coverage from low titer tissue samples (equivalent to 28.52 Cq using Li 16 S qPCR). More importantly, this method also effectively captures regions of diversity in the CLas genome, which provides precise molecular characterization of different strains.

Download Full-text

In silico whole-genome scanning of cancer-associated nonsynonymous SNPs and molecular characterization of a dynein light chain tumour variant

Oncogene ◽

10.1038/sj.onc.1208745 ◽

2005 ◽

Vol 24 (40) ◽

pp. 6133-6142 ◽

Cited By ~ 10

Author(s):

Abdel Aouacheria ◽

Vincent Navratil ◽

Wenyu Wen ◽

Ming Jiang ◽

Dominique Mouchiroud ◽

...

Keyword(s):

Molecular Characterization ◽

Light Chain ◽

In Silico ◽

Nonsynonymous Snps ◽

Whole Genome ◽

Dynein Light Chain ◽

Genome Scanning

Download Full-text

Molecular Characterization of Recurrent Partial Gene Duplications by Whole Genome Mate-Pair Sequencing (MPseq) to Improve the Accuracy of Chromosomal Microarray Reporting

Cancer Genetics ◽

10.1016/j.cancergen.2016.04.051 ◽

2016 ◽

Vol 209 (6) ◽

pp. 299-300

Author(s):

Binu Porath ◽

Sarah H. Johnson ◽

Stephanie A. Smoley ◽

Beth Pitel ◽

Troy Gliem ◽

...

Keyword(s):

Molecular Characterization ◽

Chromosomal Microarray ◽

Whole Genome ◽

Gene Duplications ◽

Mate Pair

Download Full-text

Molecular Characterization of Soybean Pterocarpan 2-Dimethylallyltransferase in Glyceollin Biosynthesis: Local Gene and Whole-Genome Duplications of Prenyltransferase Genes Led to the Structural Diversity of Soybean Prenylated Isoflavonoids

Plant and Cell Physiology ◽

10.1093/pcp/pcw178 ◽

2016 ◽

Vol 57 (12) ◽

pp. 2497-2509 ◽

Cited By ~ 24

Author(s):

Keisuke Yoneyama ◽

Tomoyoshi Akashi ◽

Toshio Aoki

Keyword(s):

Molecular Characterization ◽

Structural Diversity ◽

Whole Genome ◽

Whole Genome Duplications ◽

Genome Duplications

Download Full-text

Prevalence and Molecular Characterization of Novel Pathogenic Strains of Macrococcus Caseolyticus Isolated From External Wounds of Donkeys in Khartoum State –Sudan

10.21203/rs.3.rs-867901/v1 ◽

2021 ◽

Author(s):

Dania Ali ◽

Mushal Allam ◽

Hisham Altayb ◽

Dalia Mursi ◽

M. A Abdalla ◽

...

Keyword(s):

Sequence Analysis ◽

Molecular Characterization ◽

Genome Sequence ◽

Whole Genome Sequence ◽

Whole Genome ◽

Genome Sequence Analysis ◽

Resistant Genes ◽

Different Seasons ◽

Novel Alleles

Abstract A pathogenic strains of Macrococcus caseolyticus was isolated from wounds infection during investigation on donkeys in Khartoum State. Samples were collected from external wounds (head, abdomin, back and leg), during different seasons of the year. One isolate (124B) was identified using whole-genome sequence analysis. RAST software identified thirty-one virulent genes of disease and defense including methicillin resistant genes, TatR family and ANT(4’)-Ib. Plasmid rep22 wasidentified by PlasmidFindet-2.0 Server and a CRISPR. MILST-2.0 predicted many novel alleles. NCBI notated the genome as a novel strain of M.caseolyticus strain (DaniaSudan). The MLST-tree-V1 revealed that DaniaSudan and KM0211a strains were interrelated. Strain Daniasudan was resistant to ciprofloxacin, ceftazidime, erythromycin, oxacillin, clindamycin and kanamycin. The prevalence of the strain was 4.73%, with significant differences between collection seasons and locations of wounds. Mice modling showen bacteremia and many clinical (swelling, allergy, wounds and loss of hair). Enlarged, hyperemia, adhesions and abscesses were observed in many organs. This represents the first report of pathogenic strains of M.caseolyticus worldwide.

Download Full-text

Molecular Characterization of Novel Bacillus thuringiensis Isolate with Molluscicidal Activity Against the Intermediate Host of Schistosomes

Biotechnology(Faisalabad) ◽

10.3923/biotech.2006.413.420 ◽

2006 ◽

Vol 5 (4) ◽

pp. 413-420 ◽

Cited By ~ 7

Author(s):

Halima, H. Salem ◽

Bahy, A. Ali . ◽

Tian, H. Huang . ◽

Qing, D. Xie .

Keyword(s):

Bacillus Thuringiensis ◽

Intermediate Host ◽

Molecular Characterization ◽

Molluscicidal Activity

Download Full-text

Genomic Characterization and Phylogenetic Classification of Bovine Coronaviruses Through Whole Genome Sequence Analysis

Viruses ◽

10.3390/v12020183 ◽

2020 ◽

Vol 12 (2) ◽

pp. 183 ◽

Cited By ~ 11

Author(s):

Tohru Suzuki ◽

Yoshihiro Otake ◽

Satoko Uchimoto ◽

Ayako Hasebe ◽

Yusuke Goto

Keyword(s):

Phylogenetic Analysis ◽

Sequence Analysis ◽

Molecular Characterization ◽

Genome Sequence ◽

Whole Genome Sequence ◽

Whole Genome ◽

Wild Ruminant ◽

Genome Sequence Analysis ◽

Genomic Characterization

Bovine coronavirus (BCoV) is zoonotically transmissible among species, since BCoV-like viruses have been detected in wild ruminants and humans. BCoV causing enteric and respiratory disease is widespread in cattle farms worldwide; however, limited information is available regarding the molecular characterization of BCoV because of its large genome size, despite its significant economic impact. This study aimed to better understand the genomic characterization and evolutionary dynamics of BCoV via comparative sequence and phylogenetic analyses through whole genome sequence analysis using 67 BCoV isolates collected throughout Japan from 2006 to 2017. On comparing the genomic sequences of the 67 BCoVs, genetic variations were detected in 5 of 10 open reading frames (ORFs) in the BCoV genome. Phylogenetic analysis using whole genomes from the 67 Japanese BCoV isolates in addition to those from 16 reference BCoV strains, revealed the existence of two major genotypes (classical and US wild ruminant genotypes). All Japanese BCoV isolates originated from the US wild ruminant genotype, and they tended to form the same clusters based on the year and farm of collection, not the disease type. Phylogenetic trees on hemagglutinin-esterase protein (HE), spike glycoprotein (S), nucleocapsid protein (N) genes and ORF1 revealed clusters similar to that on whole genome, suggesting that the evolution of BCoVs may be closely associated with variations in these genes. Furthermore, phylogenetic analysis of BCoV S genes including those of European and Asian BCoVs and human enteric coronavirus along with the Japanese BCoVs revealed that BCoVs differentiated into two major types (European and American types). Moreover, the European and American types were divided into eleven and three genotypes, respectively. Our analysis also demonstrated that BCoVs with different genotypes periodically emerged and predominantly circulated within the country. These findings provide useful information to elucidate the detailed molecular characterization of BCoVs, which have spread worldwide. Further genomic analyses of BCoV are essential to deepen the understanding of the evolution of this virus.

Download Full-text