scholarly journals Genome sequencing provides insight into the reproductive biology, nutritional mode and ploidy of the fern pathogenMixia osmundae

2013 ◽  
Vol 202 (2) ◽  
pp. 554-564 ◽  
Author(s):  
Merje Toome ◽  
Robin A. Ohm ◽  
Robert W. Riley ◽  
Timothy Y. James ◽  
Katherine L. Lazarus ◽  
...  
Keyword(s):  
Reproductive Biology ◽  
Genome Sequencing ◽  
Nutritional Mode ◽  
Insight Into

scholarly journals Whole Genome Sequencing of Fusarium fujikuroi Provides Insight into the Role of Secretory Proteins and Cell Wall Degrading Enzymes in Causing Bakanae Disease of Rice

2017 ◽  
Vol 8 ◽  
Author(s):  
Bishnu M. Bashyal ◽  
Kirti Rawat ◽  
Sapna Sharma ◽  
Deepika Kulshreshtha ◽  
S. Gopala Krishnan ◽  
...  
Keyword(s):  
Cell Wall ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Fusarium Fujikuroi ◽  
Secretory Proteins ◽  
Whole Genome ◽  
Cell Wall Degrading Enzymes ◽  
Bakanae Disease ◽  
Insight Into

scholarly journals Genome sequencing of the high oil crop sesame provides insight into oil biosynthesis

2014 ◽  
Vol 15 (2) ◽  
pp. R39 ◽  
Author(s):  
Linhai Wang ◽  
Sheng Yu ◽  
Chaobo Tong ◽  
Yingzhong Zhao ◽  
Yan Liu ◽  
...  
Keyword(s):  
Genome Sequencing ◽  
Oil Crop ◽  
Oil Biosynthesis ◽  
Insight Into

scholarly journals Whole-Genome Sequencing of Tibetan Macaque (Macaca thibetana) Provides New Insight into the Macaque Evolutionary History

2014 ◽  
Vol 31 (6) ◽  
pp. 1475-1489 ◽  
Author(s):  
Zhenxin Fan ◽  
Guang Zhao ◽  
Peng Li ◽  
Naoki Osada ◽  
Jinchuan Xing ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Evolutionary History ◽  
Whole Genome ◽  
Macaca Thibetana ◽  
Tibetan Macaque ◽  
Insight Into

scholarly journals Relative Consolidation of the Kappa Variant Pre-Dates the Massive Second Wave of COVID-19 in India

Genes ◽  
2021 ◽  
Vol 12 (11) ◽  
pp. 1803
Author(s):  
Jitendra Singh ◽  
Anvita Gupta Malhotra ◽  
Debasis Biswas ◽  
Prem Shankar ◽  
Leena Lokhande ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Spike Protein ◽  
Whole Genome ◽  
The Novel ◽  
Genome Sequences ◽  
Second Wave ◽  
Insight Into

India experienced a tragic second wave after the end of March 2021, which was far more massive than the first wave and was driven by the emergence of the novel delta variant (B.1.617.2) of the SARS-CoV-2 virus. In this study, we explored the local and national landscape of the viral variants in the period immediately preceding the second wave to gain insight into the mechanism of emergence of the delta variant and thus improve our understanding of the causation of the second wave. We randomly selected 20 SARS-CoV-2 positive samples diagnosed in our lab between 3 February and 8 March 2021 and subjected them to whole genome sequencing. Nine of the 20 sequenced genomes were classified as kappa variant (B.1.617.1). The phylogenetic analysis of pan-India SARS-CoV-2 genome sequences also suggested the gradual replacement of the α variant with the kappa variant during this period. This relative consolidation of the kappa variant was significant, since it shared 3 of the 4 signature mutations (L452R, E484Q and P681R) observed in the spike protein of delta variant and thus was likely to be the precursor in its evolution. This study demonstrates the predominance of the kappa variant in the period immediately prior to the second wave and underscores its role as the “bridging variant” between the α and delta variants that drove the first and second waves of COVID-19 in India, respectively.

A compilation of soybean ESTs: generation and analysis

Genome ◽  
2002 ◽  
Vol 45 (2) ◽  
pp. 329-338 ◽  
Author(s):  
Randy Shoemaker ◽  
Paul Keim ◽  
Lila Vodkin ◽  
Ernest Retzel ◽  
Sandra W Clifton ◽  
...  
Keyword(s):  
Genome Sequencing ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Cdna Libraries ◽  
Sequence Length ◽  
Valuable Insight ◽  
Alternative Approach ◽  
Average Sequence Length ◽  
Expressed Sequence ◽  
Insight Into

Whole-genome sequencing is fundamental to understanding the genetic composition of an organism. Given the size and complexity of the soybean genome, an alternative approach is targeted random-gene sequencing, which provides an immediate and productive method of gene discovery. In this study, more than 120 000 soybean expressed sequence tags (ESTs) generated from more than 50 cDNA libraries were evaluated. These ESTs coalesced into 16 928 contigs and 17 336 singletons. On average, each contig was composed of 6 ESTs and spanned 788 bases. The average sequence length submitted to dbEST was 414 bases. Using only those libraries generating more than 800 ESTs each and only those contigs with 10 or more ESTs each, correlated patterns of gene expression among libraries and genes were discerned. Two-dimensional qualitative representations of contig and library similarities were generated based on expression profiles. Genes with similar expression patterns and, potentially, similar functions were identified. These studies provide a rich source of publicly available gene sequences as well as valuable insight into the structure, function, and evolution of a model crop legume genome.Key words: Glycine max, genome sequencing, functional genomics.

scholarly journals Draft genome sequencing and secretome analysis of fungal phytopathogen Ascochyta rabiei provides insight into the necrotrophic effector repertoire

2016 ◽  
Vol 6 (1) ◽  
Author(s):  
Sandhya Verma ◽  
Rajesh Kumar Gazara ◽  
Shadab Nizam ◽  
Sabiha Parween ◽  
Debasis Chattopadhyay ◽  
...  
Keyword(s):  
Genome Sequencing ◽  
Draft Genome ◽  
Ascochyta Rabiei ◽  
Secretome Analysis ◽  
Fungal Phytopathogen ◽  
Draft Genome Sequencing ◽  
Necrotrophic Effector ◽  
Insight Into

scholarly journals A Nonsense Mutation in Mycobacterium marinum That Is Suppressible by a Novel Mechanism

2016 ◽  
Vol 85 (2) ◽  
Author(s):  
Emily A. Williams ◽  
Felix Mba Medie ◽  
Rachel E. Bosserman ◽  
Benjamin K. Johnson ◽  
Cristal Reyna ◽  
...  
Keyword(s):  
Genome Sequencing ◽  
Nonsense Mutation ◽  
Gene Disruption ◽  
Cell Envelope ◽  
Mycobacterium Marinum ◽  
Nonsense Suppression ◽  
Whole Genome ◽  
Content Type ◽  
System 1 ◽  
Insight Into

ABSTRACT Mycobacterial pathogens use the ESAT-6 system 1 (Esx-1) exporter to promote virulence. Previously, we used gene disruption and complementation to conclude that the MMAR_0039 gene in Mycobacterium marinum is required to promote Esx-1 export. Here we applied molecular genetics, proteomics, and whole-genome sequencing to demonstrate that the MMAR_0039 gene is not required for Esx-1 secretion or virulence. These findings suggest that we initially observed an indirect mechanism of genetic complementation. We identified a spontaneous nonsense mutation in a known Esx-1-associated gene which causes a loss of Esx-1 activity. We show that the Esx-1 function was restored by nonsense suppression. Moreover, we identified a polar mutation in the ppsC gene which reduced cellular impermeability but did not impact cytotoxicity in macrophages. Our studies reveal insight into Esx-1 export, nonsense suppression, and cell envelope lipid biogenesis.

scholarly journals Insight Into Whole Genome of Aeromonas veronii Isolated From Freshwater Fish by Resistome Analysis Reveal Extensively Antibiotic Resistant Traits

2021 ◽  
Vol 12 ◽  
Author(s):  
Rungnapa Sakulworakan ◽  
Putita Chokmangmeepisarn ◽  
Nguyen Dinh-Hung ◽  
Elayaraja Sivaramasamy ◽  
Ikuo Hirono ◽  
...  
Keyword(s):  
Multidrug Resistance ◽  
Whole Genome Sequencing ◽  
Freshwater Fish ◽  
Genome Sequencing ◽  
Whole Genome ◽  
Antibiotic Resistant ◽  
Aeromonas Veronii ◽  
Insight Into

Aeromonas veronii outbreaks in tilapia farming caused relatively high mortalities, and the bacteria was resistant to many kinds of antimicrobials used in Thailand aquaculture. According to the CLSI standard, the determination of antimicrobials efficacy has been limited to phenotypic analyses, and a genomics study is required. This research aimed to analyze the resistome of A. veronii isolated from diseased tilapia in Chainat, Nong Khai, and Uttaradit provinces in Thailand. A total of 12 isolates of A. veronii were identified based on the gyrB sequencing and then, the MIC values to eight antimicrobials (AMP, AML, GEN, ENR, OXO, OTC, SXT, and FFC) were determined. According to the MIC patterns, whole genome sequencing (WGS) of five representatives and resistome analysis were performed, including 15 genomes of A. veronii isolated from freshwater fish available in the NCBI. All tilapia isolates were susceptible to FFC but resistant to AML and AMP while OTC resistance was the most dominant. In addition to the WGS analysis, 4.5 Mbp of A. veronii was characterized. A total of 20 ARGs were detected by resistome analysis and 16 genes were shared among the A. veronii population. In conclusion, A. veronii strains isolated from tilapia exhibited a resistance to several antimicrobials and multidrug resistance (MDR) which was related to the presence of multiple ARGs. Aeromonas veronii shared the ARGs in their population worldwide with a possibility of a plasmid-mediated acquisition due to the presence of resistance islands.

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