scholarly journals Genome analysis of Lysinibacillus sphaericus isolate 6.2 pathogenic to Culex quinquefasciatus Say, 1823 (Diptera: Culicidae)

2021 ◽  
Vol 22 (11) ◽  
Author(s):  
Afiannisa Viersanova ◽  
Hari Purwanto
Keyword(s):  
Phylogenetic Tree ◽  
Culex Quinquefasciatus ◽  
Genome Analysis ◽  
Genomic Analysis ◽  
Binary Toxin ◽  
Whole Genome Analysis ◽  
Lysinibacillus Sphaericus ◽  
Chitin Binding Protein ◽  
The Relationship ◽  
16Srrna Gene

Abstract. Viersanova A, Purwanto H. 2021. Genome analysis of Lysinibacillus sphaericus isolate 6.2 pathogenic to Culex quinquefasciatus Say, 1823 (Diptera: Culicidae). Biodiversitas 22: 5211-5222. Lysinibacillus sphaericus is an entomopathogenic bacteria that is specific to vector mosquitoes, especially Culex spp., and Anopheles spp., so it has been widely used as a bioinsecticide. L. sphaericus has a wide variation of toxicity efficiencies, which have led to continuous exploration of new isolates with higher toxicity and a new toxin to deal with resistance problems. This study aimed to identify the genomic characteristics and toxin characteristics of isolate 6.2 based on whole genome analysis and analyze the identification of isolate 6.2. Isolate 6.2 was previously obtained from rhizosphere in Yogyakarta. To analyze the genome and toxins, the NGS technique was used and then the analysis was carried out using a couple of freely available bioinformatics tools. Molecular identification was carried out with the 16SrRNA gene and the relationship was analyzed by reconstructing the phylogenetic tree using Neighbours-Joining. The genomic analysis of isolate 6.2 showed good results with G+C content and genome size that matched the reference genome of L. sphaericus. The result of the 16SrRNA gene blasting showed that the closest related gene of isolate 6.2 is L. fusiformis (NR_042072.1). However, the reconstructed phylogenetic tree did not show the formation of clusters according to the species. Toxin analysis indicates that isolate 6.2 has Mtx, s-layer protein, hemolysin, and chitin-binding protein genes. All of which are known to be associated with the toxicity of L. sphaericus to binary toxin resistant population of Culex quinquefasciatus.

scholarly journals Whole-genome analysis reveals the complex evolutionary dynamics of Kenyan G2P[4] human rotavirus strains

2011 ◽  
Vol 92 (9) ◽  
pp. 2201-2208 ◽  
Author(s):  
Souvik Ghosh ◽  
Noriaki Adachi ◽  
Zipporah Gatheru ◽  
James Nyangao ◽  
Dai Yamamoto ◽  
...  
Keyword(s):  
Genome Analysis ◽  
Complete Genome ◽  
Evolutionary Dynamics ◽  
Genomic Analysis ◽  
Whole Genome ◽  
Genome Sequences ◽  
Whole Genome Analysis ◽  
Human Rotavirus ◽  
Genotype Constellation ◽  
Common Causes

Although G2P[4] rotaviruses are common causes of acute childhood diarrhoea in Africa, to date there are no reports on whole genomic analysis of African G2P[4] strains. In this study, the nearly complete genome sequences of two Kenyan G2P[4] strains, AK26 and D205, detected in 1982 and 1989, respectively, were analysed. Strain D205 exhibited a DS-1-like genotype constellation, whilst strain AK26 appeared to be an intergenogroup reassortant with a Wa-like NSP2 genotype on the DS-1-like genotype constellation. The VP2-4, VP6-7, NSP1, NSP3 and NSP5 genes of strain AK26 and the VP2, VP4, VP7 and NSP1–5 genes of strain D205 were closely related to those of the prototype or other human G2P[4] strains. In contrast, their remaining genes were distantly related, and, except for NSP2 of AK26, appeared to originate from or share a common origin with rotavirus genes of artiodactyl (ruminant and camelid) origin. These observations highlight the complex evolutionary dynamics of African G2P[4] rotaviruses.

Lysinibacillus sphaericus binary toxin induces apoptosis in susceptible Culex quinquefasciatus larvae

2015 ◽  
Vol 128 ◽  
pp. 57-63 ◽  
Author(s):  
Chontida Tangsongcharoen ◽  
Nusara Chomanee ◽  
Boonhiang Promdonkoy ◽  
Panadda Boonserm
Keyword(s):  
Culex Quinquefasciatus ◽  
Binary Toxin ◽  
Lysinibacillus Sphaericus

scholarly journals GAAP: A Genome Assembly + Annotation Pipeline

2019 ◽  
Vol 2019 ◽  
pp. 1-12 ◽  
Author(s):  
Jinhwa Kong ◽  
Sun Huh ◽  
Jung-Im Won ◽  
Jeehee Yoon ◽  
Baeksop Kim ◽  
...  
Keyword(s):  
Genome Analysis ◽  
De Novo ◽  
Transcriptome Assembly ◽  
Genomic Analysis ◽  
Whole Genome ◽  
High Throughput Analysis ◽  
Whole Genome Analysis ◽  
A Genome ◽  
Base Sequences ◽  
Wide Range

Genomic analysis begins with de novo assembly of short-read fragments in order to reconstruct full-length base sequences without exploiting a reference genome sequence. Then, in the annotation step, gene locations are identified within the base sequences, and the structures and functions of these genes are determined. Recently, a wide range of powerful tools have been developed and published for whole-genome analysis, enabling even individual researchers in small laboratories to perform whole-genome analyses on their objects of interest. However, these analytical tools are generally complex and use diverse algorithms, parameter setting methods, and input formats; thus, it remains difficult for individual researchers to select, utilize, and combine these tools to obtain their final results. To resolve these issues, we have developed a genome analysis pipeline (GAAP) for semiautomated, iterative, and high-throughput analysis of whole-genome data. This pipeline is designed to perform read correction, de novo genome (transcriptome) assembly, gene prediction, and functional annotation using a range of proven tools and databases. We aim to assist non-IT researchers by describing each stage of analysis in detail and discussing current approaches. We also provide practical advice on how to access and use the bioinformatics tools and databases and how to implement the provided suggestions. Whole-genome analysis of Toxocara canis is used as case study to show intermediate results at each stage, demonstrating the practicality of the proposed method.

scholarly journals Whole-genome analysis uncovers loss of blaZ associated to carriage isolates belonging to MRSA clone ST5-VI in Cape Verde

2021 ◽  
Author(s):  
Magdalena Wysocka ◽  
Tamar Monteiro ◽  
Carine de Pina ◽  
Deisy Gonçalves ◽  
Sandrine de Pina ◽  
...  
Keyword(s):  
Genome Analysis ◽  
Cape Verde ◽  
Whole Genome ◽  
Whole Genome Analysis

scholarly journals Bacterial Toxins Active against Mosquitoes: Mode of Action and Resistance

Toxins ◽  
2021 ◽  
Vol 13 (8) ◽  
pp. 523
Author(s):  
Maria Helena Neves Lobo Silva-Filha ◽  
Tatiany Patricia Romão ◽  
Tatiana Maria Teodoro Rezende ◽  
Karine da Silva Carvalho ◽  
Heverly Suzany Gouveia de Menezes ◽  
...  
Keyword(s):  
Mode Of Action ◽  
Mosquito Control ◽  
Binary Toxin ◽  
Lysinibacillus Sphaericus ◽  
Control Programs ◽  
Resistance Selection ◽  
Single Receptor ◽  
Combined Use ◽  
Environmentally Safe ◽  
Medical Importance

Larvicides based on the bacteria Bacillus thuringiensis svar. israelensis (Bti) and Lysinibacillus sphaericus are effective and environmentally safe compounds for the control of dipteran insects of medical importance. They produce crystals that display specific and potent insecticidal activity against larvae. Bti crystals are composed of multiple protoxins: three from the three-domain Cry type family, which bind to different cell receptors in the midgut, and one cytolytic (Cyt1Aa) protoxin that can insert itself into the cell membrane and act as surrogate receptor of the Cry toxins. Together, those toxins display a complex mode of action that shows a low risk of resistance selection. L. sphaericus crystals contain one major binary toxin that display an outstanding persistence in field conditions, which is superior to Bti. However, the action of the Bin toxin based on its interaction with a single receptor is vulnerable for resistance selection in insects. In this review we present the most recent data on the mode of action and synergism of these toxins, resistance issues, and examples of their use worldwide. Data reported in recent years improved our understanding of the mechanism of action of these toxins, showed that their combined use can enhance their activity and counteract resistance, and reinforced their relevance for mosquito control programs in the future years.

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