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Last Updated: 03 September 2022

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Draft genome sequencing data of the moderately halophilic bacterium, Allobacillus halotolerans SKP2-8 from shrimp paste (ka-pi)

The bacterial species SKP2-8, a moderately halophilic, Gram-stain-positive, spore-forming rod-shaped bacterium isolated from a traditional fermented shrimp paste obtained from the market in Samut Sakhon province, Thailand, was isolated from a traditional fermented shrimp paste isolated from a spore-forming rod-shaped bacterium named SKP2-8. This isolate SKP2-8 was highly similar to Allobacillus halotolerans LMG 24826T with 99. 5 percent similarity based on the 16S rRNA gene sequence. Compared to A. halotolerans LMG 24826T, the ANIb, ANIm, AAI, and the digital DNA hybridization results of isolate SKP2-8 were 97. 22%, 97. 64%, 97. 75%, and 78. 0%, respectively.

Source link: https://doi.org/10.1016/j.dib.2022.108549


Assembly, Annotation, and Comparative Whole Genome Sequence of Fusarium verticillioides Isolated from Stored Maize Grains

Fusarium verticillioides is a plant pathogenic fungus that affects a wide variety of crops worldwide due to its toxigenic properties. The F. verticillioides BIONCL4 strain was isolated from stored maize grain samples in India and produces a high amount of fumonisin B1. We present a comparative genomic study of F. verticillioides, including basic genome information, missing genome sequence, and proteins involved in host-u2013pathogen interactions and mycotoxin biosynthesis. There are already 1447 genes related to carbohydrate active enzymes and 167 genes related to mycotoxin production. In addition, a F. verticillioides genome comparison revealed details about the species's evolution during the species's history, which was presented in F. verticillioides' genome comparison.

Source link: https://doi.org/10.3390/pathogens11070810


The First Complete Chloroplast Genome Sequence and Phylogenetic Analysis of Pistachio ( Pistacia vera)

Pistachio is one of the world's most popular nut crops. Among the genera tested, P. vera had the most simple sequence repeats, which may be useful for molecular marker research and future population studies. According to Amino acid analysis, Leucine is the most common amino acid in the chloroplast genome, followed by Isoleucine and Serine. P. vera is the most like its taxonomically close relative P. weinmaniifolia, followed by Rhus chinensis, and all are placed taxonomically in the tribe Rhoeae, according to a Phylogenetic report. The results of this chloroplast genome will be useful for future conservation studies, genetic analysis, and breeding of P. vera P. vera, as well as more detailed phylogenetic analysis of the Pistacia species and its closely related genera.

Source link: https://doi.org/10.3390/d14070577


Mitochondrial Genomes of two Lycosa spiders (Araneae, Lycosidae): Genome Description and Phylogenetic Implications

Lycosa shansia, and Lycosa singoriensis' complete mitochondrial genomes were sequenced by combining Sanger and next-generation sequencing technologies and analyzing sequenced genomes in order to determine species phylogenetic location and evolution of these species, as well as mitochondrial genome composition and evolution. L. shansia's mitochondrial genome was 14,638 bp, but L. singoriensis' was 13,686 bp. Both the mean and median values of ATP8 in both species indicated that the nucleotide compositions of the Mitogenomes of L. singoriensis and L. shansia were the highest among the 13 protein-coding genes, indicating that it may have mutated faster than the other protein-coding genes in both species.

Source link: https://doi.org/10.3390/d14070538


Genome-Wide Association Study Identifies Multiple Susceptibility Loci for Malignant Neoplasms of the Brain in Taiwan

Primary brain malignancy is a rare disease with a worldwide prevalence of less than ten per 100,000 individuals. These results reveal that genetic susceptibility to GBM or non-GBM tumors is extremely different, indicating different etiologies. RNA modification may be correlated to key risk factors in primary malignant neoplasms of the brain, according to combined signaling results.

Source link: https://doi.org/10.3390/jpm12071161


Source Attribution of Human Campylobacteriosis Using Whole-Genome Sequencing Data and Network Analysis

Campylobacter spp. We recommend network analysis models as a reliable, high-resolution source attribution scheme for human campylobacteriosis. In this study for source attribution comparing different WGS data inputs, a weighted network analysis approach was employed. The compared model inputs consisted of cgMLST and wgMLST distance matrices from 717 human and 717 animal isolates, including cattle, chickens, dogs, ducks, pigs, and turkeys. 78 percent, 79 %, and 69 percent for cgMLST, wgMLST, and SNP, respectively, according to CSC figures based on Campylobacter species. According to the various animal sources for cgMLST, wgMLST, and SNP, respectively, including human isolates in the network resulted in 88 percent, 77 percent, and 88 percent of the total human isolates being clustered. cgMLST, 52. 2 %, and 51. 2 % for cgMLST, wgMLST, and SNP distance matrices respectively, with an average attribution percentage of 52. 8 percent, 52. 2 %, and 51. 2 percent, respectively, while ducks from Denmark showed the least attribution of 0 % for all three distance matrices. The best-performing model was the one that used the wgMLST distance matrix to input data, with a CSC score of 89%. The results from our report show that the weighted network-based model for source attribution is reliable and can be used as an alternative source attribution strategy considering the model's high success. The model is also robust across the various Campylobacter species, animal sources, and WGS data types used as input.

Source link: https://doi.org/10.3390/pathogens11060645


Design of a Multi-Epitopes Based Chimeric Vaccine against Enterobacter cloacae Using Pan-Genome and Reverse Vaccinology Approaches

The new report, which acknowledges that there are currently no approved vaccine or therapeutic option for the treatment of EC, was developed to concentrate on applications based on emerging computational techniques to produce a multi-epitope-based E. cloacae peptide vaccine expressing the antigenic determinants prioritized from the EC genome. Both in vitro and in vivo experiments were found to be appropriate for both in vitro and in vivo experiments. The vaccine's 3D framework was established and the loop was refined, increasing the reliability by disulfide engineering, and the physicochemical characteristics of the recombinant vaccine sequence were determined to be excellent for both in vitro and in vivo experiments. For MHC-I, MHC-II, and TLR-4, respectively, with docked complexes considered for simulation, blind docking was then used for the prediction of the MEBEPV's predominant blinding mode with MHCII, and TLR3 native immune receptors, with MHCII, u221248. 25 kJ/mol, u221248. 25 mol, u221248. 25 mol, u2212121218121212121218121218121218181248. 201212121812121218121812181616. The docked models of MEBEPV-TLR3, MEBEPV-MHCI, and MEBEPV-MHCII were found to be stable throughout the course of the simulation, according to MD and MMGBSA's reports. According to MM-GBSA's report, the TLR3-vaccine complex contained u2212125. 4 for the MHC I-vaccine complex, u2212125. 4 for the MHC I-vaccine component, and u2212187. 94 for the MHC II-vaccine complex. U2212115. 63 binding free energy for the TLR3-vaccine complex, u2212118. 19 for the MHC I-vaccine complex, and u2212184. 61 for the MHC II-vaccine complex were estimated by MM-PBSA. Despite the fact that the suggested MEBEPV has the ability to be a powerful contender against E. cloacae-associated diseases, further research in the laboratory will be required before it can be declared safe and immunogenic.

Source link: https://doi.org/10.3390/vaccines10060886


The Complete Mitochondrial Genome of a Neglected Breed, the Peruvian Creole Cattle ( Bos taurus ), and Its Phylogenetic Analysis

Cattle flourished across the American continent during the colonization years, with originating creole breeds that were adaptable to a variety of climate conditions. Creole cattle in Peru's population is mainly due to the introduction of more popular breeds in recent years. Despite being crucial to improving productivity in the Andean area, agricultural production, and cultural traditions, little is known about the Peruvian creole cattle's genetics, despite the fact that they play a role in improving productivity in the Andean region, agricultural production, and cultural traditions. For the first time, we sequenced the mitochondrial genome of a creole bull, which also had exceptional combat skills and was employed for agricultural duties, from Arequipa's highlands. The PCC is attributed to native African breeds, according to a maximum likelihood reconstruction based on complete mitochondrial genome sequences. The annotated mitochondrial genome of PCC would be an important genetic resource for further breeding research and conservation policies.

Source link: https://doi.org/10.3390/data7060076

* Please keep in mind that all text is summarized by machine, we do not bear any responsibility, and you should always check original source before taking any actions

* Please keep in mind that all text is summarized by machine, we do not bear any responsibility, and you should always check original source before taking any actions