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Journal of Genomics

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https://www.readbyqxmd.com/read/29928467/genetic-diversity-of-bovine-major-histocompatibility-complex-class-ii-drb3-locus-in-cattle-breeds-from-asia-compared-to-those-from-africa-and-america
#1
Sunday O Peters, Tanveer Hussain, Adeyemi S Adenaike, Matthew A Adeleke, Marcos De Donato, Jordan Hazzard, Masroor E Babar, Ikhide G Imumorin
Genetic polymorphisms and diversity of BoLA-DRB3.2 are essential because of DRB3 gene's function in innate immunity and its association with infectious diseases resistance or tolerance in cattle. The present study was aimed at assessing the level of genetic diversity of DRB3 in the exon 2 (BoLA-DRB3.2) region in African, American and Asian cattle breeds. Amplification of exon 2 in 174 cattle revealed 15 haplotypes. The breeds with the highest number of haplotypes were Brangus (10), Sokoto Gudali (10) and Dajal (9), while the lowest number of haplotypes were found in Holstein and Sahiwal with 4 haplotypes each...
2018: Journal of Genomics
https://www.readbyqxmd.com/read/29928466/genome-wide-analysis-reveals-the-extrinsic-cellulolytic-and-biohydrogen-generating-abilities-of-neocallimastigomycota-fungi
#2
Ayyappa Kumar Sista Kameshwar, Wensheng Qin
Ruminating animals, especially cattle lack the carbohydrate active enzyme encoding genes which are required for the degradation of the glycosidic linkages of plant cell wall carbohydrates (such as cellulose, hemicellulose, lignin and pectin). Thus, ruminating animals are completely dependent on the microorganisms (anaerobic bacteria and fungi, methanogenic archaea and protozoa) residing in their rumen (hindgut). In this study, we have retrieved and analyzed the complete genome wide annotations of the Neocallimastigomycota division fungi such as Anaeromyces robustus, Neocallismatix californiae, Orpinomyces sp, Piromyces finnis, Piromyces sp E2...
2018: Journal of Genomics
https://www.readbyqxmd.com/read/29861788/identification-of-sex-associated-snps-of-greater-amberjack-seriola-dumerili
#3
Junya Kawase, Jun-Ya Aoki, Kazuhisa Hamada, Akiyuki Ozaki, Kazuo Araki
The sex determination systems of fish are highly diverse compared with those of mammals. Thus, performing investigations using nonmodel fish species helps to understand the highly diverse sex determination systems of fish. Because greater amberjack ( Seriola dumerili ) is one of the most important edible fish globally and knowledge of its sex determination system is economically important in the field of aquaculture, we are interested in the mechanisms of sex determination of Seriola species. In this study, we identified sex-associated SNPs of greater amberjack using SNP information of 10 males and 10 females by an association test...
2018: Journal of Genomics
https://www.readbyqxmd.com/read/29805716/isolation-and-identification-of-an-anthracimycin-analogue-from-nocardiopsis-kunsanensis-a-halophile-from-a-saltern-by-genomic-mining-strategy
#4
Fernanda L Sirota, Falicia Goh, Kia-Ngee Low, Lay-Kien Yang, Sharon C Crasta, Birgit Eisenhaber, Frank Eisenhaber, Yoganathan Kanagasundaram, Siew Bee Ng
Modern medicine is unthinkable without antibiotics; yet, growing issues with microbial drug resistance require intensified search for new active compounds. Natural products generated by Actinobacteria have been a rich source of candidate antibiotics, for example anthracimycin that, so far, is only known to be produced by Streptomyces species. Based on sequence similarity with the respective biosynthetic cluster, we sifted through available microbial genome data with the goal to find alternative anthracimycin-producing organisms...
2018: Journal of Genomics
https://www.readbyqxmd.com/read/29707046/-de-novo-assembly-of-the-burying-beetle-nicrophorus-orbicollis-coleoptera-silphidae-transcriptome-across-developmental-stages-with-identification-of-key-immune-transcripts
#5
Harim I Won, Thomas T Schulze, Emalie J Clement, Gabrielle F Watson, Sean M Watson, Rosalie C Warner, Elizabeth A M Ramler, Elias J Witte, Mark A Schoenbeck, Claudia M Rauter, Paul H Davis
Burying beetles ( Nicrophorus spp.) are among the relatively few insects that provide parental care while not belonging to the eusocial insects such as ants or bees. This behavior incurs energy costs as evidenced by immune deficits and shorter life-spans in reproducing beetles. In the absence of an assembled transcriptome, relatively little is known concerning the molecular biology of these beetles. This work details the assembly and analysis of the Nicrophorus orbicollis transcriptome at multiple developmental stages...
2018: Journal of Genomics
https://www.readbyqxmd.com/read/29707045/in-silico-designing-and-testing-of-primers-for-sanger-genome-sequencing-of-dengue-virus-types-of-asian-origin
#6
Ajay Prakash Joshi, Annette Angel, Bennet Angel, Rajendra Kumar Baharia, Suman Rathore, Neha Sharma, Karuna Yadav, Sharad Thanvi, Indu Thanvi, Vinod Joshi
Rarity in reporting whole genome sequence of Dengue virus from dengue endemic countries leaves lacunae in understanding regional pattern of virus mutation and ultimately leading to non-understanding of transmission pattern and clinical outcomes emerging at regional levels. Due to inter-serotype genomic similarity and intra-serotype genomic diversity, appropriate designing of primer pairs appears as an exhaustive exercise. Present paper reports new Dengue virus type-specific primer which may help in characterizing virus specific to Asian origin...
2018: Journal of Genomics
https://www.readbyqxmd.com/read/29576807/complete-genome-sequence-of-microcystis-aeruginosa-nies-2481-and-common-genomic-features-of-group-g-m-aeruginosa
#7
Haruyo Yamaguchi, Shigekatsu Suzuki, Yasunori Osana, Masanobu Kawachi
Microcystis aeruginosa is a freshwater bloom-forming cyanobacterium that is distributed worldwide. M. aeruginosa can be divided into at least 8 phylogenetic groups (A-G and X) at the intraspecific level. Here, we report the complete genome sequence of M. aeruginosa NIES-2481, which was isolated from Lake Kasumigaura, Japan, and is assigned to group G. The complete genome sequence of M. aeruginosa NIES-2481 comprises a 4.29-Mbp circular chromosome and a 147,539-bp plasmid; the circular chromosome and the plasmid contain 4,332 and 167 protein-coding genes, respectively...
2018: Journal of Genomics
https://www.readbyqxmd.com/read/29576806/genomic-analysis-of-propane-metabolism-in-methyl-tert-butyl-ether-degrading-mycobacterium-sp-strain-env421
#8
Peter Robert Tupa, Hisako Masuda
Methyl tert -butyl ether (MTBE) is a ground water contaminant with plausible carcinogenic properties. Mycobacterium sp. strain ENV421 cometabolically degrades MTBE and other ethers during the growth on propane as a carbon source. In this study, the 6.2 Mb genome of strain ENV421 was deciphered. The genome sequence revealed the presence of numerous putative propane catabolic genes including genes encoding hydrocarbon oxygenases and short chain alcohol dehydrogenases. These data provide the basis for the elucidation of propane metabolic pathways in strain ENV421 and its application for the remediation of ground water contaminated with toxic ethers...
2018: Journal of Genomics
https://www.readbyqxmd.com/read/29483968/high-quality-draft-genomes-of-the-type-strains-geobacillus-thermocatenulatus-dsm-730-t-g-uzenensis-dsm-23175-t-and-parageobacillus-galactosidasius-dsm-18751-t
#9
Winnie Thabisa Ramaloko, Nadine Koen, Shamara Polliack, Habibu Aliyu, Pedro Humberto Lebre, Teresa Mohr, Florian Oswald, Michaela Zwick, Daniel Ray Zeigler, Anke Neumann, Christoph Syldatk, Don Arthur Cowan, Pieter De Maayer
The thermophilic 'Geobacilli' are important sources of thermostable enzymes and other biotechnologically relevant macromolecules. The present work reports the high quality draft genome sequences of previously unsequenced type strains of Geobacillus uzenensis (DSM 23175T ), G. thermocatenulatus (DSM 730T ) and Parageobacillus galactosidasius (DSM 18751T ). Phylogenomic analyses revealed that DSM 18751T and DSM 23175T represent later heterotypic synonyms of P. toebii and G. subterraneus , respectively, while DSM 730T represents the type strain for the species G...
2018: Journal of Genomics
https://www.readbyqxmd.com/read/29290830/constructing-a-chromonome-of-yellowtail-seriola-quinqueradiata-for-comparative-analysis-of-chromosomal-rearrangements
#10
Junya Kawase, Jun-Ya Aoki, Kazuo Araki
To investigate chromosome evolution in fish species, we newly mapped 181 markers that allowed us to construct a yellowtail ( Seriola quinqueradiata ) radiation hybrid (RH) physical map with 1,713 DNA markers, which was far denser than a previous map, and we anchored the de novo assembled sequences onto the RH physical map. Finally, we mapped a total of 13,977 expressed sequence tags (ESTs) on a genome sequence assembly aligned with the physical map. Using the high-density physical map and anchored genome sequences, we accurately compared the yellowtail genome structure with the genome structures of five model fishes to identify characteristics of the yellowtail genome...
2018: Journal of Genomics
https://www.readbyqxmd.com/read/29290829/genetic-variation-in-n-and-c-terminal-regions-of-bovine-dnaja1-heat-shock-protein-gene-in-african-asian-and-american-cattle
#11
Oyeyemi O Ajayi, Sunday O Peters, Marcos De Donato, F Denis Mujibi, Waqas A Khan, Tanveer Hussain, Masroor E Babar, Ikhide G Imumorin, Bolaji N Thomas
DNAJA1 or heat shock protein 40 (Hsp40) is associated with heat adaptation in various organisms. We amplified and sequenced a total of 1,142 bp of bovine Hsp40 gene representing the critical N-terminal (NTR) and C-terminal (CTR) regions in representative samples of African, Asian and American cattle breeds. Eleven and 9 different haplotypes were observed in the NTR in Asian and African breeds respectively while in American Brangus, only two mutations were observed resulting in two haplotypes. The CTR appears to be highly conserved between cattle and yak...
2018: Journal of Genomics
https://www.readbyqxmd.com/read/29109800/exploring-effects-of-sex-and-diet-on-drosophila-melanogaster-head-gene-expression
#12
Maria D L A Jaime, Juan Hurtado, Mariana Ramirez Loustalot-Laclette, Brian Oliver, Therese Markow
Gene expression depends on sex and environment. We stringently explored the contributions of these effects in Drosophila melanogaster by rearing three distinct wildtype genotypes on isocaloric diets either high in protein or sugar followed by expression profiling of heads from the sexes. By using different genotypes as replicates we developed robust sex- and diet-biased expression responses.
2017: Journal of Genomics
https://www.readbyqxmd.com/read/29109799/draft-genome-sequence-of-a-biosurfactant-producing-bacillus-aquimaris-strain-samm-mcc-3014-isolated-from-indian-arabian-coastline-sea-water
#13
Samadhan Waghmode, Laxmikant Dama, Tejashri Hingamire, Nidhi Bharti, Swapnil Doijad, Mangesh Suryavanshi
Bacillus aquimaris strain SAMM, a biosurfactant producing moderately halophilic marine bacterium was isolated from Indian Arabian coastline sea water. The strain was found to tolerate up to 2.7 M NaCl indicating osmotic stress sustainable physiological systems. We report here the draft genome sequence of B. aquimaris SAMM, as a candidate bacterium for bioactive surfactant producer. The whole genome sequence with 161 scaffolds, 4,414,932 bp and 44.8% of G+C content for SAMM was obtained using Illumina MiSeq sequencing technology...
2017: Journal of Genomics
https://www.readbyqxmd.com/read/28943973/permanent-draft-genome-sequence-for-frankia-sp-strain-cci49-a-nitrogen-fixing-bacterium-isolated-from-casuarina-cunninghamiana-that-infects-elaeagnaceae
#14
Samira Mansour, Erik Swanson, Zakkary McNutt, Céline Pesce, Kelsey Harrington, Feseha Abebe-Alele, Stephen Simpson, Krystalynne Morris, W Kelley Thomas, Louis S Tisa
Frankia sp. strain CcI49 was isolated from Casuarina cunninghamiana nodules. However the strain was unable to re-infect Casuarina, but was able to infect other actinorhizal plants including Elaeagnaceae. Here, we report the 9.8-Mbp draft genome sequence of Frankia sp. strain CcI49 with a G+C content of 70.5 % and 7,441 candidate protein-encoding genes. Analysis of the genome revealed the presence of a bph operon involved in the degradation of biphenyls and polychlorinated biphenyls.
2017: Journal of Genomics
https://www.readbyqxmd.com/read/28943972/small-non-coding-rna-abundance-in-adrenocortical-carcinoma-a-footprint-of-a-rare-cancer
#15
Srinivas V Koduru, Ashley N Leberfinger, Dino J Ravnic
BACKGROUND: Adrenocortical carcinoma (ACC) is a relatively rare, but aggressive type of cancer, which affects both children and adults. OBJECTIVE: Small non-coding RNAs (sncRNAs) play important roles and may serve as biomarkers for disease diagnosis, prognosis and treatment. METHODS: In our study, we sought to identify sncRNAs associated with malignant adrenal tumors. We obtained publicly available, small RNA sequencing data derived from 45 ACC and 30 benign tumors arising from the cortex of the adrenal gland, adrenocortical adenomas (ACA), and compared their sncRNA expression profiles...
2017: Journal of Genomics
https://www.readbyqxmd.com/read/28943971/genome-comparison-of-pseudomonas-fluorescens-um270-with-related-fluorescent-strains-unveils-genes-involved-in-rhizosphere-competence-and-colonization
#16
Julie E Hernández-Salmerón, Gabriel Moreno-Hagelsieb, Gustavo Santoyo
Pseudomonas fluorescens UM270 is a rhizosphere-colonizing bacterium that produces multiple diffusible and volatile compounds involved in plant growth-promoting activities. Strain UM270 exhibits excellent biocontrol capacities against diverse fungal pathogens . In a previous study, the general UM270 genome characteristics were published. Here, we report a deeper analysis of its gene content and compare it to other P. fluorescens strains to unveil the genetic elements that might explain UM270's great colonizing and plant growth-promoting capabilities...
2017: Journal of Genomics
https://www.readbyqxmd.com/read/28698739/complete-genome-sequence-of-actinomadura-parvosata-subsp-kistnae-a-rich-source-of-novel-natural-product-bio-chemistry
#17
Kalina Kusserow, Tobias A M Gulder
The soil dwelling actinomycete strain Actinomadura parvosata subsp. kistnae is the producer of the antiviral antibiotics kistamicin A and B. Genome sequencing and bioinformatic analysis revealed the presence of the kistamycin biosynthetic gene cluster responsible for the formation of these non-ribosomal peptides as well as an impressive number of yet uncharacterized biosynthetic pathways. This includes polyketide, ribosomal and non-ribosomal peptide and a large number of terpenoid biosynthetic loci encoding yet unknown natural products...
2017: Journal of Genomics
https://www.readbyqxmd.com/read/28698738/complete-genome-sequence-and-comparative-genomics-of-a-streptococcus-pyogenes-emm3-strain-m3-b-isolated-from-a-japanese-patient-with-streptococcal-toxic-shock-syndrome
#18
Kohei Ogura, Shinya Watanabe, Teruo Kirikae, Tohru Miyoshi-Akiyama
Epidemiologic typing of Streptococcus pyogenes (GAS) is frequently based on the genotype of the emm gene, which encodes M/Emm protein. In this study, the complete genome sequence of GAS emm3 strain M3-b, isolated from a patient with streptococcal toxic shock syndrome (STSS), was determined. This strain exhibited 99% identity with other complete genome sequences of emm3 strains MGAS315, SSI-1, and STAB902. The complete genomes of five additional strains isolated from Japanese patients with and without STSS were also sequences...
2017: Journal of Genomics
https://www.readbyqxmd.com/read/28698737/draft-genome-sequence-of-a-virulent-strain-of-pasteurella-multocida-isolated-from-alpaca
#19
Raquel Enma Hurtado, Flavia Aburjaile, Diego Mariano, Marcus Vinicius Canário, Leandro Benevides, Daniel Antonio Fernandez, Nataly Olivia Allasi, Rocio Rimac, Julio Eduardo Juscamayta, Jorge Enrique Maximiliano, Raul Hector Rosadio, Vasco Azevedo, Lenin Maturrano
Pasteurella multocida is one of the most frequently isolated bacteria in acute pneumonia cases, being responsible for high mortality rates in Peruvian young alpacas, with consequent social and economic costs. Here we report the genome sequence of P. multocida strain UNMSM, isolated from the lung of an alpaca diagnosed with pneumonia, in Peru. The genome consists of 2,439,814 base pairs assembled into 82 contigs and 2,252 protein encoding genes, revealing the presence of known virulence-associated genes (ompH, ompA, tonB, tbpA, nanA, nanB, nanH, sodA, sodC, plpB and toxA)...
2017: Journal of Genomics
https://www.readbyqxmd.com/read/28698736/draft-genome-sequence-of-the-symbiotic-frankia-sp-strain-kb5-isolated-from-root-nodules-of-casuarina-equisetifolia
#20
Céline Pesce, Erik Swanson, Stephen Simpson, Krystalynne Morris, W Kelley Thomas, Louis S Tisa, Anita Sellstedt
Frankia sp. strain KB5 was isolated from Casuarina equisetifolia and previous studies have shown both nitrogenase and uptake hydrogenase activities under free-living conditions. Here, we report 5.5-Mbp draft genome sequence with a G+C content of 70.03 %, 4,958 candidate protein-encoding genes, and 2 rRNA operons.
2017: Journal of Genomics
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