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Journal of Genomics

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https://read.qxmd.com/read/30820259/selfies-and-cellfies-whole-genome-sequencing-and-annotation-of-five-antibiotic-resistant-bacteria-isolated-from-the-surfaces-of-smartphones-an-inquiry-based-laboratory-exercise-in-a-genomics-undergraduate-course-at-the-rochester-institute-of-technology
#1
Anutthaman Parthasarathy, Narayan H Wong, Amanda N Weiss, Susan Tian, Sara E Ali, Nicole T Cavanaugh, Tyler M Chinsky, Chelsea E Cramer, Aditya Gupta, Rakshanda Jha, Loryn K Johnson, Elizabeth D Tuason, Lauren M Klafehn, Varada Krishnadas, Ryan J Musich, Jennifer M Pfaff, Spencer C Richman, Alexandria J Shumway, André O Hudson
Are touchscreen devices a public health risk for the transmission of pathogenic bacteria, especially those that are resistant to antibiotics? To investigate this, we embarked on a project aimed at isolating and identifying bacteria that are resistant to antibiotics from the screens of smartphones. Touchscreen devices have become ubiquitous in society, and it is important to evaluate the potential risks they pose towards public health, especially as it pertains to the harboring and transmission of pathogenic bacteria that are resistant to antibiotics...
2019: Journal of Genomics
https://read.qxmd.com/read/30820258/complete-genome-sequence-of-arthrobacter-sp-strain-mn05-02-a-uv-resistant-bacterium-from-a-manganese-deposit-in-the-sonoran-desert
#2
Konosuke Mark Ii, Nobuaki Kono, Ivan Glaucio Paulino-Lima, Masaru Tomita, Lynn Justine Rothschild, Kazuharu Arakawa
Arthrobacter sp. strain MN05-02 is a UV-resistant bacterium isolated from a manganese deposit in the Sonoran Desert, Arizona, USA. The LD10 of this strain is 123 Jm-2 , which is twice that of Escherichia coli , and therefore can be a useful resource for comparative study of UV resistance and the role of manganese on this phenotype. Its complete genome is comprised of a chromosome of 3,488,433 bp and a plasmid of 154,991 bp. The chromosome contains 3,430 putative genes, including 3,366 protein coding genes, 52 tRNA and 12 rRNA genes...
2019: Journal of Genomics
https://read.qxmd.com/read/30820257/genome-sequencing-and-annotation-of-bacillus-subtilis-ubbs-14-to-ensure-probiotic-safety
#3
Ayesha Sulthana, Suvarna G Lakshmi, Ratna Sudha Madempudi
Bacillus subtilis is a rod shaped, gram positive, spore producing bacterium. They are the normal flora of gastrointestinal tract of humans and it is the best characterized model organism for endospore formation. It has the ability to withstand environmental stress, and synthesize beneficial compounds, therefore, it is recognized as a high-quality probiotic supplement. To ensure the probiotic safety and the efficiency, we report the whole genome sequence (WGS) of Bacillus subtilis UBBS-14 strain. The draft genome sequence of Bacillus subtilis UBBS-14 consists of 4,048,984 bp and 4,017 genes, respectively...
2019: Journal of Genomics
https://read.qxmd.com/read/30820256/draft-genome-sequence-of-the-oleaginous-yeast-apiotrichum-porosum-syn-trichosporon-porosum-dsm-27194
#4
Olga Gorte, Habibu Aliyu, Anke Neumann, Katrin Ochsenreither
Here, we present the draft genome sequence of Apiotrichum porosum DSM 27194 generated on PacBio platform. Characterization of this oleaginous yeast originally collected from the grassland in Karlsruhe Germany, revealed potential for its utilization as a source of single cell oil (SCO) and gluconic acid (GA). The availability of the genome sequence provides a valuable resource for the elucidation of the genetic processes determining SCO and GA biosynthesis.
2019: Journal of Genomics
https://read.qxmd.com/read/30662570/complete-genome-sequence-of-novel-sulfitobacter-pseudonitzschiae-strain-smr1-isolated-from-a-culture-of-the-marine-diatom-skeletonema-marinoi
#5
Mats Töpel, Matthew I M Pinder, Oskar N Johansson, Olga Kourtchenko, Adrian K Clarke, Anna Godhe
When studying diatoms, an important consideration is the role of associated bacteria in the diatom-microbiome holobiont. To that end, bacteria isolated from a culture of Skeletonema marinoi strain R05AC were sequenced, one of which being bacterial strain SMR1, presented here. The genome consists of a circular chromosome and seven circular plasmids, totalling 5,121,602 bp. After phylotaxonomic analysis and 16S rRNA sequence comparison, we place this strain in the taxon Sulfitobacter pseudonitzschiae on account of similarity to the type strain...
2019: Journal of Genomics
https://read.qxmd.com/read/30662569/genomic-insights-into-a-novel-alkalitolerant-nitrogen-fixing-bacteria-azonexus-sp-strain-zs02
#6
Zohier B Salah, Christopher J Charles, Paul N Humphreys, Andrew P Laws, Simon P Rout
Alkaline environments represent a significant challenge to the growth of micro-organisms. Despite this, there are a number of alkaline environments which contain active microbial communities. Here we describe the genome of a diazotrophic, alkalitolerant strain of Azonexus, which was isolated from a microcosm seeded with hyperalkaline soils resulting from lime depositions. The isolate has a genome size 3.60 Mb with 3431 protein coding genes. The proteome indicated the presence of genes associated with the cycling of nitrogen, in particular the fixation of atmospheric nitrogen...
2019: Journal of Genomics
https://read.qxmd.com/read/30510598/-de-novo-male-gonad-transcriptome-draft-for-the-marine-mussel-perumytilus-purpuratus-with-a-focus-on-its-reproductive-related-proteins
#7
Carolina Briones, José J Nuñez, Montse Pérez, Daniela Espinoza-Rojas, Cristian Molina-Quiroz, Ricardo Guiñez
Perumytilus purpuratus is a marine mussel considered a bioengineer species with a broad distribution in the Pacific and Atlantic coast of South America. Studies have shown two geographically and genetically differentiated subpopulations at molecular level and in sperm morphological traits. To open avenues for molecular research on P. purpuratus , a global de novo transcriptome from gonadal tissue of mature males was sequenced using the Illumina platform. From a total of 126.38 million reads, 37,765 transcripts were successfully annotated...
2018: Journal of Genomics
https://read.qxmd.com/read/30510597/genomic-analysis-of-rhodococcus-sp-br-6-a-bromate-reducing-bacterium-isolated-from-soil-in-chiba-japan
#8
Kohei Ito, Masafumi Harada, Nobuyoshi Nakajima, Shigeki Yamamura, Masaru Tomita, Haruo Suzuki, Seigo Amachi
Bromate is a byproduct of the ozone disinfection of drinking water. It is a genotoxic carcinogen and causes renal cell tumors in rats. Physicochemical removal of bromate is very difficult, making microbial reduction of bromate to bromide a promising approach to eliminate bromate from water. Rhodococcus sp. Br-6, isolated from soil, can efficiently reduce bromate by using acetate as an electron donor. We determined the draft genome sequence of Rhodococcus sp. Br-6 for the potential practical application of the bromate-reducing bacterium...
2018: Journal of Genomics
https://read.qxmd.com/read/30310525/isolation-and-genomic-characterization-of-six-endophytic-bacteria-isolated-from-saccharum-sp-sugarcane-insights-into-antibiotic-secondary-metabolite-and-quorum-sensing-metabolism
#9
Anutthaman Parthasarathy, Han Ming Gan, Narayan H Wong, Michael A Savka, KayLee K Steiner, Kurtis R Henry, André O Hudson
Six endophytic bacteria were isolated from Saccharum sp (sugarcane) grown in the parish of Westmoreland on the island of Jamaica located in the West Indies. Whole genome sequence and annotation of the six bacteria show that three were from the genus Pseudomonas and the other three were from the genera Pantoea , Pseudocitrobacter , and Enterobacter . A scan of each genome using the antibiotics and secondary metabolite analysis shell (antiSMASH4.0) webserver showed evidence that the bacteria were able to produce a variety of secondary metabolites...
2018: Journal of Genomics
https://read.qxmd.com/read/30310524/whole-genome-sequence-of-the-novel-antarctobacter-heliothermus-strain-sms3-found-in-association-with-the-marine-diatom-skeletonema-marinoi
#10
Mats Töpel, Matthew I M Pinder, Oskar N Johansson, Olga Kourtchenko, Anna Godhe, Adrian K Clarke
As part of an ongoing investigation into the microbiome of the marine diatom Skeletonema marinoi , the bacterial strain SMS3 was isolated from a culture of S. marinoi strain ST54, which had been propagated from a sample of top layer marine sediments taken from the Swedish west coast. We present here the sequenced genome of this bacterium, which we place in the taxon Antarctobacter heliothermus , based on a phylotaxonomic analysis and its high 16S rRNA sequence similarity to the A. heliothermus type strain DSM 11445T ...
2018: Journal of Genomics
https://read.qxmd.com/read/29973960/expression-and-network-analysis-of-ybx1-interactors-for-identification-of-new-drug-targets-in-lung-adenocarcinoma
#11
Suriya Narayanan Murugesan, Birendra Singh Yadav, Pramod Kumar Maurya, Amit Chaudhary, Swati Singh, Ashutosh Mani
Y-Box Binding protein 1 (YBX-1) is known to be involved in various types of cancers. It's interactors also play major role in various cellular functions. Present work aimed to study the expression profile of the YBX-1 interactors during lung adenocarcinoma (LUAD). The differential expression analysis involved 57 genes from 95 lung adenocarcinoma samples, construction of gene network and topology analysis. A Total of 43 genes were found to be differentially expressed from which 17 genes were found to be down regulated and 26 genes were up-regulated...
2018: Journal of Genomics
https://read.qxmd.com/read/29973959/mitochondrial-genomes-of-the-south-american-frogs-eupsophus-vertebralis-and-e-emiliopugini-neobatrachia-alsodidae-and-their-phylogenetic-relationships
#12
Elkin Y Suárez-Villota, Camila A Quercia, José J Nuñez
We report the sequencing and compare the mitochondrial genomes of the South American ground frogs Eupsophus vertebralis and E. emiliopugini and reconstruct phylogenetic relationships among Eupsophus species. These genomes consist of 16,156 and 16,711 bp in length, respectively and contain 13 protein-coding genes, two ribosomal RNA genes, 22 transfer RNA genes (tRNA), and partial non-coding D-loop region. Both genomes share 94.5% identity with 879 variable sites. A phylogenetic analysis with other available mitogenomes recovered both species as the sister clade of Alsodes gargola...
2018: Journal of Genomics
https://read.qxmd.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
#13
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://read.qxmd.com/read/29928466/genome-wide-analysis-reveals-the-extrinsic-cellulolytic-and-biohydrogen-generating-abilities-of-neocallimastigomycota-fungi
#14
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://read.qxmd.com/read/29861788/identification-of-sex-associated-snps-of-greater-amberjack-seriola-dumerili
#15
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://read.qxmd.com/read/29805716/isolation-and-identification-of-an-anthracimycin-analogue-from-nocardiopsis-kunsanensis-a-halophile-from-a-saltern-by-genomic-mining-strategy
#16
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://read.qxmd.com/read/29707046/-de-novo-assembly-of-the-burying-beetle-nicrophorus-orbicollis-coleoptera-silphidae-transcriptome-across-developmental-stages-with-identification-of-key-immune-transcripts
#17
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://read.qxmd.com/read/29707045/in-silico-designing-and-testing-of-primers-for-sanger-genome-sequencing-of-dengue-virus-types-of-asian-origin
#18
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://read.qxmd.com/read/29576807/complete-genome-sequence-of-microcystis-aeruginosa-nies-2481-and-common-genomic-features-of-group-g-m-aeruginosa
#19
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://read.qxmd.com/read/29576806/genomic-analysis-of-propane-metabolism-in-methyl-tert-butyl-ether-degrading-mycobacterium-sp-strain-env421
#20
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
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