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Journal of Genomics

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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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