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Journal of Genomics

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https://www.readbyqxmd.com/read/29290830/constructing-a-chromonome-of-yellowtail-seriola-quinqueradiata-for-comparative-analysis-of-chromosomal-rearrangements
#1
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
#2
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
#3
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
#4
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
#5
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
#6
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
#7
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
#8
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
#9
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
#10
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
#11
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
https://www.readbyqxmd.com/read/28611852/cnv-analysis-of-host-responses-to-porcine-reproductive-and-respiratory-syndrome-virus-infection
#12
El Hamidi A Hay, Igseo Choi, Lingyang Xu, Yang Zhou, Robert R R Rowland, Joan K Lunney, George E Liu
Porcine reproductive and respiratory syndrome (PRRS) is a devastating disease with a significant impact on the swine industry causing major economic losses. The objective of this study is to examine copy number variations (CNVs) associated with the group-specific host responses to PRRS virus infection. We performed a genome-wide CNV analysis using 660 animals genotyped with on the porcine SNP60 BeadChip and discovered 7097 CNVs and 271 CNV regions (CNVRs). For this study, we used two established traits related to host response to the virus, i...
2017: Journal of Genomics
https://www.readbyqxmd.com/read/28529652/de-novo-assembly-of-the-liver-transcriptome-of-the-european-starling-sturnus-vulgaris
#13
Mark F Richardson, William B Sherwin, Lee A Rollins
The European starling, Sturnus vulgaris, is a prolific and worldwide invasive species that also has served as an important model for avian ecological and invasion research. Although the genome sequence recently has become available, no transcriptome data have been published for this species. Here, we have sequenced and assembled the S. vulgaris liver transcriptome, which will provide a foundational resource for further annotation and validation of the draft genome. Moreover, it will be important for ecological and evolutionary studies investigating the genetic factors underlying rapid evolution and invasion success in this global invader...
2017: Journal of Genomics
https://www.readbyqxmd.com/read/28529651/draft-genome-sequence-of-roseovarius-sp-a-2-an-iodide-oxidizing-bacterium-isolated-from-natural-gas-brine-water-chiba-japan
#14
Tri Yuliana, Nobuyoshi Nakajima, Shigeki Yamamura, Masaru Tomita, Haruo Suzuki, Seigo Amachi
Roseovarius sp. A-2 is a heterotrophic iodide (I(-))-oxidizing bacterium isolated from iodide-rich natural gas brine water in Chiba, Japan. This strain oxidizes iodide to molecular iodine (I2) by means of an extracellular multicopper oxidase. Here we report the draft genome sequence of strain A-2. The draft genome contained 46 tRNA genes, 1 copy of a 16S-23S-5S rRNA operon, and 4,514 protein coding DNA sequences, of which 1,207 (27%) were hypothetical proteins. The genome contained a gene encoding IoxA, a multicopper oxidase previously found to catalyze the oxidation of iodide in Iodidimonas sp...
2017: Journal of Genomics
https://www.readbyqxmd.com/read/28348643/whole-genome-sequencing-of-vibrio-sinaloensis-t47-a-tropical-marine-isolate-with-quorum-sensing-properties
#15
Nur Izzati Mohamad, Kah Yan How, Wai-Fong Yin, Kok-Gan Chan
A large number of Vibrio sp. thrive in the marine environment and they are notable to cause food borne infection associated with undercooked seafood. In this study, we report the whole genome sequence of Vibrio sinaloensis T47 which was isolated from coastal marine water in Morib Beach, Hulu Selangor. The genome is made up of approximately 4.59 Mbp with 80 contigs and 46% G+C content. From the annotated genome, genes associated with quorum sensing (QS) were identified. This research provides a genetic basis for better understanding of QS pathway which contributes to the physiological traits of strain T47 to thrive in the marine environment...
2017: Journal of Genomics
https://www.readbyqxmd.com/read/28348642/metagenomic-analysis-of-a-complex-community-present-in-pond-sediment
#16
Vivek Negi, Rup Lal
The metagenomic profiling of complex communities is gaining immense interest across the scientific community. A complex community present in the pond sediment of a water body located close to a hexachlorocyclohexane (HCH) production site of the Indian Pesticide Limited (IPL) (Chinhat, Lucknow) was selected in an attempt to identify and analyze the unique microbial diversity and functional profile of the site. In this study, we supplement the metagenomic study of pond sediment with a variety of binning approaches along with an in depth functional analysis...
2017: Journal of Genomics
https://www.readbyqxmd.com/read/28348641/complete-genome-sequence-and-functional-study-of-the-fibrinolytic-enzyme-producing-bacterium-leuconostoc-holzapfelii-5h4-a-silage-probiotic
#17
Hye Sun Kim, Ouk Kyu Han, Youn-Sig Kwak
To process silage, rye is usually removed before the heading stage but the rye biomass increased up to 30% after the heading stage. However, after the heading stage, lignification rapidly accelerated and it resulted in a poor NDF digestibility problem. This has led to a demand for a strong fibrinolytic enzyme-producing probiotic for rye silage. The Gram-positive Leuconostoc holzapfelii 5H4 was selected as a fibrinolytic enzyme-producing probiotic to overcome lignification of rye silage. The L. holzapfelii 5H4 has a relatively small circular chromosome (1,885,398 bp), but the strain has one cellulase, two xylanase, and five esterase in its genome sequence...
2017: Journal of Genomics
https://www.readbyqxmd.com/read/28348640/exploration-of-small-rna-seq-data-for-small-non-coding-rnas-in-human-colorectal-cancer
#18
Srinivas V Koduru, Amit K Tiwari, Sprague W Hazard, Milind Mahajan, Dino J Ravnic
Background: Improved healthcare and recent breakthroughs in technology have substantially reduced cancer mortality rates worldwide. Recent advancements in next-generation sequencing (NGS) have allowed genomic analysis of the human transcriptome. Now, using NGS we can further look into small non-coding regions of RNAs (sncRNAs) such as microRNAs (miRNAs), Piwi-interacting-RNAs (piRNAs), long non-coding RNAs (lncRNAs), and small nuclear/nucleolar RNAs (sn/snoRNAs) among others. Recent studies looking at sncRNAs indicate their role in important biological processes such as cancer progression and predict their role as biomarkers for disease diagnosis, prognosis, and therapy...
2017: Journal of Genomics
https://www.readbyqxmd.com/read/28138345/genomic-characterization-of-eight-ensifer-strains-isolated-from-pristine-caves-and-a-whole-genome-phylogeny-of-ensifer-sinorhizobium
#19
Heerman Kumar Sandra Kumar, Han Ming Gan, Mun Hua Tan, Wilhelm Wei Han Eng, Hazel A Barton, André O Hudson, Michael A Savka
A total of eight Ensifer sp. strains were isolated from two pristine cave environments. One strain was isolated from a cave water pool located in the Wind Cave National Park, South Dakota, USA and the remaining seven strains were isolated from Lechuguilla Cave of Carlsbad Caverns National Park, New Mexico, USA. Whole genome sequencing and comparative genomic analyses of the eight isolates compared to various type strains from the genera Ensifer and Sinorhizobium demonstrates that although members in these genera can be phylogenetically separated into two distinct clades, the percentage of conserved proteins (POCP) between various type strains from Ensifer and Sinorhizobium are consistently higher than 50%, providing strong genomic evidence to support the classification of the genera Ensifer and Sinorhizobium into a single genus...
2017: Journal of Genomics
https://www.readbyqxmd.com/read/28138344/detection-of-intestinal-pathogens-in-river-shore-and-drinking-water-in-lima-peru
#20
David C Grothen, Sydney J Zach, Paul H Davis
Water quality management is an ongoing struggle for many locations worldwide. Current testing of water supplies can be time-consuming, expensive, and lack sensitivity. This study describes an alternative, easy-to-use, and inexpensive method to water sampling and testing at remote locations. This method was employed to detect a number of intestinal pathogens in various locations of Lima, Peru. A total of 34 PCR primer pairs were tested for specificity and high-yield amplification for 12 different pathogens using known DNA templates...
2017: Journal of Genomics
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