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Journal of Genomics

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https://www.readbyqxmd.com/read/27672405/whole-genome-sequence-analysis-of-an-alachlor-and-endosulfan-degrading-micrococcus-sp-strain-2385-isolated-from-ochlockonee-river-florida
#1
Ashish Pathak, Ashvini Chauhan, Ayman Y I Ewida, Paul Stothard
We recently isolated Micrococcus sp. strain 2385 from Ochlockonee River, Florida and demonstrated potent biodegradative activity against two commonly used pesticides- alachlor [(2-chloro-2`,6`-diethylphenyl-N (methoxymethyl)acetanilide)] and endosulfan [(6,7,8,9,10,10-hexachloro-1,5,5a,6,9,9a-hexahydro-6,9methano-2,3,4-benzo(e)di-oxathiepin-3-oxide], respectively. To further identify the repertoire of metabolic functions possessed by strain 2385, a draft genome sequence was obtained, assembled, annotated and analyzed...
2016: Journal of Genomics
https://www.readbyqxmd.com/read/27672404/de-novo-assembly-and-analysis-of-the-chilean-pencil-catfish-trichomycterus-areolatus-transcriptome
#2
Thomas T Schulze, Jonathan M Ali, Maggie L Bartlett, Madalyn M McFarland, Emalie J Clement, Harim I Won, Austin G Sanford, Elyssa B Monzingo, Matthew C Martens, Ryan M Hemsley, Sidharta Kumar, Nicolas Gouin, Alan S Kolok, Paul H Davis
Trichomycterus areolatus is an endemic species of pencil catfish that inhabits the riffles and rapids of many freshwater ecosystems of Chile. Despite its unique adaptation to Chile's high gradient watersheds and therefore potential application in the investigation of ecosystem integrity and environmental contamination, relatively little is known regarding the molecular biology of this environmental sentinel. Here, we detail the assembly of the Trichomycterus areolatus transcriptome, a molecular resource for the study of this organism and its molecular response to the environment...
2016: Journal of Genomics
https://www.readbyqxmd.com/read/27512520/pseudomonas-lini-strain-zbg1-revealed-carboxylic-acid-utilization-and-copper-resistance-features-required-for-adaptation-to-vineyard-soil-environment-a-draft-genome-analysis
#3
Kok-Gan Chan, Teik-Min Chong, Tan-Guan-Sheng Adrian, Heng Leong Kher, Catherine Grandclément, Denis Faure, Wai-Fong Yin, Yves Dessaux, Kar-Wai Hong
Pseudomonas lini strain ZBG1 was isolated from the soil of vineyard in Zellenberg, France and the draft genome was reported in this study. Bioinformatics analyses of the genome revealed presence of genes encoding tartaric and malic acid utilization as well as copper resistance that correspond to the adaptation this strain in vineyard soil environment.
2016: Journal of Genomics
https://www.readbyqxmd.com/read/27512519/draft-genome-sequence-of-carotenoid-producing-yellow-pigmented-planococcus-maritimus-mku009
#4
Ashok Ganapathy, Sridhar Jayavel, Sivakumar Natesan
Planococcus maritimus MKU009 is a Gram positive cocci and a moderate halophilic bacterium isolated from marine water of Pichavaram, South East Coast of India. Here we report the draft genome of Planococcus maritimus MKU009 with a total size of 3,251,644 bp with N50 value of 1681571 bp. The overall G+C content of the genome was 47.27%. The carotenoid producing crtN, crtB, crtP and crtI genes were located within the first contig of the genome assembly. This genome source will provide insights into functional genomics of carotenoid production and metabolic engineering...
2016: Journal of Genomics
https://www.readbyqxmd.com/read/27512518/external-rna-controls-consortium-beta-version-update
#5
Hangnoh Lee, P Scott Pine, Jennifer McDaniel, Marc Salit, Brian Oliver
Spike-in RNAs are valuable controls for a variety of gene expression measurements. The External RNA Controls Consortium developed test sets that were used in a number of published reports. Here we provide an authoritative table that summarizes, updates, and corrects errors in the test version that ultimately resulted in the certified Standard Reference Material 2374. We have noted existence of anti-sense RNA controls in the material, corrected sub-pool memberships, and commented on control RNAs that displayed inconsistent behavior...
2016: Journal of Genomics
https://www.readbyqxmd.com/read/27326264/draft-genome-sequence-of-kocuria-rhizophila-strain-tpw45-an-actinobacterium-isolated-from-freshwater
#6
Tan-Guan-Sheng Adrian, Pui-Wan Tan, Jian-Woon Chen, Wai-Fong Yin, Kok-Gan Chan
Kocuria rhizophila is a ubiquitous bacterium which is well known for its industrial value. Here, we present the draft genome of Kocuria rhizophila strain TPW45 which was isolated from Sungai Gabai, Selangor, Malaysia. The assembled genome comprised of 46 contigs and the estimated genome size is 2.7 Mb. Based on the RAST annotation, a gene cluster responsible for aromatic compound degradation was identified in this strain.
2016: Journal of Genomics
https://www.readbyqxmd.com/read/27326263/draft-genome-sequence-of-paracoccus-sp-mku1-a-new-bacterial-strain-isolated-from-an-industrial-effluent-with-potential-for-bioremediation
#7
Kamaldeen Nasrin Nisha, Jayavel Sridhar, Perumal Varalakshmi, Balasubramaniem Ashokkumar
Paracoccus sp. MKU1, a novel dimethylformamide degrading bacterial strain was originally isolated from an industrial effluent, Tirupur region, Tamil Nadu, India. Here, we report the draft genome sequence of Paracoccus sp. MKU1, which could provide the genetic insights on its evolution and application of this versatile bacterium for effective degradation of xenobiotics and thus in bioremediation.
2016: Journal of Genomics
https://www.readbyqxmd.com/read/27026792/draft-genome-sequence-of-providencia-sneebia-strain-st1-a-quorum-sensing-bacterium-associated-with-marine-microalgae
#8
Jin Zhou, Yong-Min Lao, Zhong-Hua Cai
Providencia sneebia strain ST1 is a symbiotic bacterium (belonging to phylum gammaproteobacteria) with marine microalgae. This bacterium exhibits the ability to produce N-Acyl homoserine lactone signal molecule. To date, no genome that originates from marine Providencia spp. has been reported. In this study, we present the genome sequence of this strain. It has a genome size of 4.89 M, with 19 contigs and an average G+C of 51.97%. The function of 4,631 proteins was predicted, and 3,652 proteins were assigned to COG functional categories...
2016: Journal of Genomics
https://www.readbyqxmd.com/read/26958092/draft-genome-sequences-of-two-pathogenic-corynebacterial-species-isolated-from-cows
#9
Luis Carlos Guimarães, Thiago Lopes, Rommel Thiago Jucá Ramos, Adriana Ribeiro Carneiro, Ana Lídia Queiroz Cavalcante, Diego Barreto, Pablo Caracciolo Gomes de Sá, Adonney Allan Oliveira Veras, Flávia Souza Rocha, Priscilla Bagano, Felipe Luiz Pereira, Fernanda Alves Dorella, Carlos Augusto Leal, Alex Fiorini Carvalho, Chantal Bizet, Nicole Guiso, Edgar Badell, Henrique César Pereira Figueiredo, Vasco Azevedo, Artur Silva
The species Corynebacterium renale, Corynebacterium pilosum, and Corynebacterium cystitidis were initially thought to be the same species C. renale, but with different immunological types. These bacteria are the causative agent of cystitis, urethritis and pyelonephritis and are found usually as constituents of the normal flora in the lower urogenital tract of cattle. Therefore, we present the draft genome sequences of two pathogenic Corynebacterium species: C. renale CIP 52.96 and C. pilosum CIP 103422. The genome sequences of these species have 2,322,762 bp with 2,218 protein encoding genes and 2,548,014 bp with 2,428 protein encoding genes, respectively...
2016: Journal of Genomics
https://www.readbyqxmd.com/read/26958091/draft-genome-sequence-of-brevibacillus-borstelensis-cifa_chp40-a-thermophilic-strain-having-biotechnological-importance
#10
Swetaleena Tripathy, Soumesh Kumar Padhi, Rinil Sen, Ushajyoti Maji, Mrinal Samanta, Sriprakash Mohanty, Nikhil Kumar Maiti
Brevibacillus borstelensis cifa_chp40 is a thermophilic, strictly aerobic gram positive motile bacteria isolated from the alkaline hot water spring located in the Eastern Ghats zone of India. It could grow in a wide range of temperature and degrade low-density polythene at 37°C. The strain cifa_chp40 produces essential enzymes like protease, lipase, esterase and amidase at 50°C. Here, we report the draft genome sequence of B. borstelensis cifa_chp40 which will provide further insight into the metabolic capabilities, function and evolution of this important organism...
2016: Journal of Genomics
https://www.readbyqxmd.com/read/26958090/draft-genome-sequence-of-colletotrichum-falcatum-a-prelude-on-screening-of-red-rot-pathogen-in-sugarcane
#11
Rasappa Viswanathan, Chandrasekaran Naveen Prasanth, Palaniyandi Malathi, Amalraj Ramesh Sundar
Colletotrichum falcatum, a concealed fungal ascomycete causes red rot, which is a serious disease in sugarcane. It infects economically important stalk tissues, considered as store house of sugar in sugarcane. The study is to find genetic complexities of C. falcatum in establishing this as a stalk infecting pathogen and to decipher the unique lifestyle of this pathogen using NGS technology. We report the draft genome of C. falcatum of about 48.16 Mb in size with 12,270 genes. The genome sequences were compared with other fungal species which revealed that C...
2016: Journal of Genomics
https://www.readbyqxmd.com/read/26816553/draft-genome-of-multidrug-resistant-klebsiella-pneumoniae-223-14-carrying-kpc-6-isolated-from-a-general-hospital-in-malaysia
#12
Norazah Ahmad, Teik Min Chong, Rohaidah Hashim, Surianti Shukor, Wai-Fong Yin, Kok-Gan Chan
We performed whole genome sequencing on a clinical multidrug-resistant Klebsiella pneumoniae strain 223/14. Investigation into its draft genome revealed the presence of KPC-6 variant, suggesting carbapenemase is present in this isolate. We found a plasmid-borne KPC gene (882 bp) inserted between two transposase genes in the genome of K. pneumoniae 223/14.
2015: Journal of Genomics
https://www.readbyqxmd.com/read/26816552/draft-genome-sequences-of-two-brucella-abortus-strains-isolated-from-cattle-and-pig
#13
Narinder Singh Sharma, Thakhur Sunita, A K Arora, Chandra Mudit, Paviter Kaur, Jagadesan Sankarasubramanian, Udayakumar S Vishnu, Paramasamy Gunasekaran, Jeyaprakash Rajendhran
We report the draft genome sequences of two Brucella abortus strains LMN1 and LMN2 isolated from cattle and pig. The LMN1 and LMN2 have the genome size of 3,395,952 bp and 3,334,792 bp, respectively. In addition to the conserved genes of Brucella, few novel regions showing similarity to the phages were identified in both strains.
2015: Journal of Genomics
https://www.readbyqxmd.com/read/26516375/whole-genome-sequence-of-the-soybean-aphid-endosymbiont-buchnera-aphidicola-and-genetic-differentiation-among-biotype-specific-strains
#14
Bryan J Cassone, Jacob A Wenger, Andrew P Michel
Endosymbiosis with microorganisms is common in insects, with more than 10% of species requiring the metabolic capabilities of intracellular bacteria for their nutrient acquisition. Aphids harbor an obligate mutualism with the vertically transferred endosymbiont, Buchnera aphidicola, which produces key nutrients lacking in the aphid's phloem-based diet that are necessary for normal development and reproduction. It is thought that, in some groups of insects, bacterial symbionts may play key roles in biotype evolution against host-plant resistance...
2015: Journal of Genomics
https://www.readbyqxmd.com/read/26516374/draft-genome-sequences-of-two-species-of-difficult-to-identify-human-pathogenic-corynebacteria-implications-for-better-identification-tests
#15
Luis G C Pacheco, Ana L Mattos-Guaraldi, Carolina S Santos, Adonney A O Veras, Luis C Guimarães, Vinícius Abreu, Felipe L Pereira, Siomar C Soares, Fernanda A Dorella, Alex F Carvalho, Carlos G Leal, Henrique C P Figueiredo, Juliana N Ramos, Veronica V Vieira, Eric Farfour, Nicole Guiso, Raphael Hirata, Vasco Azevedo, Artur Silva, Rommel T J Ramos
Non-diphtheriae Corynebacterium species have been increasingly recognized as the causative agents of infections in humans. Differential identification of these bacteria in the clinical microbiology laboratory by the most commonly used biochemical tests is challenging, and normally requires additional molecular methods. Herein, we present the annotated draft genome sequences of two isolates of "difficult-to-identify" human-pathogenic corynebacterial species: C. xerosis and C. minutissimum. The genome sequences of ca...
2015: Journal of Genomics
https://www.readbyqxmd.com/read/26157507/glad-an-online-database-of-gene-list-annotation-for-drosophila
#16
Yanhui Hu, Aram Comjean, Lizabeth A Perkins, Norbert Perrimon, Stephanie E Mohr
We present a resource of high quality lists of functionally related Drosophila genes, e.g. based on protein domains (kinases, transcription factors, etc.) or cellular function (e.g. autophagy, signal transduction). To establish these lists, we relied on different inputs, including curation from databases or the literature and mapping from other species. Moreover, as an added curation and quality control step, we asked experts in relevant fields to review many of the lists. The resource is available online for scientists to search and view, and is editable based on community input...
2015: Journal of Genomics
https://www.readbyqxmd.com/read/26157506/antibiotic-resistant-and-virulence-determinants-of-staphylococcus-haemolyticus-c10a-as-revealed-by-whole-genome-sequencing
#17
Kok-Gan Chan, Kim Tien Ng, Teik Min Chong, Yong Kek Pang, Adeeba Kamarulzaman, Wai-Fong Yin, Kok Keng Tee
Staphylococcus haemolyticus is one of the pathogens that harbor a high level of antibiotic resistance. Here, we highlighted the potential determinants for multidrug resistance and virulence from the draft genome of Staphylococcus haemolyticus strain C10A, isolated from a patient with chronic obstructive pulmonary disease exacerbation.
2015: Journal of Genomics
https://www.readbyqxmd.com/read/25874016/map-based-comparative-genomic-analysis-of-virulent-haemophilus-parasuis-serovars-4-and-5
#18
Paulraj Lawrence, Russell Bey
Haemophilus parasuis is a commensal bacterium of the upper respiratory tract of healthy pigs. However, in conjunction with viral infections in immunocompromised animals H. parasuis can transform into a pathogen that is responsible for causing Glasser's disease which is typically characterized by fibrinous polyserositis, polyarthritis, meningitis and sometimes acute pneumonia and septicemia in pigs. Haemophilus parasuis serovar 5 is highly virulent and more frequently isolated from respiratory and systemic infection in pigs...
2015: Journal of Genomics
https://www.readbyqxmd.com/read/25874015/draft-genome-sequence-of-multidrug-resistant-salmonella-enterica-serovar-weltevreden-isolated-from-seafood
#19
Vijaya Kumar Deekshit, Krishna Kumar Ballamoole, Praveen Rai, Madhushankara, Iddya Karunasagar, Indrani Karunasagar
Salmonella enterica subsp. enterica serovar Weltevereden is the most frequent serovar isolated from Asia. Here, we report a draft genome sequence of multidrug resistant Salmonella Weltevreden 9 isolated from seafood. Whole-genome of this isolate and annotation will help enhance the understanding of this pathogenic multidrug-resistant serovar.
2015: Journal of Genomics
https://www.readbyqxmd.com/read/25874014/genetic-variability-of-microrna-genes-in-15-animal-species
#20
Minja Zorc, Jana Obsteter, Peter Dovc, Tanja Kunej
MicroRNAs (miRNA) are a class of non-coding RNAs important in posttranscriptional regulation of target genes. Previous studies have proven that genetic variability of miRNA genes (miR-SNP) has an impact on phenotypic variation and disease susceptibility in human, mice and some livestock species. MicroRNA gene polymorphisms could therefore represent biomarkers for phenotypic traits also in other animal species. We upgraded our previously developed tool miRNA SNiPer to the version 4.0 which enables the search of miRNA genetic variability in 15 animal genomes: http://www...
2015: Journal of Genomics
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