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Genomics Data

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https://www.readbyqxmd.com/read/28856101/draft-genome-sequence-of-an-endophytic-bacterium-paenibacillus-tyrfis-strain-suk123-isolated-from-santiria-apiculata-stem
#1
Emmanuel Haruna, Noraziah M Zin, Jonathan M Adams
Here we report the draft genome sequence of an endophytic Paenibacillus tyrfis strain isolated from the Universiti Kebangsaan Malaysia reserve forest, Malaysia. The genome size was approximately 8.04 Mb, and the assembly consisted of 107 scaffolds with 168 contigs, and had a G + C content of 53%. Phylogenetic analysis of strain SUK123 using the 16S rRNA gene revealed that it belonged to the family Paenibacillaceae with the highest similarity to Paenibacillus elgii SD(T) (99%). Whole genome comparison of SUK123 with related species using average nucleotide identity (ANI) analysis revealed a similarity of 98% to Paenibacillus tyrfis Mst1(T), 94% to Paenibacillus elgii B69(T), 91% to Paenibacillus ehimensis A2(T), 68% to Paenibacillus polymyxa SC2(T) and 69% to Paenibacillus alvei DMS29(T)...
December 2017: Genomics Data
https://www.readbyqxmd.com/read/28856100/genome-of-pseudomonas-nitroreducens-df05-from-dioxin-contaminated-sediment-downstream-of-the-san-jacinto-river-waste-pits-reveals-a-broad-array-of-aromatic-degradation-gene-determinants
#2
Rupa Iyer, Brian Iken, Ashish Damania
P. nitroreducens DF05 is a Gram negative, motile, aerobic, rod-shaped and psychrotrophic bacterium that was isolated from contaminated San Jacinto River sediment near River Terrace Park in Channelview, Texas. The draft genome of strain DF05 consists of a total of 192 contigs assembled at the scaffold level totaling 6,487,527 bp and encoding for 5862 functional proteins, 1116 of which are annotated as hypothetical proteins. The bacterial chromosome has a GC content of 65.15% and contains 22 rRNA and 70 tRNA loci...
December 2017: Genomics Data
https://www.readbyqxmd.com/read/28856099/rna-seq-data-comparisons-of-wild-soybean-genotypes-in-response-to-soybean-cyst-nematode-heterodera-glycines
#3
Hengyou Zhang, Bao-Hua Song
Soybean [Glycine max (L.) Merr.] is an important crop rich in vegetable protein and oil, and is a staple food for human and animals worldwide. However, soybean plants have been challenged by soybean cyst nematode (SCN, Heterodera glycines), one of the most damaging pests found in soybean fields. Applying SCN-resistant cultivars is the most efficient and environmentally friendly strategy to manage SCN. Currently, soybean breeding and further improvement in soybean agriculture are hindered by severely limited genetic diversity in cultivated soybeans...
December 2017: Genomics Data
https://www.readbyqxmd.com/read/28856098/gene-expression-profiling-of-ramie-roots-during-hydroponic-induction-and-adaption-to-aquatic-environment
#4
Gang Gao, Heping Xiong, Kunmei Chen, Jikang Chen, Ping Chen, Chunming Yu, Aiguo Zhu
Ramie (Boehmeria nivea (L.) Gaud.) is a traditionally terrestrial fiber crop. However, hydroponic technology can enhance the quantity and quality of disease free Ramie plant seedlings for field cultivation. To date, few studies have attempted to examine the hydroponic induction of ramie roots and the molecular responses of ramie roots to aquatic environment. In this study, ramie tender stems was grown in the soil or in a hydroponic water solution, and cultured in the same environmental conditions. Root samples of terrestrial ramie, and different developmental stages of hydroponic ramie (5 days, 30 days), were firstly pooled for reference transcriptome sequencing by Illumina Hiseq 2000...
December 2017: Genomics Data
https://www.readbyqxmd.com/read/28840100/genome-wide-identification-and-tissue-specific-expression-analysis-of-nucleotide-binding-site-leucine-rich-repeat-gene-family-in-cicer-arietinum-kabuli-chickpea
#5
Ranu Sharma, Vimal Rawat, C G Suresh
The nucleotide binding site-leucine rich repeat (NBS-LRR) proteins play an important role in the defense mechanisms against pathogens. Using bioinformatics approach, we identified and annotated 104 NBS-LRR genes in chickpea. Phylogenetic analysis points to their diversification into two families namely TIR-NBS-LRR and non-TIR-NBS-LRR. Gene architecture revealed intron gain/loss events in this resistance gene family during their independent evolution into two families. Comparative genomics analysis elucidated its evolutionary relationship with other fabaceae species...
December 2017: Genomics Data
https://www.readbyqxmd.com/read/28831381/draft-genome-sequence-of-a-monokaryotic-model-brown-rot-fungus-postia-rhodonia-placenta-sb12
#6
Jill Gaskell, Phil Kersten, Luis F Larrondo, Paulo Canessa, Diego Martinez, David Hibbett, Monika Schmoll, Christian P Kubicek, Angel T Martinez, Jagjit Yadav, Emma Master, Jon Karl Magnuson, Debbie Yaver, Randy Berka, Kathleen Lail, Cindy Chen, Kurt LaButti, Matt Nolan, Anna Lipzen, Andrea Aerts, Robert Riley, Kerrie Barry, Bernard Henrissat, Robert Blanchette, Igor V Grigoriev, Dan Cullen
No abstract text is available yet for this article.
December 2017: Genomics Data
https://www.readbyqxmd.com/read/28831380/draft-genome-sequence-of-the-halophilic-halobacillus-mangrovi-ktb-131-isolated-from-topan-salt-of-the-jeon-nam-in-korea
#7
Mingyeong Woo, Sun-Hee Park, Kyounghee Park, Min-Kyu Park, Ji-Yeon Kim, Han-Seung Lee, Jae Hak Sohn, Dong-Woo Lee, Gaewon Nam, Kee-Sun Shin, Sang-Jae Lee
The draft genome sequence of the halophilic bacterium Halobacillus mangrovi KTB 131, isolated from Topan salt of the Jeon-nam in Korea, was established. The genome comprises 4,151,649 bp, with a G + C content of 41.6%. The strain displays a high number of genes responsible for secondary metabolite biosynthesis, transport, and catabolism compared to other Halobacillus bacterial genus members. Numerous genes responsible for various transport systems, solute accumulation, and aromatic/sulfur decomposition were detected...
December 2017: Genomics Data
https://www.readbyqxmd.com/read/28794989/comparative-metagenomics-reveals-alterations-in-the-soil-bacterial-community-driven-by-n-fertilizer-and-amino-16%C3%A2-application-in-lettuce
#8
Apostolos Kalivas, Ioannis Ganopoulos, Fotis Psomopoulos, Ioannis Grigoriadis, Aliki Xanthopoulou, Evangelos Hatzigiannakis, Maslin Osathanunkul, Athanasios Tsaftaris, Panagiotis Madesis
Nutrients in the form of fertilizers and/or other additives such as amino acids, dramatically influence plant development and growth, plant nutrient composition and the level of soil pollution. Moreover, the treatment of soil microbiota is emerging as a new strategy in plant breeding to achieve desirable traits. Thus, integrated study of fertilizer application and soil microbiota might lead to a better understanding of soil-plant interactions and inform the design of novel ways to fertilize plants. Herein we report metagenomics data for soil microbiota in lettuce (Lactuca sativa) treated with fertilizer, amino acids or their combinations as follows: N-fertilizer + Amino16®, Amino16®, N-fertilizer and no treatment control...
December 2017: Genomics Data
https://www.readbyqxmd.com/read/28794988/whole-genome-sequencing-of-microbacterium-sp-aiso3-from-polluted-san-jacinto-river-sediment-reveals-high-bacterial-mobility-metabolic-versatility-and-heavy-metal-resistance
#9
Rupa Iyer, Ashish Damania, Brian Iken
The genus Microbacterium is composed of high GC content, Gram-positive bacteria of the phylum Acintobacteria known for their antibiotic production. Microbacterium species commonly colonize agricultural rhizospheres and more infrequently have been found to colonize and infect human tissues as well. Here we report the 3,696,310 bp draft genome (chromosome and plasmids) sequence assembled at the scaffold level from 232 contigs of Microbacterium sp. strain AISO3, isolated from polluted San Jacinto River sediment in Channelview, Texas...
December 2017: Genomics Data
https://www.readbyqxmd.com/read/28794987/whole-genome-of-klebsiella-aerogenes-px01-isolated-from-san-jacinto-river-sediment-west-of-baytown-texas-reveals-the-presence-of-multiple-antibiotic-resistance-determinants-and-mobile-genetic-elements
#10
Rupa Iyer, Brian Iken, Ashish Damania
Klebsiella aerogenes is a Gram-negative bacterium of the family Enterobacteriaceae which is widely distributed in water, air and soil. It also forms part of the normal microbiota found in human and animal gastrointestinal tracts. Here we report the draft genome sequence (chromosome and 1 plasmid) of K. aerogenes strain PX01 compiled at the scaffold level from 97 contigs totaling 5,262,952 bp. K. aerogenes PX01 was isolated from sediment along the northern face of Burnet Bay west of Baytown, Texas. The nucleotide sequence of this genome was deposited into NCBI GenBank under the accession NJBB00000000...
December 2017: Genomics Data
https://www.readbyqxmd.com/read/28761813/rna-seq-data-from-different-developmental-stages-of-rafflesia-cantleyi-floral-buds
#11
Safoora Amini, Halimah Alias, Mohd Afiq Aizat-Juhari, Mohd-Noor Mat-Isa, Jumaat Haji Adam, Hoe-Han Goh, Kiew-Lian Wan
Rafflesia cantleyi, known as one of the world's largest flowers, is a specialised holoparasite due to dramatic morphological modifications. It possesses highly reduced vegetative structure and only appears as a flower for sexual reproduction. Moreover, it has an unusual life cycle in that its floral bud development takes up to nine months. In order to fully understand the highly modified floral organ structure and long life cycle of R. cantleyi, we used Illumina sequencing technology (HiSeq) for sequence generation followed by de novo assembly of sequence reads...
December 2017: Genomics Data
https://www.readbyqxmd.com/read/28736703/genome-wide-mirna-gene-and-methylation-analysis-of-triple-negative-breast-cancer-to-identify-changes-associated-with-lymph-node-metastases
#12
Kelly A Avery-Kiejda, Andrea Mathe, Rodney J Scott
Triple negative breast cancer (TNBC) is a particularly important breast cancer subtype with an aggressive clinical phenotype that is associated with a higher likelihood of metastasis. This subtype is characterized by an absence of the estrogen (ER) and progesterone (PR) receptors, as well as the human epidermal growth factor receptor 2 (HER2/HER neu). The absence of the three receptors significantly reduces targeted treatment options for patients with TNBC and as such, there is an urgent need to identify novel treatment targets...
December 2017: Genomics Data
https://www.readbyqxmd.com/read/28736702/cultivar-specific-transcriptome-prediction-and-annotation-in-ficus-carica-l
#13
Liceth Solorzano Zambrano, Gabriele Usai, Alberto Vangelisti, Flavia Mascagni, Tommaso Giordani, Rodolfo Bernardi, Andrea Cavallini, Riccardo Gucci, Giovanni Caruso, Claudio D'Onofrio, Mike Frank Quartacci, Piero Picciarelli, Barbara Conti, Andrea Lucchi, Lucia Natali
The availability of transcriptomic data sequence is a key step for functional genomics studies. Recently, a repertoire of predicted genes of a Japanese cultivar of fig (Ficus carica L.) was released. Because of the great phenotypic variability that can be found in this species, we decided to study another fig genotype, the Italian cv. Dottato, in order to perform comparative studies between the two cultivars and extend the pan genome of this species. We isolated, sequenced and assembled fig genomic DNA from young fruits of cv...
September 2017: Genomics Data
https://www.readbyqxmd.com/read/28736701/a-comparative-genome-analysis-of-cercospora-sojina-with-other-members-of-the-pathogen-genus-mycosphaerella-on-different-plant-hosts
#14
Fanchang Zeng, Xin Lian, Guirong Zhang, Xiaoman Yu, Carl A Bradley, Ray Ming
Fungi are the causal agents of many of the world's most serious plant diseases causing disastrous consequences for large-scale agricultural production. Pathogenicity genomic basis is complex in fungi as multicellular eukaryotic pathogens. Here, we report the genome sequence of C. sojina, and comparative genome analysis with plant pathogen members of the genus Mycosphaerella (Zymoseptoria. tritici (synonyms M. graminicola), M. pini, M. populorum and M. fijiensis - pathogens of wheat, pine, poplar and banana, respectively)...
September 2017: Genomics Data
https://www.readbyqxmd.com/read/28736700/profiling-and-characterization-of-a-longissimus-dorsi-muscle-microrna-dataset-from-an-f2-duroc%C3%A2-%C3%A3-%C3%A2-pietrain-pig-resource-population
#15
Kaitlyn R Daza, Juan P Steibel, Deborah Velez-Irizarry, Nancy E Raney, Ronald O Bates, Catherine W Ernst
To elucidate the effects of microRNA (miRNA) regulation in skeletal muscle of adult pigs, miRNA expression profiling was performed with RNA extracted from longissimus dorsi (LD) muscle samples from 174 F2 pigs (~ 5.5 months of age) from a Duroc × Pietrain resource population. Total RNA was extracted from LD samples, and libraries were sequenced on an Illumina HiSeq 2500 platform in 1 × 50 bp format. After processing, 232,826,977 total reads were aligned to the Sus scrofa reference genome (v10.2.79), with 74...
September 2017: Genomics Data
https://www.readbyqxmd.com/read/28725557/genome-assembly-of-chryseobacterium-sp-strain-ihbb-10212-from-glacier-top-surface-soil-in-the-indian-trans-himalayas-with-potential-for-hydrolytic-enzymes
#16
Mohinder Pal, Mohit Kumar Swarnkar, Hena Dhar, Sanjay Chhibber, Arvind Gulati
The cold-active esterases are gaining importance due to their catalytic activities finding applications in chemical industry, food processes and detergent industry as additives, and organic synthesis of unstable compounds as catalysts. In the present study, the complete genome sequence of 4,843,645 bp with an average 34.08% G + C content and 4260 protein-coding genes are reported for the low temperature-active esterase-producing novel strain of Chrysobacterium isolated from the top-surface soil of a glacier in the cold deserts of the Indian trans-Himalayas...
September 2017: Genomics Data
https://www.readbyqxmd.com/read/28725556/de-novo-transcriptome-assembly-for-the-lung-of-the-ornamented-pygmy-frog-microhyla-fissipes
#17
Lusha Liu, Shouhong Wang, Lanying Zhao, Jianping Jiang
Microhyla fissipes, belonging to Neobatrachia, is a new model organism to study developmental biology, adaptive mechanisms from aquatic to terrestrial life, environmental toxicology, and human disease. M. fissipes use of lungs soon after hatching makes it extremely valuable for the study of lung function and development mechanisms. However, our knowledge of genes and pathways associated with lung development in M. fissipes is very limited. In this study, we conducted de novo transcriptome assembly for the lung of M...
September 2017: Genomics Data
https://www.readbyqxmd.com/read/28725555/genome-sequence-of-the-type-strain-clib-1764-t-%C3%A2-cbs-14374-t-of-the-yeast-species-kazachstania-saulgeensis-isolated-from-french-organic-sourdough
#18
Véronique Sarilar, Lieven Sterck, Saki Matsumoto, Noémie Jacques, Cécile Neuvéglise, Colin R Tinsley, Delphine Sicard, Serge Casaregola
Kazachstania saulgeensis is a recently described species isolated from French organic sourdough. Here, we report the high quality genome sequence of a monosporic segregant of the type strain of this species, CLIB 1764(T) (= CBS 14374(T)). The genome has a total length of 12.9 Mb and contains 5326 putative protein-coding genes, excluding pseudogenes and transposons. The nucleotide sequences were deposited into the European Nucleotide Archive under the genome assembly accession numbers FXLY01000001-FXLY01000017...
September 2017: Genomics Data
https://www.readbyqxmd.com/read/28721334/draft-genome-sequence-of-bradyrhizobium-paxllaeri-lmtr-21-t-isolated-from-lima-bean-phaseolus-lunatus-in-peru
#19
Ernesto Ormeño-Orrillo, Luis Rey, David Durán, Carlos A Canchaya, Marco A Rogel, Doris Zúñiga-Dávila, Juan Imperial, Tomás Ruiz-Argüeso, Esperanza Martínez-Romero
Bradyrhizobium paxllaeri is a prevalent species in root nodules of the Lima bean (Phaseolus lunatus) in Peru. LMTR 21(T) is the type strain of the species and was isolated from a root nodule collected in an agricultural field in the Peruvian central coast. Its 8.29 Mbp genome encoded 7635 CDS, 71 tRNAs and 3 rRNAs genes. All genes required to stablish a nitrogen-fixing symbiosis with its host were present. The draft genome sequence and annotation have been deposited at GenBank under the accession number MAXB00000000...
September 2017: Genomics Data
https://www.readbyqxmd.com/read/28702356/genome-sequence-of-bradyrhizobium-sp-lmtr-3-a-diazotrophic-symbiont-of-lima-bean-phaseolus-lunatus
#20
Ernesto Ormeño-Orrillo, Luis Rey, David Durán, Carlos A Canchaya, Doris Zúñiga-Dávila, Juan Imperial, Esperanza Martínez-Romero, Tomás Ruiz-Argüeso
Bradyrhizobium sp. LMTR 3 is a representative strain of one of the geno(species) of diazotrophic symbionts associated with Lima bean (Phaseolus lunatus) in Peru. Its 7.83 Mb genome was sequenced using the Illumina technology and found to encode a complete set of genes required for nodulation and nitrogen fixation, and additional genes putatively involved in root colonization. Its draft genome sequence and annotation have been deposited at GenBank under the accession number MAXC00000000.
September 2017: Genomics Data
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