scholarly journals Genome Sequences of Both Organelles of the Grapevine Rootstock Cultivar ‘Börner’

2020 ◽  
Vol 9 (15) ◽  
Author(s):  
Bianca Frommer ◽  
Daniela Holtgräwe ◽  
Ludger Hausmann ◽  
Prisca Viehöver ◽  
Bruno Huettel ◽  
...  
Keyword(s):  
Rna Editing ◽  
Mitochondrial Genes ◽  
Genome Sequences ◽  
Content Type ◽  
Vitis Riparia ◽  
Long Reads ◽  
Organelle Genomes

Genomic long reads of the interspecific grapevine rootstock cultivar ‘Börner’ (Vitis riparia GM183 × Vitis cinerea Arnold) were used to assemble its chloroplast and mitochondrion genome sequences. We annotated 133 chloroplast and 172 mitochondrial genes, including the RNA editing sites. The organelle genomes in ‘Börner’ were maternally inherited from Vitis riparia.

scholarly journals Genome sequences of both organelles of the grapevine rootstock cultivar 'Börner'

2020 ◽  
Author(s):  
Bianca Frommer ◽  
Daniela Luise Holtgräwe ◽  
Ludger Hausmann ◽  
Prisca Viehöver ◽  
Bruno Hüttel ◽  
...  
Keyword(s):  
Rna Editing ◽  
Mitochondrial Genes ◽  
Genome Sequences ◽  
Vitis Riparia ◽  
Organellar Genomes ◽  
Long Reads

Genomic long reads of the interspecific grapevine rootstock cultivar 'Börner' (Vitis riparia GM183 x Vitis cinerea Arnold) were used to assemble its chloroplast and mitochondrion genome sequences. We annotated 133 chloroplast and 172 mitochondrial genes including the RNA-editing sites. The organellar genomes were maternally inherited to 'Börner' from Vitis riparia.

scholarly journals Complete Circular Genome Sequences of Three Bacillus cereus Group Strains Isolated from Positive Blood Cultures from Preterm and Immunocompromised Infants Hospitalized in France

2021 ◽  
Vol 10 (41) ◽  
Author(s):  
Mariem Ben Khedher ◽  
Fredrik Nindo ◽  
Alicia Chevalier ◽  
Stéphane Bonacorsi ◽  
Gregory Dubourg ◽  
...  
Keyword(s):  
Intensive Care ◽  
Bacillus Cereus ◽  
Complete Genome ◽  
Blood Cultures ◽  
Genome Sequences ◽  
Bacillus Cereus Group ◽  
Illumina Hiseq ◽  
Content Type ◽  
Long Reads ◽  
Oxford Nanopore

We report here the complete genome sequences of three Bacillus cereus group strains isolated from blood cultures from premature and immunocompromised infants hospitalized in intensive care units in three French hospitals. These complete genome sequences were obtained from a combination of Illumina HiSeq X Ten short reads and Oxford Nanopore MinION long reads.

scholarly journals Complete Genome Sequences of 12 Quinolone-Resistant Escherichia coli Strains Containing qnrS1 Based on Hybrid Assemblies

2021 ◽  
Vol 10 (4) ◽  
Author(s):  
Håkon Kaspersen ◽  
Thomas H. A. Haverkamp ◽  
Hanna Karin Ilag ◽  
Øivind Øines ◽  
Camilla Sekse ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Complete Genome ◽  
Flow Cell ◽  
Hybrid Assembly ◽  
Genome Sequences ◽  
Content Type ◽  
Short Reads ◽  
Long Reads ◽  
Long Read ◽  
Hybrid Assemblies

ABSTRACT In total, 12 quinolone-resistant Escherichia coli (QREC) strains containing qnrS1 were submitted to long-read sequencing using a FLO-MIN106 flow cell on a MinION device. The long reads were assembled with short reads (Illumina) and analyzed using the MOB-suite pipeline. Six of these QREC genome sequences were closed after hybrid assembly.

scholarly journals PREPACT 2.0: Predicting C-to-U and U-to-C RNA Editing in Organelle Genome Sequences with Multiple References and Curated RNA Editing Annotation

2013 ◽  
Vol 7 ◽  
pp. BBI.S11059 ◽  
Author(s):  
Henning Lenz ◽  
Volker Knoop
Keyword(s):  
Rna Editing ◽  
Genome Sequences ◽  
Computer Tool ◽  
Organelle Genome ◽  
Chloroplast Genomes ◽  
Organelle Genomes ◽  
Genetic Systems ◽  
Analysis Computer ◽  
New Commons ◽  
Multiple References

RNA editing is vast in some genetic systems, with up to thousands of targeted C-to-U and U-to-C substitutions in mitochondria and chloroplasts of certain plants. Efficient prognoses of RNA editing in organelle genomes will help to reveal overlooked cases of editing. We present PREPACT 2.0 ( http://www.prepact.de ) with numerous enhancements of our previously developed Plant RNA Editing Prediction & Analysis Computer Tool. Reference organelle transcriptomes for editing prediction have been extended and reorganized to include 19 curated mitochondrial and 13 chloroplast genomes, now allowing to distinguish RNA editing sites from “pre-edited” sites. Queries may be run against multiple references and a new “commons” function identifies and highlights orthologous candidate editing sites congruently predicted by multiple references. Enhancements to the BLASTX mode in PREPACT 2.0 allow querying of complete novel organelle genomes within a few minutes, identifying protein genes and candidate RNA editing sites simultaneously without prior user analyses.

scholarly journals Whole-Genome Sequencing and De Novo Assembly of 61 Staphylococcus pseudintermedius Isolates from Healthy Dogs and Dogs with Pyoderma

2021 ◽  
Vol 10 (16) ◽  
Author(s):  
O. Francino ◽  
D. Pérez ◽  
J. Viñes ◽  
R. Fonticoba ◽  
S. Madroñero ◽  
...  
Keyword(s):  
Genome Sequencing ◽  
De Novo ◽  
Noncoding Rnas ◽  
Whole Genome ◽  
Genome Sequences ◽  
Staphylococcus Pseudintermedius ◽  
Coding Sequences ◽  
Content Type ◽  
Long Reads ◽  
Healthy Dogs

ABSTRACT We have de novo assembled and polished 61 Staphylococcus pseudintermedius genome sequences with Nanopore-only long reads. Completeness was 99.25%. The average genome size was 2.70 Mbp, comprising 2,506 coding sequences, 19 complete rRNAs, 56 to 59 tRNAs, and 4 noncoding RNAs (ncRNAs), as well as CRISPR arrays.

scholarly journals Complete Mitochondrial and Plastid Genomes of the Green Microalga Trebouxiophyceae sp. Strain MX-AZ01 Isolated from a Highly Acidic Geothermal Lake

2012 ◽  
Vol 11 (11) ◽  
pp. 1417-1418 ◽  
Author(s):  
Luis E. Servín-Garcidueñas ◽  
Esperanza Martínez-Romero
Keyword(s):  
Green Algae ◽  
Genome Sequence ◽  
Hot Springs ◽  
Geothermal Field ◽  
Genome Sequences ◽  
Toxic Heavy Metal ◽  
Content Type ◽  
Plastid Genomes ◽  
Organelle Genomes ◽  
Green Microalga

ABSTRACTWe report the complete organelle genome sequences ofTrebouxiophyceaesp. strain MX-AZ01, an acidophilic green microalga isolated from a geothermal field in Mexico. This eukaryote has the remarkable ability to thrive in a particular shallow lake with emerging hot springs at the bottom, extremely low pH, and toxic heavy metal concentrations.Trebouxiophyceaesp. MX-AZ01 represents one of few described photosynthetic eukaryotes living in such a hostile environment. The organelle genomes ofTrebouxiophyceaesp. MX-AZ01 are remarkable. The plastid genome sequence currently presents the highest G+C content for a trebouxiophyte. The mitochondrial genome sequence is the largest reported to date for theTrebouxiophyceaeclass of green algae. The analysis of the genome sequences presented here provides insight into the evolution of organelle genomes of trebouxiophytes and green algae.

scholarly journals Draft Genome Sequences of 12 Mycolicibacterium smegmatis Strains Resistant to Imidazo[1,2-b][1,2,4,5]Tetrazines

2019 ◽  
Vol 8 (16) ◽  
Author(s):  
Aleksey A. Vatlin ◽  
Kirill V. Shur ◽  
Valery N. Danilenko ◽  
Dmitry A. Maslov
Keyword(s):  
Draft Genome ◽  
Transcriptional Repressor ◽  
Antituberculosis Drug ◽  
Genome Sequences ◽  
Content Type ◽  
Drug Candidates

Here, we report 12 draft genome sequences of mutant Mycolicibacterium smegmatis strains resistant to imidazo[1,2-b][1,2,4,5]tetrazines, which are antituberculosis drug candidates. We have identified 7 different mutations in the MSMEG_1380 gene, which encodes the AcrR/TetR_N transcriptional repressor, which may activate efflux-mediated resistance.

scholarly journals Draft Genome Sequences of Three Flavobacterium psychrophilum Strains Isolated from Diseased Ayu (Plecoglossus altivelis altivelis) Caught at Three Sites in the Kagami River in Kochi, Japan

2019 ◽  
Vol 8 (34) ◽  
Author(s):  
Hazuki Yamashita ◽  
Takayuki Wada ◽  
Yusuke Kato ◽  
Takuji Ikeda ◽  
Masayuki Imajoh
Keyword(s):  
Draft Genome ◽  
Psychrophilic Bacterium ◽  
Genome Sequences ◽  
Plecoglossus Altivelis ◽  
Gram Negative ◽  
Content Type ◽  
Flavobacterium Psychrophilum ◽  
Skin Ulcers ◽  
The Family

Flavobacterium psychrophilum is a Gram-negative, psychrophilic bacterium within the family Flavobacteriaceae. Here, we report the draft genome sequences of three F. psychrophilum strains isolated from skin ulcers of diseased ayu caught by tomozuri angling at three sites in the Kagami River in Japan.

scholarly journals Draft Genome Sequences of Escherichia coli Strains FP2 and FP3, Isolated from the Canada Goose (Branta canadensis)

2018 ◽  
Vol 7 (9) ◽  
Author(s):  
Allison L. Denny ◽  
Susan E. Arruda
Keyword(s):  
Escherichia Coli ◽  
Draft Genome ◽  
Branta Canadensis ◽  
Canada Goose ◽  
Genome Sequences ◽  
Content Type

Draft genomes of two strains of Escherichia coli, FP2 and FP3, isolated from the feces of the Canada goose (Branta canadensis), were sequenced. Genome sizes were 5.26 Mb with a predicted G+C content of 50.54% (FP2) and 5.07 Mb with a predicted G+C content of 50.41% (FP3).

scholarly journals Genome Sequences of a Staphylococcus aureus Clinical Isolate, Strain SMA0034-04 (UGA22), from Siaya County Referral Hospital in Siaya, Kenya

2019 ◽  
Vol 8 (17) ◽  
Author(s):  
Gary Xie ◽  
Qiuying Cheng ◽  
Hajnalka Daligault ◽  
Karen Davenport ◽  
Cheryl Gleasner ◽  
...  
Keyword(s):  
Staphylococcus Aureus ◽  
Clinical Isolate ◽  
Referral Hospital ◽  
Genome Sequences ◽  
Content Type

Here, we report the genome sequences of a Staphylococcus aureus clinical isolate, strain SMA0034-04 (UGA22), which contains one chromosome and one plasmid. We also reveal that isolate SMA0034-04 (UGA22) contains loci in the genome that encode multiple exotoxins.

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