“Omics” Analyses of Cyanidioschyzon merolae Based on Complete Genome Information

2017 ◽  
pp. 73-85
Author(s):  
Masaki Yoshida ◽  
Takayuki Fujiwara
Keyword(s):  
Complete Genome ◽  
Cyanidioschyzon Merolae ◽  
Genome Information

scholarly journals Complete Genome Sequence of Streptococcus mutans Strain MD, Which Produces Highly Potent Mutacins

2020 ◽  
Vol 9 (33) ◽  
Author(s):  
Saswati Biswas ◽  
Indranil Biswas
Keyword(s):  
Streptococcus Mutans ◽  
Genome Sequence ◽  
Complete Genome Sequence ◽  
Complete Genome ◽  
Comparative Genomic ◽  
Content Type ◽  
Genomic Study ◽  
Comparative Genomic Study ◽  
Genome Information

ABSTRACT Here, we report the complete genome sequence of Streptococcus mutans strain MD, which produces potent mutacins capable of inhibiting streptococci. MD is a relatively uncharacterized strain whose genome information was unavailable. This study provides useful information for comparative genomic study and for understanding the repertoire of mutacins in S. mutans.

scholarly journals Complete Genome and Plasmid Sequences of Raphidiopsis curvispora Strain GIHE-G1, Isolated from a Drinking Water Reservoir in South Korea

2020 ◽  
Vol 9 (47) ◽  
Author(s):  
Ju-Yong Jeong ◽  
Mi-Ra Yun ◽  
Seung-Eun Oh ◽  
Seon-Min Hwang ◽  
Chan-Won Hwang ◽  
...  
Keyword(s):  
Drinking Water ◽  
South Korea ◽  
Complete Genome ◽  
Water Reservoir ◽  
Content Type ◽  
Drinking Water Reservoir ◽  
Genome Information

ABSTRACT The complete genome and plasmid sequences of Raphidiopsis curvispora strain GIHE-G1, a coiled filamentous heterocyst-forming cyanobacterium isolated from a drinking water reservoir in South Korea, are reported here. The genome information is expected to improve understanding of this species.

scholarly journals Genome Sequence of Prosthecochloris sp. Strain CIB 2401 of the Phylum Chlorobi

2016 ◽  
Vol 4 (6) ◽  
Author(s):  
Shaza Nabhan ◽  
Boyke Bunk ◽  
Cathrin Spröer ◽  
Zhenfeng Liu ◽  
Donald A. Bryant ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Complete Genome Sequence ◽  
Complete Genome ◽  
Phylogenetic Diversity ◽  
Green Sulfur Bacteria ◽  
Sulfur Bacteria ◽  
The Family ◽  
Green Sulfur ◽  
Genome Information

To date, only 13 genomes of green sulfur bacteria (family Chlorobiaceae ) have been sequenced. The sequenced strains do not cover the full phylogenetic diversity of the family. We determined the complete genome sequence of Prosthecochloris sp. strain CIB 2401, thereby increasing the genome information for the poorly represented marine Chlorobiaceae .

scholarly journals Complete genome sequence analysis of a novel granaticin producer, Streptomyces sp. A1013Y

2020 ◽  
Author(s):  
Shenglan Zheng ◽  
Yunping Zhu ◽  
Kaifeng Liu ◽  
Jinlong Li
Keyword(s):  
Complete Genome ◽  
Deletion Mutant ◽  
Gc Content ◽  
Rrna Genes ◽  
Trna Genes ◽  
Genome Sequence Analysis ◽  
Streptomyces Sp ◽  
Fermentation Liquid ◽  
Complete Genome Sequence Analysis ◽  
Genome Information

Abstract Granaticin is a kind of antibiotics with the function of anticancer, antibacterial, anticoccidial. Streptomyces sp. A1013Y is a new strain isolated from soil with granaticin-producing ability. The genome information was analyzed for the further study of granaticin. The present work reported the complete genome of S. sp. A1013Y, which contains a 7,646,296 bp chromosome with an average GC content of 71.59%. A total of 7361 CDSs, including 66 tRNA genes, 18 rRNA genes and 23 clusters, were identified in the genome. With homologous recombination, an in-frame deletion mutant was constructed to confirm the granaticin cluster. The fermentation liquid of the mutant did not contain granaticin based on HPLC and LC-MS analysis, indicating that S. sp. A1013Y is a granaticin producer. Comparing the granaticin biosynthesis cluster of S. sp. A1013Y with Streptomycesviolaceoruber Tü22 and Streptomyces vietnamensis GIMV4.0001T, which were sequenced and produce granaticin, the similarity between the granaticin clusters was 78% and 83% respectively, but some genes still weren’t identified in the granaticin biosynthesis cluster. The phylogenetic analysis and ANI value between S. sp. A1013Y and other Streptomyces species, including S. vietnamensis GIMV4.0001T, were all below 85%, which showed that S. sp. A1013Y was probably a novel streptomyces strain that produced granaticin. The whole genome information of S. sp. A1013Y provides a valuable foundation for future granaticin analyses as well as biomedicine applications.

scholarly journals Near-Complete Genome Assembly of Alternaria brassicae—A Necrotrophic Pathogen of Brassica Crops

2019 ◽  
Vol 32 (8) ◽  
pp. 928-930 ◽  
Author(s):  
Sivasubramanian Rajarammohan ◽  
Deepak Pental ◽  
Jagreet Kaur
Keyword(s):  
Genome Assembly ◽  
Fungal Pathogen ◽  
Complete Genome ◽  
Alternaria Brassicae ◽  
Necrotrophic Pathogen ◽  
Alternaria Blight ◽  
Brassica Crops ◽  
Genome Information ◽  
Important Disease ◽  
Chromosome Level

Alternaria brassicae, a necrotrophic fungal pathogen, causes Alternaria blight, an important disease of brassica crops. Although many Alternaria spp. have been sequenced, no genome information is available for A. brassicae, a monotypic lineage within the Alternaria genus. A highly contiguous genome assembly of A. brassicae has been generated using Nanopore MinION sequencing with an N50 of 2.98 Mb, yielding nine full chromosome-level sequences. This study adds to the current genomic resources available for the genus Alternaria and will provide opportunities for further analyses to unravel the mechanisms underlying pathogenicity of this important necrotrophic pathogen.

scholarly journals Complete Genome of the Chitin-Degrading Bacterium, Paenibacillus xylanilyticus W4

2019 ◽  
Vol 11 (11) ◽  
pp. 3252-3255 ◽  
Author(s):  
Weifang Liao ◽  
Pulin Liu ◽  
Weijie Liao ◽  
Lihong Miao
Keyword(s):  
Complete Genome ◽  
Gc Content ◽  
Circular Chromosome ◽  
Chitin Degradation ◽  
Degrading Bacterium ◽  
Degradation Activity ◽  
Genome Information ◽  
Taxonomic Characterization ◽  
Single Circular Chromosome ◽  
Genome Distance

Abstract Chitinases possess an extraordinary ability to directly hydrolyze highly insoluble chitin polymers to low-molecular-weight chito-oligomers, which possess particular biological functions, such as elicitor action and antitumor activity. A novel strain, Paenibacillus xylanilyticus W4, which was isolated from soil, showed strong chitin degradation activity. Here, we first reported the complete genome information of P. xylanilyticus. Paenibacillus xylanilyticus W4 contains a 5,532,141 bp single circular chromosome with 47.33% GC content. The genome contains 5,996 genes, including 39 rRNA- and 109 tRNA-coding genes. Phylogenetic analysis and Genome-to-Genome Distance revealed its taxonomic characterization into a separate family. Six glycoside hydrolase 18 (GH18) and 2 GH23 enzymes involved in chitin degradation. Although many of the chitinases were conserved in Paenibacillus, several GH18 chitinases share high similarity with Bacillus circulans. The genome information provided here could benefit for understanding the chitin-degrading properties of P. xylanilyticus as well as its potential application in biotechnological and pharmaceutical fields.

scholarly journals Complete Genome Sequence of Cyanobacterium Leptolyngbya sp. NIES-3755

2016 ◽  
Vol 4 (2) ◽  
Author(s):  
Yuu Hirose ◽  
Takatomo Fujisawa ◽  
Yoshiyuki Ohtsubo ◽  
Mitsunori Katayama ◽  
Naomi Misawa ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Complete Genome Sequence ◽  
Complete Genome ◽  
Diverse Species ◽  
University Of Technology ◽  
Genome Information ◽  
Cyanobacterial Genus

Cyanobacterial genus Leptolyngbya comprises genetically diverse species, but the availability of their complete genome information is limited. Here, we isolated Leptolyngbya sp. strain NIES-3755 from soil at the Toyohashi University of Technology, Japan. We determined the complete genome sequence of the NIES-3755 strain, which is composed of one chromosome and three plasmids.

scholarly journals Complete Genome Sequence of Stenotrophomonas sp. Strain WZN-1, Which Is Capable of Degrading Polybrominated Diphenyl Ethers

2017 ◽  
Vol 5 (31) ◽  
Author(s):  
Zhineng Wu ◽  
Mark Bartlam ◽  
Yingying Wang
Keyword(s):  
Genome Sequence ◽  
Complete Genome Sequence ◽  
Polybrominated Diphenyl Ethers ◽  
Complete Genome ◽  
Waste Recycling ◽  
Diphenyl Ethers ◽  
Genome Information

ABSTRACT Stenotrophomonas sp. strain WZN-1, isolated from an e-waste recycling area in Tianjin, China, is capable of degrading polybrominated diphenyl ethers (PBDEs). The complete genome of strain WZN-1 consists of 4,512,703 bp. This genome information will provide important information about the biodegradation pathways and mechanisms of PBDEs.

scholarly journals Draft Genome Sequence of Leishmania tarentolae Parrot Tar II, Obtained by Single-Molecule Real-Time Sequencing

2020 ◽  
Vol 9 (21) ◽  
Author(s):  
Yasuyuki Goto ◽  
Akihiro Kuroki ◽  
Kengo Suzuki ◽  
Junya Yamagishi
Keyword(s):  
Real Time ◽  
Genome Sequence ◽  
Single Molecule ◽  
Genome Assembly ◽  
Complete Genome ◽  
Draft Genome ◽  
Protozoan Parasite ◽  
Leishmania Tarentolae ◽  
Content Type ◽  
Genome Information

ABSTRACT Leishmania tarentolae is a protozoan parasite of lizards and is nonpathogenic to mammals. Genome information for the nonpathogenic species will facilitate an understanding of the pathology caused by species pathogenic to mammals. Here, we report resequencing of the L. tarentolae genome with a single-molecule real-time (SMRT) sequencer to provide a more complete genome assembly.

Methods for protein identification using expressed sequence tags and peptide mass fingerprinting for seed crops without complete genome sequences

2010 ◽  
Vol 20 (4) ◽  
pp. 257-262 ◽  
Author(s):  
Liming Yang ◽  
Yuming Luo ◽  
Jifu Wei ◽  
Chongmiao Ren ◽  
Xin Zhou ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Complete Genome ◽  
Protein Identification ◽  
Peptide Mass Fingerprinting ◽  
Mass Spectrometry Data ◽  
Peptide Mass ◽  
Species Specific ◽  
Seed Crops ◽  
Genome Information ◽  
Expressed Sequence

AbstractProteomic approaches based on two-dimensional gel electrophoresis, mass spectrometry and database search are widely used to address questions about the development, physiology and quality of seeds. Identification of proteins is of great importance in proteomic analyses. For seed crops without full genome information, cross-species protein identification by mass spectrometry-driven sequence similarity search can be used. However, this approach is risky due to protein polymorphism between different species. Species-specific expressed sequence tag (EST) databases are an invaluable resource, which complements mass spectrometry data analysis for protein identification. Here, we illustrate a modified method of protein identification and characterization using species-specific EST databases and peptide mass fingerprinting with an example of protein identification. This method is reliable, supplements the existing methods, and improves the efficiency and accuracy of protein identification for seed crops for which complete genome information is not available.

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