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

2019 ◽  
Author(s):  
Shenglan Zheng ◽  
Yunping Zhu ◽  
Kaifeng Liu ◽  
Jinlong Li
Keyword(s):  
Complete Genome ◽  
Deletion Mutant ◽  
Gc Content ◽  
Rrna Genes ◽  
Trna Genes ◽  
Streptomyces Species ◽  
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 Complete genome sequence of Chryseobacterium sp. ZHDP1 with protease activity

2021 ◽  
Author(s):  
Huanshuai Zhao ◽  
Jianxin Wang ◽  
Jiamao Huang ◽  
Yuncheng Ma ◽  
Yunfei Chen ◽  
...  
Keyword(s):  
Complete Genome ◽  
Protease Activity ◽  
Fermentation Broth ◽  
Gc Content ◽  
Rrna Genes ◽  
Trna Genes ◽  
Rrna Gene ◽  
The Novel ◽  
Maximum Similarity ◽  
Insight Into

Abstract This study reported a complete genome of Chryseobacterium sp. ZHDP1 isolated from the soils of a seafood market. The ZHDP1 genome with a size of 4,917,748 bp and a GC content of 35.95% possessed 4,478 coding genes, 5 rRNA genes, 26 sRNA genes, and 89 tRNA genes. The 16S rRNA gene sequence of ZHDP1 had a maximum similarity of 99.07% with that of C. gambrini 5-1St1a. The maximum values of average nucleotide identity and DNA-DNA hybridization of ZHDP1 genome were 91.39 and 47.8, respectively, which were lower than the thresholds for a new genome. Different protease genes were annotated in the genome of ZHDP1, and the protease activity was also detected in the fermentation broth of ZHDP1. Furthermore, the activity of protease in the fermentation broth was optimized through temperature, pH, and metal irons, and the results showed that 60°C and pH 7.0 were the optimum conditions and Fe3+ could positively increase the protease activity of ZHDP1. This study provides the first insight into the novel genomic information of Chryseobacterium sp. ZHDP1 and its protein-degrading ability, thereby broadening our knowledge of the industrial potentials in genus Chryseobacterium strains.

scholarly journals Complete Genome Sequence of Megamonas funiformis Strain 1CBH44, Isolated from Human Feces

2021 ◽  
Vol 10 (48) ◽  
Author(s):  
Yusuke Ogata ◽  
Mitsuo Sakamoto ◽  
Naveen Kumar ◽  
Moriya Ohkuma ◽  
Masahira Hattori ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Complete Genome Sequence ◽  
Complete Genome ◽  
Gc Content ◽  
Rrna Genes ◽  
Trna Genes ◽  
Human Feces ◽  
Circular Chromosome ◽  
Protein Coding ◽  
Content Type

Here, we report the complete genome sequence of Megamonas funiformis strain 1CBH44, which was isolated from the feces of a healthy Japanese person. The genome consists of a circular chromosome (2,310,709 bp, with a GC content of 31.5%) and possesses 2,170 putative protein-coding genes, 18 rRNA genes, and 54 tRNA genes.

scholarly journals Complete genome sequence and evolution analysis of Psychrobacter sp. YP14 from Gammaridea Gastrointestinal Microbiota of Yap Trench

2019 ◽  
Author(s):  
Wei Jiaqiang ◽  
Gao Zhiyuan ◽  
Liu Whenfeng ◽  
Chen Hao
Keyword(s):  
Stress Response ◽  
Complete Genome ◽  
Genome Structure ◽  
Gc Content ◽  
Rrna Genes ◽  
Trna Genes ◽  
Psychrophilic Bacterium ◽  
Putative Open Reading Frame ◽  
Gastrointestinal Microbiota ◽  
Circular Chromosome

AbstractPsychrobacter sp. YP14, a moderately psychrophilic bacterium belonging to the class Gammaproteobacteria, was isolated from Gammaridea Gastrointestinal Microbiota of Yap Trench. The strain has one circular chromosome of 2,895,311 bp with a 44.66% GC content, consisting of 2333 protein-coding genes, 53 tRNA genes and 9 rRNA genes. Four plasmids were completely assembled and their sizes were 13,712 bp, 19711 bp, 36270 bp, 8194 bp, respectively. In particular, a putative open reading frame (ORF) for dienelactone hydrolase (DLH) related to degradation of chlorinated aromatic hydrocarbons. To get an better understanding of the evolution of Psychrobacter sp. YP14 in this genus, six Psychrobacter strains (G, PRwf-1, DAB_AL43B, AntiMn-1,P11G5, P2G3), with publicly available complete genome, were selected and comparative genomics analysis were performed among them. The closest phylogenetic relationship was identified between strains G and K5 based on 16s gene and ANI (average nucleotide identity) values. Analysis of the pan-genome structure found that YP14 has fewer COG clusters associated with transposons and prophage which indicates fewer sequence rearrangements compared with PRwf-1. Besides, stress response-related genes of strain YP14 demonstrates that it has less strategies to cope with extreme environment, which is consistent with its intestinal habitat. The difference of metabolism and strategies coped with stress response of YP14 are more conducive to the study of microbial survival and metabolic mechanisms in deep sea environment.

scholarly journals Complete Genome Sequence of Cupriavidus necator H16 (DSM 428)

2019 ◽  
Vol 8 (37) ◽  
Author(s):  
Gareth T. Little ◽  
Muhammad Ehsaan ◽  
Christian Arenas-López ◽  
Kamran Jawed ◽  
Klaus Winzer ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Complete Genome Sequence ◽  
Complete Genome ◽  
Cupriavidus Necator ◽  
Rrna Genes ◽  
Trna Genes ◽  
Protein Coding ◽  
Content Type ◽  
Protein Coding Genes ◽  
Cupriavidus Necator H16

The hydrogen-utilizing strain Cupriavidus necator H16 (DSM 428) was sequenced using a combination of PacBio and Illumina sequencing. Annotation of this strain reveals 6,543 protein-coding genes, 263 pseudogenes, 64 tRNA genes, and 15 rRNA genes.

scholarly journals First Complete Genome Sequence of Brucella abortus 2308 isolated from an abortion storm in a dairy farm in India

2021 ◽  
Author(s):  
Amit Kumar ◽  
Malyaj R Prajapati ◽  
Surendra Upadhyay ◽  
Anamika Bhordia ◽  
Vinod Kumar Singh ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Dna Sequences ◽  
Brucella Abortus ◽  
Complete Genome Sequence ◽  
Complete Genome ◽  
Messenger Rna ◽  
Gc Content ◽  
Dairy Farm ◽  
Rrna Genes ◽  
Sequence Length

Abstract The present report communicates the first complete genome sequence of Brucella abortus 2308 strain isolated from a an abortion storm in a dairy farm located at Kanpur, Uttar Pradesh in India. It caused the last trimester abortions of 32 animals out of 100 cows in a dairy over a period of 60 days. The bacteria were isolated in pure culture from the placenta of aborted cows. The genome sequence length of isolated bacteria is 3,285,606 bp with a 57.25 % GC content, an N50 value of 296,426, L50 value of 4 containing 3,119 coding DNA sequences (CDSs), 49 tRNAs, 1 transfer messenger RNA (mRNA), and 3 rRNA genes. It is the first report of Brucella abortus 2308 isolation and complete genome sequence from Indian subcontinent.

scholarly journals Complete Genome Sequence of Thiohalobacter sp. Strain COW1, Isolated from Activated Sludge Treating Coke Oven Wastewater

2021 ◽  
Vol 10 (7) ◽  
Author(s):  
Kentaro Miyazaki ◽  
Hikaru Suenaga ◽  
Mamoru Oshiki ◽  
Shuichi Kawano ◽  
Toshikazu Fukushima
Keyword(s):  
Activated Sludge ◽  
Genome Sequence ◽  
Complete Genome Sequence ◽  
Complete Genome ◽  
Coke Oven ◽  
Rrna Genes ◽  
Trna Genes ◽  
Circular Chromosome ◽  
Protein Coding ◽  
Degrading Bacterium

ABSTRACT A thiocyanate-degrading bacterium, Thiohalobacter sp. strain COW1, was isolated from activated sludge treating coke oven wastewater, and the complete genome sequence was determined. COW1 contained a single circular chromosome (3.23 Mb; G+C content, 63.4%) in which 2,788 protein-coding genes, 39 tRNA genes, and 3 rRNA genes were identified.

scholarly journals Complete Chloroplast Genomes from Sanguisorba: Identity and Variation Among Four Species

Molecules ◽  
2018 ◽  
Vol 23 (9) ◽  
pp. 2137 ◽  
Author(s):  
Xiang-Xiao Meng ◽  
Yan-Fang Xian ◽  
Li Xiang ◽  
Dong Zhang ◽  
Yu-Hua Shi ◽  
...  
Keyword(s):  
Gc Content ◽  
Single Copy ◽  
Rrna Genes ◽  
Trna Genes ◽  
Protein Coding ◽  
Future Studies ◽  
Chloroplast Genomes ◽  
Close Relationship ◽  
Cp Genome ◽  
Sanguisorba Officinalis

The genus Sanguisorba, which contains about 30 species around the world and seven species in China, is the source of the medicinal plant Sanguisorba officinalis, which is commonly used as a hemostatic agent as well as to treat burns and scalds. Here we report the complete chloroplast (cp) genome sequences of four Sanguisorba species (S. officinalis, S. filiformis, S. stipulata, and S. tenuifolia var. alba). These four Sanguisorba cp genomes exhibit typical quadripartite and circular structures, and are 154,282 to 155,479 bp in length, consisting of large single-copy regions (LSC; 84,405–85,557 bp), small single-copy regions (SSC; 18,550–18,768 bp), and a pair of inverted repeats (IRs; 25,576–25,615 bp). The average GC content was ~37.24%. The four Sanguisorba cp genomes harbored 112 different genes arranged in the same order; these identical sections include 78 protein-coding genes, 30 tRNA genes, and four rRNA genes, if duplicated genes in IR regions are counted only once. A total of 39–53 long repeats and 79–91 simple sequence repeats (SSRs) were identified in the four Sanguisorba cp genomes, which provides opportunities for future studies of the population genetics of Sanguisorba medicinal plants. A phylogenetic analysis using the maximum parsimony (MP) method strongly supports a close relationship between S. officinalis and S. tenuifolia var. alba, followed by S. stipulata, and finally S. filiformis. The availability of these cp genomes provides valuable genetic information for future studies of Sanguisorba identification and provides insights into the evolution of the genus Sanguisorba.

Complete genome sequence analysis of the Malacosoma neustria nucleopolyhedrovirus from Turkey

Virus Genes ◽  
2018 ◽  
Vol 54 (5) ◽  
pp. 706-718 ◽  
Author(s):  
Donus Gencer ◽  
Remziye Nalcacioglu ◽  
Zihni Demirbag ◽  
Ismail Demir
Keyword(s):  
Sequence Analysis ◽  
Genome Sequence ◽  
Complete Genome Sequence ◽  
Complete Genome ◽  
Genome Sequence Analysis ◽  
Complete Genome Sequence Analysis
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