Metabacillus indicus LMG 22858
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ABSTRACT:
PROVIDER: PRJNA237198 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Metabacillus indicus strain:DSM 16189 Genome sequencing and assembly
| PRJNA252001 | ENA
Project description:Background: Pantoea ananatis LMG 2665T synthesizes and utilizes acyl homoserine lactones (AHLs) for signaling. In this strain, short chain AHLs (C4 to C8) are produced by the EanI/R quorum sensing (QS) system that is involved in pathogenicity and biofilm formation. The complete set of genes regulated by the EanI/R system in P. ananatis LMG 2665T is still not fully known. In the present study, RNA-seq was used to analyze the transcriptome profiles controlled by the EanI/R system in this strain by comparing the wild type strain and its QS mutant 2665T ean∆I/R during lag and log stages. The RNA seq data was validated by RT qPCR. Results: The results showed that the EanI/R regulon in P. ananatis LMG 2665T comprised 144 genes, constituting 3.3% of the whole transcriptome under the experimental conditions in this study. The majority of genes regulated by the EanI/R system included genes for flagella assembly, bacterial chemotaxis, pyruvate metabolism, two component system, metabolic pathways, microbial metabolism and biosynthesis of secondary metabolites. Conclusions: This is the first study to identify the EanI/R QS regulon in P. ananatis LMG 2665T. Functional analysis of genes regulated the EanI/R system in LMG 2665T could help unveil genes that play a vital role in pathogenesis and survival strategies of this pathogen.
2018-10-31 | GSE87207 | GEO
Project description:Background: The Malnad Gidda are unique dwarf Bos indicus cattle native to heavy rainfall Malnad and coastal areas of Karnataka in India. These cattle are highly adapted to harsh climatic conditions and are more resistant to Foot and Mouth disease as compared to other breeds of B.indicus. Since the first genome reference became available from B.taurus Hereford breed, only a few other breeds have been genotyped using high-throughput platforms. Also despite the known reports on high diversity within indicine breeds as compared to taurine breeds, only one draft genome of Nellore and horn transcriptome of Kankrej breed were sequenced at base level resolution. Because of the special characteristics Malnad Gidda possess, it becomes the choice of breed among many indicine cows to study at molecular level and genotyping. Results: Sequencing mRNA from the PBMCs isolated from blood of one selected Malnad Gidda bull resulted in generation of 55 million paired-end reads of 100bp length. Raw sequencing data is processed to trim the adaptor and low quality bases, and are aligned against the whole genome and transcript assemblies of Bos taurus UMD 3.1 and Bos indicus (Nellore breed) respectively. About 72% of the sequenced reads from our study could be mapped against the B.taurus genome where as only 41% of reads could be mapped against the Bos indicus transcript assembly. Transcript assembly from the alignment carried out against the annotated B.taurus UMD 3.1 genome resulted in identification of ~10,000 genes with significant expression (FPKM>1). In a similar analysis against the B.indicus Kankrej assembled transcripts we could identify only ~6,000 transcripts. From the variant analysis of the sequencing data we found ~10,000 SNPs in coding regions among which ~9,000 are novel and ~6,400 are amino acid changing. Conclusions: For the first time we have genotyped and explored the transcriptome of B.indicus Malnad Gidda breed. A comparative analysis of mapping the RNA-Seq data against the available reference genome and transcript sequences is demonstrated. An enhanced utility of transcript sequencing could be achieved by improving or completing the sequence assembly of any B.indicus breed to better characterize the indicine breeds for productivity features and selective breeding.
2016-12-31 | GSE71182 | GEO
Project description:Metabacillus sp. DBTR6 Genome sequencing and assembly
| PRJNA762435 | ENA
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| PRJNA639428 | ENA
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| PRJNA683090 | ENA
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| PRJNA560168 | ENA
Project description:Metabacillus sp. GX 13764 Genome sequencing and assembly
| PRJNA785483 | ENA