Detail publikace

Analysis of Clostridium beijerinckii NRRL B-598 coding regions using RNA-Seq data of a closely related strain

Originální název

Analysis of Clostridium beijerinckii NRRL B-598 coding regions using RNA-Seq data of a closely related strain

Anglický název

Analysis of Clostridium beijerinckii NRRL B-598 coding regions using RNA-Seq data of a closely related strain

Jazyk

en

Originální abstrakt

Modern research in biotechnology utilizes methods of molecular biology and associated bioinformatics techniques more than in the past. Genome mining of biotechnologically relevant organisms became a standard procedure. After a genome is sequenced and annotated, more information regarding its genes, including their variant calling, and the analysis of their expression needs to be acquired. This can be achieved by additional sequencing of the transcriptome, so-called RNA-Seq. Here, we present the analysis of the coding regions for a recently reidentified strain Clostridium beijerinckii NRRL B-598, formerly misidentified as C. pasteurianum, using RNA-Seq expression data of a closely related strain C. beijerinckii NCIMB 8052. We confirm the correctness of its reidentification as the majority of reads match the genome. Although expression levels or single nucleotide variants cannot be properly explored, we are able to analyze in silico the annotation of this genome, which supports the annotation of biotechnologically relevant genes. Although this kind of analysis does not allow us to reannotate the genome, nor to reconstruct any gene regulatory networks, it still provides us with valuable information for planning our own RNA-Seq experiments that will be performed in the near future.

Anglický abstrakt

Modern research in biotechnology utilizes methods of molecular biology and associated bioinformatics techniques more than in the past. Genome mining of biotechnologically relevant organisms became a standard procedure. After a genome is sequenced and annotated, more information regarding its genes, including their variant calling, and the analysis of their expression needs to be acquired. This can be achieved by additional sequencing of the transcriptome, so-called RNA-Seq. Here, we present the analysis of the coding regions for a recently reidentified strain Clostridium beijerinckii NRRL B-598, formerly misidentified as C. pasteurianum, using RNA-Seq expression data of a closely related strain C. beijerinckii NCIMB 8052. We confirm the correctness of its reidentification as the majority of reads match the genome. Although expression levels or single nucleotide variants cannot be properly explored, we are able to analyze in silico the annotation of this genome, which supports the annotation of biotechnologically relevant genes. Although this kind of analysis does not allow us to reannotate the genome, nor to reconstruct any gene regulatory networks, it still provides us with valuable information for planning our own RNA-Seq experiments that will be performed in the near future.

BibTex


@inproceedings{BUT141681,
  author="Karel {Sedlář} and Barbora {Branská} and Kristýna {Kupková} and Pavlína {Cicková} and Jan {Kolek} and Maryna {Vasylkivska} and Petra {Patáková} and Ivo {Provazník}",
  title="Analysis of Clostridium beijerinckii NRRL B-598 coding regions using RNA-Seq data of a closely related strain",
  annote="Modern research in biotechnology utilizes methods of molecular biology and associated bioinformatics techniques more than in the past. Genome mining of biotechnologically relevant organisms became a standard procedure. After a genome is sequenced and annotated, more information regarding its genes, including their variant calling, and the analysis of their expression needs to be acquired. This can be achieved by additional sequencing of the transcriptome, so-called RNA-Seq. Here, we present the analysis of the coding regions for a recently reidentified strain Clostridium beijerinckii NRRL B-598, formerly misidentified as C. pasteurianum, using RNA-Seq expression data of a closely related strain C. beijerinckii NCIMB 8052. We confirm the correctness of its reidentification as the majority of reads match the genome. Although expression levels or single nucleotide variants cannot be properly explored, we are able to analyze in silico the annotation of this genome, which supports the annotation of biotechnologically relevant genes. Although this kind of analysis does not allow us to reannotate the genome, nor to reconstruct any gene regulatory networks, it still provides us with valuable information for planning our own RNA-Seq experiments that will be performed in the near future.",
  address="Ocean Design",
  booktitle="Proceedings of the 5th International Conference on Chemical Technology",
  chapter="141681",
  edition="1",
  howpublished="online",
  institution="Ocean Design",
  year="2017",
  month="october",
  pages="87--91",
  publisher="Ocean Design",
  type="conference paper"
}