Complete genome sequence of the sand-sediment actinobacterium Nocardioides dokdonensis FR1436T

Min Jung Kwak, Soon Kyeong Kwon, Jihyun F. Kim

Research output: Contribution to journalArticle

Abstract

Nocardioides dokdonensis, belonging to the class Actinobacteria, was first isolated from sand sediment of a beach in Dokdo, Korea, in 2005. In this study, we determined the genome sequence of FR1436, the type strain of N. dokdonensis, and analyzed its gene contents. The genome sequence is the second complete one in the genus Nocardioides after that of Nocardioides sp. JS614. It is composed of a 4,376,707-bp chromosome with a G + C content of 72.26%. From the genome sequence, 4,104 CDSs, three rRNA operons, 51 tRNAs, and one tmRNA were predicted, and 71.38% of the genes were assigned putative functions. Through the sequence analysis, dozens of genes involved in steroid metabolism, especially its degradation, were detected. Most of the identified genes were located in large gene clusters, which showed high similarities with the gene clusters in Pimelobacter simplex VKM Ac-2033D. Genomic features of N. dokdonensis associated with steroid catabolism indicate that it could be used for research and application of steroids in science and industry.

Original languageEnglish
Article number44
JournalStandards in Genomic Sciences
Volume12
Issue number1
DOIs
Publication statusPublished - 2017 Jul 25

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Actinobacteria
Genome
Steroids
Multigene Family
Genes
rRNA Operon
Base Composition
Korea
Transfer RNA
Sequence Analysis
Industry
Chromosomes
Research

All Science Journal Classification (ASJC) codes

  • Genetics

Cite this

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abstract = "Nocardioides dokdonensis, belonging to the class Actinobacteria, was first isolated from sand sediment of a beach in Dokdo, Korea, in 2005. In this study, we determined the genome sequence of FR1436, the type strain of N. dokdonensis, and analyzed its gene contents. The genome sequence is the second complete one in the genus Nocardioides after that of Nocardioides sp. JS614. It is composed of a 4,376,707-bp chromosome with a G + C content of 72.26{\%}. From the genome sequence, 4,104 CDSs, three rRNA operons, 51 tRNAs, and one tmRNA were predicted, and 71.38{\%} of the genes were assigned putative functions. Through the sequence analysis, dozens of genes involved in steroid metabolism, especially its degradation, were detected. Most of the identified genes were located in large gene clusters, which showed high similarities with the gene clusters in Pimelobacter simplex VKM Ac-2033D. Genomic features of N. dokdonensis associated with steroid catabolism indicate that it could be used for research and application of steroids in science and industry.",
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Complete genome sequence of the sand-sediment actinobacterium Nocardioides dokdonensis FR1436T . / Kwak, Min Jung; Kwon, Soon Kyeong; Kim, Jihyun F.

In: Standards in Genomic Sciences, Vol. 12, No. 1, 44, 25.07.2017.

Research output: Contribution to journalArticle

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