Draft Genome Sequence and Comparative Analysis of the Superb Aromatic-Hydrocarbon Degrader Rhodococcus sp. Strain DK17

Yoo, Miyoun; Kim, Dockyu; Choi, Ki Young; Chae, Jong Chan; Zylstra, Gerben J.; Kim, Eungbin

doi:10.1128/jb.00844-12

Cited by 17 publications

(10 citation statements)

References 8 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…WGM utilize singlemolecule restriction examination to acquire results concerning the magnitude of the control splinter and their substantial positions beside the DNA strand [45]. Whole genome has been exploit in a number of functions, which comprised of phylogenetic analyses and genotyping of associated with microbial isolates [46,47], discovery of outsized genomic structural rearrangements or variations [48,49], and quality control or verification for genome sequences which were assembled [50,51]. Physical genome maps based a restriction also having the potential to be used as a model for the exact arrangement of NGS contigs and to assist concluding the spaces between mapped contig.…”

Section: Whole Genome/targeted Re-sequencingmentioning

confidence: 99%

High Throughput Sequencing Advances and Future Challenges

Pervaiz¹,

Lotfi²,

Haider³

et al. 2017

J Plant Biochem Physiol

View full text Add to dashboard Cite

High throughput sequencing (HTS) technologies were developed into indispensable for genomic investigation and recent hottest topic for research in the field of genomics, which can generate over 100 times more data in comparison with the most complicated capillary sequencers. Recent advances and developments in HTS using next generation sequencing techniques have become essential in the studies of digital gene expression profiling, in epigenomics, genomics, and transcriptomics. These methodologies are dexterous of sequencing multiple DNA molecules in corresponding; facilitate hundreds of millions of DNA molecules to be sequenced within a short period of time. Though, the expenses and time period have been significantly reduced; the inaccurate profiles and boundaries of the new policy differ considerably from those of earlier reported sequencing techniques. The technical developments and decreasing cost of NGS (Next Generation Sequencing) technology have made RNA sequencing (RNA-seq) as a worldwide popular technique for gene expression projects. Various approaches have been done for the standardization of RNA sequencing data, which have been materialized in the reports, contradictory, both in the type of bias modification and in the statistical approach. On the other hand, as data persistently build up, there has been no apparent consensus on the proper normalization techniques to be used or the impact of chosen methods on the downstream analysis. In the present article, we mentioned the key features of HT-NGS like, Key HTS platforms and different sequencing applications, ethical limitation and future prospective.

show abstract

Section: Whole Genome/targeted Re-sequencingmentioning

confidence: 99%

High Throughput Sequencing Advances and Future Challenges

Pervaiz¹,

Lotfi²,

Haider³

et al. 2017

J Plant Biochem Physiol

View full text Add to dashboard Cite

show abstract

“…A comparison between the draft genome of 311R and the 12 genomes/draft genomes of Rhodococcus sp. DK17 ( 17 ), Rhodococcus sp. JVH1 ( 18 ), R. jostii RHA1 ( 19 ), R. erythropolis PR4 ( 20 ), R. erythropolis SK121 (BioProject PRJNA55853), R. erythropolis CCM2595 ( 21 ), R. erythropolis R138 ( 22 ), R. opacus B4 ( 3 ), R. opacus PD630 ( 7 ), R. equi 103S ( 8 ), R. pyridinivorans SB3094 ( 23 ), and Rhodococcus sp.…”

Section: Genome Announcementmentioning

confidence: 99%

Draft Genome Sequence of Rhodococcus sp. Strain 311R

et al. 2015

View full text Add to dashboard Cite

show abstract

“…strain DK17 is also able to utilize phthalate as a growth substrate via the Gram-positive pathway [6,7]. DK17 possesses three megaplasmids (380 kb pDK1, 330 kb pDK2, and 750 kb pDK3), and the phthalate operons in DK17 are duplicated and are present on both pDK2 and pDK3 [6,8]. It was previously shown that both copies of the phthalate operon are equally functional in DK17 [9].…”

Section: Introductionmentioning

confidence: 99%

Functional Identification of OphR, an IclR Family Transcriptional Regulator Involved in the Regulation of the Phthalate Catabolic Operon in Rhodococcus sp. Strain DK17

et al. 2015

Self Cite

View full text Add to dashboard Cite

A putative gene for a transcriptional regulator (ophR) was detected near each copy of the duplicated phthalate-degrading operon of Rhodococcus sp. DK17. Sequence analysis and molecular modeling indicate that OphR belongs to the IclR family of transcriptional regulators and possesses the N-terminal DNA-binding and C-terminal effector-binding domains. DNA-binding assays demonstrate that OphR regulates the phthalate operon by binding to the ophA1-ophR intergenic region.

show abstract

Draft Genome Sequence and Comparative Analysis of the Superb Aromatic-Hydrocarbon Degrader Rhodococcus sp. Strain DK17

Cited by 17 publications

References 8 publications

High Throughput Sequencing Advances and Future Challenges

High Throughput Sequencing Advances and Future Challenges

Draft Genome Sequence of Rhodococcus sp. Strain 311R

Functional Identification of OphR, an IclR Family Transcriptional Regulator Involved in the Regulation of the Phthalate Catabolic Operon in Rhodococcus sp. Strain DK17

Contact Info

Product

Resources

About