2017
Sablok, G.; Chen, T. -W.; Lee, C. -C.; Yang, C.; Gan, R. -C.; Wegrzyn, J. L.; Porta, N. La; Nayak, K. C.; Huang, P. -J.; Varotto, C.; Tang, P.
ChloroMitoCU: Codon patterns across organelle genomes for functional genomics and evolutionary applications Journal Article
In: DNA Research, 24 (3), pp. 327-332, 2017, ISSN: 13402838, (cited By 1).
Abstract | Links | BibTeX | 標籤: Chloroplast; Genome, Chloroplasts; Codon; Eukaryota; Evolution, codon, Mitochondrial; Genomics; Mitochondria; Software, Molecular; Genome
@article{Sablok2017327,
title = {ChloroMitoCU: Codon patterns across organelle genomes for functional genomics and evolutionary applications},
author = {G. Sablok and T. -W. Chen and C. -C. Lee and C. Yang and R. -C. Gan and J. L. Wegrzyn and N. La Porta and K. C. Nayak and P. -J. Huang and C. Varotto and P. Tang},
url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85021349951&doi=10.1093%2fdnares%2fdsw044&partnerID=40&md5=1319adee5d716b5947e7e72134e23f93},
doi = {10.1093/dnares/dsw044},
issn = {13402838},
year = {2017},
date = {2017-01-01},
journal = {DNA Research},
volume = {24},
number = {3},
pages = {327-332},
publisher = {Oxford University Press},
abstract = {Organelle genomes are widely thought to have arisen from reduction events involving cyanobacterial and archaeal genomes, in the case of chloroplasts, or α-proteobacterial genomes, in the case of mitochondria. Heterogeneity in base composition and codon preference has long been the subject of investigation of topics ranging from phylogenetic distortion to the design of overexpression cassettes for transgenic expression. From the overexpression point of view, it is critical to systematically analyze the codon usage patterns of the organelle genomes. In light of the importance of codon usage patterns in the development of hyper-expression organelle transgenics, we present ChloroMitoCU, the first-ever curated, web-based reference catalog of the codon usage patterns in organelle genomes. ChloroMitoCU contains the pre-compiled codon usage patterns of 328 chloroplast genomes (29,960 CDS) and 3,502 mitochondrial genomes (49,066 CDS), enabling genome-wide exploration and comparative analysis of codon usage patterns across species. ChloroMitoCU allows the phylogenetic comparison of codon usage patterns across organelle genomes, the prediction of codon usage patterns based on user-submitted transcripts or assembled organelle genes, and comparative analysis with the pre-compiled patterns across species of interest. ChloroMitoCU can increase our understanding of the biased patterns of codon usage in organelle genomes across multiple clades. ChloroMitoCU can be accessed at: http://chloromitocu.cgu.edu.tw/ © The Author 2017. Published by Oxford University Press on behalf of Kazusa DNA Research Institute.},
note = {cited By 1},
keywords = {Chloroplast; Genome, Chloroplasts; Codon; Eukaryota; Evolution, codon, Mitochondrial; Genomics; Mitochondria; Software, Molecular; Genome},
pubstate = {published},
tppubtype = {article}
}
Organelle genomes are widely thought to have arisen from reduction events involving cyanobacterial and archaeal genomes, in the case of chloroplasts, or α-proteobacterial genomes, in the case of mitochondria. Heterogeneity in base composition and codon preference has long been the subject of investigation of topics ranging from phylogenetic distortion to the design of overexpression cassettes for transgenic expression. From the overexpression point of view, it is critical to systematically analyze the codon usage patterns of the organelle genomes. In light of the importance of codon usage patterns in the development of hyper-expression organelle transgenics, we present ChloroMitoCU, the first-ever curated, web-based reference catalog of the codon usage patterns in organelle genomes. ChloroMitoCU contains the pre-compiled codon usage patterns of 328 chloroplast genomes (29,960 CDS) and 3,502 mitochondrial genomes (49,066 CDS), enabling genome-wide exploration and comparative analysis of codon usage patterns across species. ChloroMitoCU allows the phylogenetic comparison of codon usage patterns across organelle genomes, the prediction of codon usage patterns based on user-submitted transcripts or assembled organelle genes, and comparative analysis with the pre-compiled patterns across species of interest. ChloroMitoCU can increase our understanding of the biased patterns of codon usage in organelle genomes across multiple clades. ChloroMitoCU can be accessed at: http://chloromitocu.cgu.edu.tw/ © The Author 2017. Published by Oxford University Press on behalf of Kazusa DNA Research Institute.