ChloroMitoCU: Codon patterns across organelle genomes for functional genomics and evolutionary applications

Sablok, G; Chen, TW; Lee, CC; Yang, C; Gan, RC; Wegrzyn, JL; La Porta, N; Nayak, KC; Huang, PJ; Varotto, C; Tang, P

ChloroMitoCU: Codon patterns across organelle genomes for functional genomics and evolutionary applications

Sablok, G

Chen, TW Lee, CC Yang, C Gan, RC Wegrzyn, JL La Porta, N Nayak, KC Huang, PJ Varotto, C Tang, P

Permalink

Publication Type:: Journal Article
Citation:: DNA Research, 2017, 24 (3), pp. 327 - 332
Issue Date:: 2017-06-01

Open Access

Copyright Clearance Process

Recently Added
In Progress
Open Access

This item is open access.

Adobe PDF

Download Published VersionAdobe PDF (561.19 kB)

View on publisher's site

View statistics

Full metadata record

Field	Value	Language
dc.contributor.author	Sablok, G https://orcid.org/0000-0002-4157-9405	en_US
dc.contributor.author	Chen, TW	en_US
dc.contributor.author	Lee, CC	en_US
dc.contributor.author	Yang, C	en_US
dc.contributor.author	Gan, RC	en_US
dc.contributor.author	Wegrzyn, JL	en_US
dc.contributor.author	La Porta, N	en_US
dc.contributor.author	Nayak, KC	en_US
dc.contributor.author	Huang, PJ	en_US
dc.contributor.author	Varotto, C	en_US
dc.contributor.author	Tang, P	en_US
dc.date.available	2016-09-14	en_US
dc.date.issued	2017-06-01	en_US
dc.identifier.citation	DNA Research, 2017, 24 (3), pp. 327 - 332	en_US
dc.identifier.issn	1340-2838	en_US
dc.identifier.uri	http://hdl.handle.net/10453/125780
dc.description.abstract	© The Author 2017. Published by Oxford University Press on behalf of Kazusa DNA Research Institute. 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/	en_US
dc.relation.ispartof	DNA Research	en_US
dc.relation.isbasedon	10.1093/dnares/dsw044	en_US
dc.subject.classification	Plant Biology & Botany	en_US
dc.subject.mesh	Mitochondria	en_US
dc.subject.mesh	Chloroplasts	en_US
dc.subject.mesh	Codon	en_US
dc.subject.mesh	Genomics	en_US
dc.subject.mesh	Evolution, Molecular	en_US
dc.subject.mesh	Software	en_US
dc.subject.mesh	Genome, Chloroplast	en_US
dc.subject.mesh	Genome, Mitochondrial	en_US
dc.subject.mesh	Eukaryota	en_US
dc.title	ChloroMitoCU: Codon patterns across organelle genomes for functional genomics and evolutionary applications	en_US
dc.type	Journal Article
utslib.citation.volume	3	en_US
utslib.citation.volume	24	en_US
utslib.for	0604 Genetics	en_US
pubs.embargo.period	Not known	en_US
pubs.organisational-group	/University of Technology Sydney
pubs.organisational-group	/University of Technology Sydney/Faculty of Science
pubs.organisational-group	/University of Technology Sydney/Strength - C3 - Climate Change Cluster
utslib.copyright.status	open_access
pubs.issue	3	en_US
pubs.publication-status	Published	en_US
pubs.volume	24	en_US

Abstract:

© The Author 2017. Published by Oxford University Press on behalf of Kazusa DNA Research Institute. 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/

Please use this identifier to cite or link to this item:

http://hdl.handle.net/10453/125780