CGAP: a new comprehensive platform for the comparative analysis of chloroplast genomes
© Cheng et al.; licensee BioMed Central Ltd. 2013
Received: 22 October 2012
Accepted: 11 February 2013
Published: 14 March 2013
Chloroplast is an essential organelle in plants which contains independent genome. Chloroplast genomes have been widely used for plant phylogenetic inference recently. The number of complete chloroplast genomes increases rapidly with the development of various genome sequencing projects. However, no comprehensive platform or tool has been developed for the comparative and phylogenetic analysis of chloroplast genomes. Thus, we constructed a comprehensive platform for the comparative and phylogenetic analysis of complete chloroplast genomes which was named as chloroplast genome analysis platform (CGAP).
CGAP is an interactive web-based platform which was designed for the comparative analysis of complete chloroplast genomes. CGAP integrated genome collection, visualization, content comparison, phylogeny analysis and annotation functions together. CGAP implemented four web servers including creating complete and regional genome maps of high quality, comparing genome features, constructing phylogenetic trees using complete genome sequences, and annotating draft chloroplast genomes submitted by users.
Both CGAP and source code are available at http://www.herbbol.org:8000/chloroplast. CGAP will facilitate the collection, visualization, comparison and annotation of complete chloroplast genomes. Users can customize the comparative and phylogenetic analysis using their own unpublished chloroplast genomes.
KeywordsChloroplast genomes Comparative and phylogenetic analysis Web-based platform
The chloroplast is an essential organelle in plants which performs photosynthesis. Chloroplast contains independent genome derived from a cyanobacterial ancestor . Chloroplast genome typically consists of circular double-stranded DNA molecules of 110-200 kb size, including 100-200 unique genes. Most chloroplast genomes contain two large inverted repeats (IRs) of 6-76 kb which are highly conserved and divide the genomes into one large and one small single-copy region (called LSC and SSC, respectively) . The chloroplast genomes contain important genes involved in photosystems and biosynthetic pathways. Many coding and non-coding sequences of chloroplast genomes have been used for the phylogeny analysis of plants, including: rbcL, matK and psbA-trnH[3, 4]. Because of the conserved nature, appropriate size, persistent gene organization and potential ability for plant phylogenetic inference and transgenic expression, chloroplast genomes have been widely sequenced and used for the comparison and phylogeny analysis [5-7].
As the number of sequenced chloroplast genomes increases rapidly, bioinformatics tools become more critical for the analysis of complete chloroplast genomes. GenBank, EMBL and DDBJ are the primary nucleotide sequences databases. The chloroplast genome database (CGDB: http://nar.oxfordjournals.org/content/34/suppl_1/D692.full) and GOBASE (http://gobase.bcm.umontreal.ca/) are specialized chloroplast repositories [8, 9]. Dual organelle genome annotator (DOGMA: http://dogma.ccbb.utexas.edu/) is a web-based annotation tool for chloroplast and mitochondrial genomes . GeneOrder (http://binf.gmu.edu:8080/GeneOrder3.0/) and BADGER (http://badger.duq.edu/manual2/models.html) can be used for comparative analysis of gene arrangements in small genomes . GRAPPA (http://www.cs.unm.edu/~moret/GRAPPA/) and MGR (http://grimm.ucsd.edu/MGR/) perform phylogenetic analysis based on gene order changes [12-14]. Several tools offer the option to create chloroplast genome maps (e.g. PlasMapper, CGView and OGDRAW) [15-17]. However, there is no comprehensive platform or tool which can be used for the comparative and phylogenetic analysis of chloroplast genomes. We aim to construct a platform which integrates genome collection, visualization, comparison, phylogenetic analysis and annotation functions together. It will facilitate the comparative and phylogenetic analysis of complete chloroplast genomes.
Results and discussion
CGAP collected 284 complete chloroplast genomes from NCBI Organelle Genome Resources (http://www.ncbi.nlm.nih.gov/genomes). According to the annotation information stored in the GenBank format file, CGAP extracted all types of genome features including Gene, CDS, tRNA, rRNA, Exon, Intron, Promoter, RepeatRegion, StemLoop, -10 Signal and -35 Signal. Complete chloroplast genomes and all genome features were stored in CGAP chloroplast database. You can view and download all genomes and features in Fasta format online.
Visualization of genomes
Comparison of genome features
Where, N mat denotes the number of nucleotides matched between genomes A and B, L max is the max length of all genomes analyzed.
CGAP saved the distance matrix of the genomes as three kinds of formats, including the standard Nexus format and distance formats used in MEGA and PHYLIP [25, 26]. CGAP also drew a tree map for the overview of the phylogenetic relationship (see Additional file 3), and saved the phylogeny tree as standard Newick and Nexus formats. Optionally, you can supply your unpublished genomes and customize the chloroplast genomes used in your phylogeny analysis. In this situation, users need to submit a txt file, the first part of the file contains all names of organisms or accession numbers of the published genomes used in the analysis process, and the second part of the file contains the unpublished complete genomes in Fasta format.
Meanings of the fields in annotation entry
Fields of annotation entry
Meanings of the fields
Normalized feature name of a segment sequence of the genome
Starting position of the segment sequence on the chloroplast genome
Ending position of the segment sequence on the chloroplast genome
Potential feature name or location identifier of the segment sequence of the genome
|End-Start|/L, L indicated the length of the feature sequence compared to the segment sequence of the genome
Nmatch/Nmissmatch, Nmatch and Nmissmatch indicated the number of match and mismatch bases of the segment sequence respectively in sequence alignment
Score obtained in sequence alignment
Expectation value computed in sequence alignment
CGAP was developed for the comparative analysis of complete chloroplast genomes. It integrated genome collection, visualization, content comparison, phylogeny analysis and annotation functions together. CGAP implemented feature content comparison of chloroplast genomes and a novel alignment-free method for the phylogenetic analysis. Users can customize the comparative and phylogenetic analysis using their own unpublished genomes. To our knowledge, CGAP represents the first comprehensive platform for the comparative analysis of chloroplast genomes. It would facilitate the researches and applications of complete chloroplast genomes.
Availability and requirements
Project name: CGAP
Project home page: http://www.herbbol.org:8000/chloroplast
Operating system(s): Linux for the distributed source code and operating system independent for the web servers
Programming language: Python 2.6
License: Free for academic use
Chloroplast genome analysis platform
This work was supported by National Natural Science Foundation of China (81102746, 81100077, 31201768), Beijing Natural Science Foundation (5113033, 6133033), Special Foundation of China Postdoctoral Science (2012T50067), China Postdoctoral Science Foundation funded project (2011M500014, 2012M510011), Scientific Research Foundation of the State Human Resource Ministry and the Education Ministry for Returned Chinese Scholars, PUMC Youth Fund, the Fundamental Research Funds for the Central Universities, the Research Fund for the Doctoral Program of Higher Education (20111106120028), “Major Drug Discovery” major science and technology research “12nd Five-Year Plan” (2012ZX09301-002-001-025), Basic Scientific Research Operation Cost of State-Leveled Public Welfare Scientific Research Courtyard (YZ-12-15), China Medical Board of New York (A2009001), Program for New Century Excellent Talents in University (NCET-12-0074) granted to Zhihua Liu.
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