GOBASE--a database of mitochondrial and chloroplast information

O'Brien, Emmet A.; Badidi, Elarbi; Barbasiewicz, Ania; deSousa, Cristina; Lang, B. Franz; Burger, Gertraud

doi:10.1093/nar/gkg090

Cited by 28 publications

(11 citation statements)

References 6 publications

(2 reference statements)

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“…Otherwise, the secondary structures of the mitochondrial and eubacterial homologs are essentially superimposable. Secondary structures are provided through GOBASE, the Organelle Genome Database [(37), ].…”

Section: Resultsmentioning

confidence: 99%

The Rhodomonas salina mitochondrial genome: bacteria-like operons, compact gene arrangement and complex repeat region

Hauth

Maier²,

Lang³

et al. 2005

Nucleic Acids Research

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To gain insight into the mitochondrial genome structure and gene content of a putatively ancestral group of eukaryotes, the cryptophytes, we sequenced the complete mitochondrial DNA of Rhodomonas salina. The 48 063 bp circular-mapping molecule codes for 2 rRNAs, 27 tRNAs and 40 proteins including 23 components of oxidative phosphorylation, 15 ribosomal proteins and two subunits of tat translocase. One potential protein (ORF161) is without assigned function. Only two introns occur in the genome; both are present within cox1 belong to group II and contain RT open reading frames. Primitive genome features include bacteria-like rRNAs and tRNAs, ribosomal protein genes organized in large clusters resembling bacterial operons and the presence of the otherwise rare genes such as rps1 and tatA. The highly compact gene organization contrasts with the presence of a 4.7 kb long, repeat-containing intergenic region. Repeat motifs ∼40–700 bp long occur up to 31 times, forming a complex repeat structure. Tandem repeats are the major arrangement but the region also includes a large, ∼3 kb, inverted repeat and several potentially stable ∼40–80 bp long hairpin structures. We provide evidence that the large repeat region is involved in replication and transcription initiation, predict a promoter motif that occurs in three locations and discuss two likely scenarios of how this highly structured repeat region might have evolved.

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Section: Resultsmentioning

confidence: 99%

The Rhodomonas salina mitochondrial genome: bacteria-like operons, compact gene arrangement and complex repeat region

Hauth

Maier²,

Lang³

et al. 2005

Nucleic Acids Research

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“…Bacterial and mitochondrial sequences with homology to the deduced Micavibrio proteins were searched using BLASTP, TBLASTN (Altschul et al ., 1997), GOBASE (O’Brien et al ., 2003) and GOLD (Bernal et al ., 2001). Bacterial sequences mostly originated from complete or ongoing genomic projects.…”

Section: Methodsmentioning

confidence: 99%

A new α‐proteobacterial clade of Bdellovibrio‐like predators: implications for the mitochondrial endosymbiotic theory

Davidov¹,

Huchon

Koval

et al. 2006

Environmental Microbiology

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Bdellovibrio-and-like organisms (BALOs) are peculiar, ubiquitous, small-sized, highly motile Gram-negative bacteria that are obligatory predators of other bacteria. Typically, these predators invade the periplasm of their prey where they grow and replicate. To date, BALOs constitute two highly diverse families affiliated with the delta-proteobacteria class. In this study, Micavibrio spp., a BALO lineage of epibiotic predators, were isolated from soil. These bacteria attach to digest and grow at the expense of other prokaryotes, much like other BALOs. Multiple phylogenetic analyses based on six genes revealed that they formed a deep branch within the alpha-proteobacteria, not affiliated with any of the alpha-proteobacterial orders. The presence of BALOs deep among the alpha-proteobacteria suggests that their peculiar mode of parasitism maybe an ancestral character in this proteobacterial class. The origin of the mitochondrion from an alpha-proteobacterium endosymbiont is strongly supported by molecular phylogenies. Accumulating data suggest that the endosymbiont's host was also a prokaryote. As prokaryotes are unable to phagocytose, the means by which the endosymbiont gained access into its host remains mysterious. We here propose a scenario based on the BALO feeding-mode to hypothesize a mechanism at play at the origin of the mitochondrial endosymbiosis.

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“…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.…”

Section: Introductionmentioning

confidence: 99%

CGAP: a new comprehensive platform for the comparative analysis of chloroplast genomes

Cheng

Ren

et al. 2013

BMC Bioinformatics

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BackgroundChloroplast 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).ResultsCGAP 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.ConclusionsBoth 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.

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GOBASE--a database of mitochondrial and chloroplast information

Cited by 28 publications

References 6 publications

The Rhodomonas salina mitochondrial genome: bacteria-like operons, compact gene arrangement and complex repeat region

The Rhodomonas salina mitochondrial genome: bacteria-like operons, compact gene arrangement and complex repeat region

A new α‐proteobacterial clade of Bdellovibrio‐like predators: implications for the mitochondrial endosymbiotic theory

CGAP: a new comprehensive platform for the comparative analysis of chloroplast genomes

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