OrganellarGenomeDRAW (OGDRAW): a tool for the easy generation of high-quality custom graphical maps of plastid and mitochondrial genomes

Lohse, Marc; Drechsel, Oliver; Bock, Ralph

doi:10.1007/s00294-007-0161-y

Cited by 1,074 publications

(758 citation statements)

References 20 publications

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“…54; Table S3) were used to amplify fragments of the mitochondrial rrnL, cob, and cox1 regions from sea slug egg DNA and then in various combinations to amplify the entire mtDNA. The mitochondrial sequence was annotated using Dual Organellar GenoMe Annotator (DOGMA) (55), and the map was drawn using OrganellarGenome-DRAW (OGDRAW) (56). Additional information, including analysis for HGT, is provided in SI Methods.…”

Section: Race and Phylogenetic Analysis Of Psbomentioning

confidence: 99%

Horizontal gene transfer of the algal nuclear gene psbO to the photosynthetic sea slug Elysia chlorotica

Rumpho

Worful²,

Lee³

et al. 2008

Proc. Natl. Acad. Sci. U.S.A.

241

169

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The sea slug Elysia chlorotica acquires plastids by ingestion of its algal food source Vaucheria litorea. Organelles are sequestered in the mollusc's digestive epithelium, where they photosynthesize for months in the absence of algal nucleocytoplasm. This is perplexing because plastid metabolism depends on the nuclear genome for >90% of the needed proteins. Two possible explanations for the persistence of photosynthesis in the sea slug are (i) the ability of V. litorea plastids to retain genetic autonomy and/or (ii) more likely, the mollusc provides the essential plastid proteins. Under the latter scenario, genes supporting photosynthesis have been acquired by the animal via horizontal gene transfer and the encoded proteins are retargeted to the plastid. We sequenced the plastid genome and confirmed that it lacks the full complement of genes required for photosynthesis. In support of the second scenario, we demonstrated that a nuclear gene of oxygenic photosynthesis, psbO, is expressed in the sea slug and has integrated into the germline. The source of psbO in the sea slug is V. litorea because this sequence is identical from the predator and prey genomes. Evidence that the transferred gene has integrated into sea slug nuclear DNA comes from the finding of a highly diverged psbO 3 flanking sequence in the algal and mollusc nuclear homologues and gene absence from the mitochondrial genome of E. chlorotica. We demonstrate that foreign organelle retention generates metabolic novelty (''green animals'') and is explained by anastomosis of distinct branches of the tree of life driven by predation and horizontal gene transfer.symbiosis ͉ Vaucheria litorea ͉ evolution ͉ plastid ͉ stramenopile

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Section: Race and Phylogenetic Analysis Of Psbomentioning

confidence: 99%

Horizontal gene transfer of the algal nuclear gene psbO to the photosynthetic sea slug Elysia chlorotica

Rumpho

Worful²,

Lee³

et al. 2008

Proc. Natl. Acad. Sci. U.S.A.

241

169

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“…Composition skewness was calculated according to the formulas: GC skew=(G%−C%)/ (G%+C%), AT skew=(A%−T%)/(A%+T%) [25]. The gene map of the mitochondrial genome was created with OGDRAW v1.1 [26] and modified manually.…”

Section: Sequence Analysismentioning

confidence: 99%

Characterization of mitochondrial genome of sea cucumber Stichopus horrens: A novel gene arrangement in Holothuroidea

Fan

Wen

et al. 2011

Sci. China Life Sci.

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The complete mitochondrial DNA sequence contains useful information for phylogenetic analyses of metazoa. In this study, the complete mitochondrial DNA sequence of sea cucumber Stichopus horrens (Holothuroidea: Stichopodidae: Stichopus) is presented. The complete sequence was determined using normal and long PCRs. The mitochondrial genome of Stichopus horrens is a circular molecule 16257 bps long, composed of 13 protein-coding genes, two ribosomal RNA genes and 22 transfer RNA genes. Most of these genes are coded on the heavy strand except for one protein-coding gene (nad6) and five tRNA genes (tRNA Ser(UCN) , tRNA Gln , tRNA Ala , tRNA Val , tRNA Asp ) which are coded on the light strand. The composition of the heavy strand is 30.8% A, 23.7% C, 16.2% G, and 29.3% T bases (AT skew=0.025; GC skew=−0.188). A non-coding region of 675 bp was identified as a putative control region because of its location and AT richness. The intergenic spacers range from 1 to 50 bp in size, totaling 227 bp. A total of 25 overlapping nucleotides, ranging from 1 to 10 bp in size, exist among 11 genes. All 13 protein-coding genes are initiated with an ATG. The TAA codon is used as the stop codon in all the protein coding genes except nad3 and nad4 that use TAG as their termination codon. The most frequently used amino acids are Leu (16.29%), Ser (10.34%) and Phe (8.37%). All of the tRNA genes have the potential to fold into typical cloverleaf secondary structures. We also compared the order of the genes in the mitochondrial DNA from the five holothurians that are now available and found a novel gene arrangement in the mitochondrial DNA of Stichopus horrens.

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“…Eventually, a complete C. micranthum cp genome was obtained and deposited in the NCBI database (KT833081). The cp genome circle map was drawn with OGDRAW (Lohse et al 2007). …”

Section: Next-generationmentioning

confidence: 99%

Comparative analysis of the complete chloroplast genomic sequence and chemical components of Cinnamomum micranthum and Cinnamomum kanehirae

Chu

et al. 2017

Holzforschung

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Cinnamomum micranthum (Hayata) Hayata is a tree species that is often confused with Cinnamomum kanehirae Hayata, which is an endemic species in Taiwan and the sole natural host of the valuable medicinal fungus Antrodia cinnamomea. However, the two species are highly similar in morphology and difficult to distinguish based on traditional vegetative structures or wood anatomical methods. The aim of the present study was to identify of these two species by DNA and chemical analysis. The complete chloroplast genome of C. micranthum has been determined and compared with that of C. kanehirae. The leaf methanol extracts of these species were also analyzed by ultra-performance liquid chromatography (UPLC). The length of the C. micranthum chloroplast genome was 152 675 bp, i.e. 25 bp shorter than that of C. kanehirae. In phylogenetic analysis, C. micranthum was more closely related to C. kanehirae than other six Lauracea species. Six validated insertion/deletions of bases in the DNA (InDels) are suitable for differentiation of the two species. Moreover, high amounts of linalool and sesamin were present in the leaves of C. kanehirae, but not in C. micranthum. Overall, this study provided new insight for distinguishing the two species on the basis of the chemical composition of the leaves and the InDel markers.

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OrganellarGenomeDRAW (OGDRAW): a tool for the easy generation of high-quality custom graphical maps of plastid and mitochondrial genomes

Cited by 1,074 publications

References 20 publications

Horizontal gene transfer of the algal nuclear gene psbO to the photosynthetic sea slug Elysia chlorotica

Horizontal gene transfer of the algal nuclear gene psbO to the photosynthetic sea slug Elysia chlorotica

Characterization of mitochondrial genome of sea cucumber Stichopus horrens: A novel gene arrangement in Holothuroidea

Comparative analysis of the complete chloroplast genomic sequence and chemical components of Cinnamomum micranthum and Cinnamomum kanehirae

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