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      Complete Sequences of the Mitochondrial DNA of the Wild Gracilariopsis lemaneiformis and Two Mutagenic Cultivated Breeds (Gracilariaceae, Rhodophyta)

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          Abstract

          The complete mitochondrial DNA (mtDNA) of Gracilariopsis lemaneiformis was sequenced (25883 bp) and mapped to a circular model. The A+T composition was 72.5%. Forty six genes and two potentially functional open reading frames were identified. They include 24 protein-coding genes, 2 rRNA genes, 20 tRNA genes and 2 ORFs ( orf60, orf142). There is considerable sequence synteny across the five red algal mtDNAs falling into Florideophyceae including Gr. lemaneiformis in this study and previously sequenced species. A long stem-loop and a hairpin structure were identified in intergenic regions of mt genome of Gr. lemaneiformis, which are believed to be involved with transcription and replication. In addition, the mtDNAs of two mutagenic cultivated breeds (“981” and “07-2”) were also sequenced. Compared with the mtDNA of wild Gr. lemaneiformis, the genome size and gene length and order of three strains were completely identical except nine base mutations including eight in the protein-coding genes and one in the tRNA gene. None of the base mutations caused frameshift or a premature stop codon in the mtDNA genes. Phylogenetic analyses based on mitochondrial protein-coding genes and rRNA genes demonstrated Gracilariopsis andersonii had closer phylogenetic relationship with its parasite Gracilariophila oryzoides than Gracilariopsis lemaneiformis which was from the same genus of Gracilariopsis.

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          Most cited references38

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          Isolation of plant DNA from faesh tissue

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            The mitochondrial genome of Arabidopsis thaliana contains 57 genes in 366,924 nucleotides.

            We have determined the complete sequence of the mitochondrial DNA in the model plant species Arabidopsis thaliana, affording access to the first of its three genomes. The 366,924 nucleotides code for 57 identified genes, which cover only 10% of the genome. Introns in these genes add about 8%, open reading frames larger than 100 amino acids represent 10% of the genome, duplications account for 7%, remnants of retrotransposons of nuclear origin contribute 4% and integrated plastid sequences amount to 1%-leaving 60% of the genome unaccounted for. With the significant contribution of duplications, imported foreign DNA and the extensive background of apparently functionless sequences, the mosaic structure of the Arabidopsis thaliana mitochondrial genome features many aspects of size-relaxed nuclear genomes.
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              Replication of animal mitochondrial DNA.

              D Clayton (1982)
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                Author and article information

                Contributors
                Role: Editor
                Journal
                PLoS One
                PLoS ONE
                plos
                plosone
                PLoS ONE
                Public Library of Science (San Francisco, USA )
                1932-6203
                2012
                29 June 2012
                : 7
                : 6
                : e40241
                Affiliations
                [1 ]College of Marine Life Sciences, Ocean University of China, Qingdao, Shandong, People’s Republic of China
                [2 ]Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, People’s Republic of China
                Leuven University, Belgium
                Author notes

                Conceived and designed the experiments: TL LZ. Performed the experiments: LZ. Analyzed the data: LZ HQ. Contributed reagents/materials/analysis tools: XMW HQ SC CL TL. Wrote the paper: LZ TL.

                Article
                PONE-D-12-07573
                10.1371/journal.pone.0040241
                3386957
                22768261
                26cc533f-a227-479f-84fe-5f10ba87fdf6
                Zhang et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
                History
                : 15 March 2012
                : 3 June 2012
                Page count
                Pages: 7
                Categories
                Research Article
                Biology
                Evolutionary Biology
                Evolutionary Systematics
                Phylogenetics
                Comparative Genomics
                Evolutionary Genetics
                Genomic Evolution
                Genomics
                Genome Analysis Tools
                Gene Prediction
                Sequence Assembly Tools
                Genome Databases
                Genome Sequencing
                Marine Biology
                Plant Science
                Plants
                Algae

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