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. 2015 Apr 7;10(4):e0121020.
doi: 10.1371/journal.pone.0121020. eCollection 2015.

The complete chloroplast and mitochondrial genomes of the green macroalga Ulva sp. UNA00071828 (Ulvophyceae, Chlorophyta)

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The complete chloroplast and mitochondrial genomes of the green macroalga Ulva sp. UNA00071828 (Ulvophyceae, Chlorophyta)

James T Melton 3rd et al. PLoS One. .

Abstract

Sequencing mitochondrial and chloroplast genomes has become an integral part in understanding the genomic machinery and the phylogenetic histories of green algae. Previously, only three chloroplast genomes (Oltmannsiellopsis viridis, Pseudendoclonium akinetum, and Bryopsis hypnoides) and two mitochondrial genomes (O. viridis and P. akinetum) from the class Ulvophyceae have been published. Here, we present the first chloroplast and mitochondrial genomes from the ecologically and economically important marine, green algal genus Ulva. The chloroplast genome of Ulva sp. was 99,983 bp in a circular-mapping molecule that lacked inverted repeats, and thus far, was the smallest ulvophycean plastid genome. This cpDNA was a highly compact, AT-rich genome that contained a total of 102 identified genes (71 protein-coding genes, 28 tRNA genes, and three ribosomal RNA genes). Additionally, five introns were annotated in four genes: atpA (1), petB (1), psbB (2), and rrl (1). The circular-mapping mitochondrial genome of Ulva sp. was 73,493 bp and follows the expanded pattern also seen in other ulvophyceans and trebouxiophyceans. The Ulva sp. mtDNA contained 29 protein-coding genes, 25 tRNA genes, and two rRNA genes for a total of 56 identifiable genes. Ten introns were annotated in this mtDNA: cox1 (4), atp1 (1), nad3 (1), nad5 (1), and rrs (3). Double-cut-and-join (DCJ) values showed that organellar genomes across Chlorophyta are highly rearranged, in contrast to the highly conserved organellar genomes of the red algae (Rhodophyta). A phylogenomic investigation of 51 plastid protein-coding genes showed that Ulvophyceae is not monophyletic, and also placed Oltmannsiellopsis (Oltmannsiellopsidales) and Tetraselmis (Chlorodendrophyceae) closely to Ulva (Ulvales) and Pseudendoclonium (Ulothrichales).

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Conflict of interest statement

Competing Interests: The authors have declared that no competing interests exist.

Figures

Fig 1
Fig 1. Gene map of Ulva sp. UNA00071828 chloroplast genome using OGDRAW.
Genes in the clockwise direction are on the inside of the map, and genes in the counterclockwise direction are on the outside of the map. Annotated genes are colored according to the functional categories shown in the legend (bottom left).
Fig 2
Fig 2. Gene map of Ulva sp. UNA00071828 mitochondrial genome using OGDRAW.
Genes in the clockwise direction are on the inside of the map, and genes in the counterclockwise direction are on the outside of the map. Annotated genes are colored according to the functional categories shown in the legend (bottom left).
Fig 3
Fig 3. Bayesian majority rule tree showing all compatible partitions, inference from the nucleotide alignment of 51 concatenated chloroplast genes (first two codon positions: 28,167 nucleotide positions and 52 terminal taxa).
Node support is given as Bayesian posterior probabilities and maximum-likelihood (ML) bootstrap values of the nucleotide analyses (above branches), and the amino acid analyses (below branches); values <0.9 and 50, respectively, are not shown; asterisks indicated full support in both the Bayesian and ML analyses.

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