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).
Highlights
The green algae are comprised of two main clades, Chlorophyta and Streptophyta
In order to help answer the phylogenetic questions that remain for the green algae and to gain a better understanding of the organellar genomic composition of these organisms, plastid and mitochondrial genomes have been sequenced throughout most of the major chlorophyte lineages, and many more organellar genomes are expected to be published in the near future
We present the first complete chloroplast and mitochondrial genomes of Ulva
Summary
The green algae are comprised of two main clades, Chlorophyta and Streptophyta. Chlorophyta includes a wide diversity of marine, freshwater and terrestrial green algae. In order to help answer the phylogenetic questions that remain for the green algae and to gain a better understanding of the organellar genomic composition of these organisms, plastid and mitochondrial genomes have been sequenced throughout most of the major chlorophyte lineages, and many more organellar genomes are expected to be published in the near future. Green algae have shown to have a wide range of organellar genome sizes, content (e.g. GC%, number of genes, and number of introns), and organization of genes [2],[7],[8]. Some Ulva species are notorious for forming harmful algal blooms called green tides in eutrophic conditions [24],[25] These macroalgae are either monostromatic and tubular, distromatic blades, or distromatic with hollow monostromatic margins [26]. We performed a phylogenomic investigation to assess the monophyly of the Ulvophyceae and relationships of ulvophytes with other core chlorophytan clades
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