Maximum likelihood tree and schematic diagrams of heme oxygenase proteins.

Maximum likelihood (ML) tree based on an alignment of 510 heme oxygenase amino acid sequences from 1,678 taxa. Red algal heme oxygenases had three isotypes of heme oxygenase; HMOX1, HMOX2, and pbsA. HMOX1 and HMOX2 were located in the nuclear genome whereas the pbsA was encoded in the plastid genome in red algae.</p

Comparison of general features for 102 florideophycean plastid genomes.

<p>Comparison of general features for 102 florideophycean plastid genomes.</p

Plastid genome analysis of three Nemaliophycidae red algal species suggests environmental adaptation for iron limited habitats

<div><p>The red algal subclass Nemaliophycidae includes both marine and freshwater taxa that contribute to more than half of the freshwater species in Rhodophyta. Given that these taxa inhabit diverse habitats, the Nemaliophycidae is a suitable model for studying environmental adaptation. For this purpose, we characterized plastid genomes of two freshwater species, <i>Kumanoa americana</i> (Batrachospermales) and <i>Thorea hispida</i> (Thoreales), and one marine species <i>Palmaria palmata</i> (Palmariales). Comparative genome analysis identified seven genes (<i>ycf</i>34, <i>ycf</i>35, <i>ycf</i>37, <i>ycf</i>46, <i>ycf</i>91, <i>grx</i>, and <i>pbs</i>A) that were different among marine and freshwater species. Among currently available red algal plastid genomes (127), four genes (<i>pbs</i>A, <i>ycf</i>34, <i>ycf</i>35, <i>ycf</i>37) were retained in most of the marine species. Among these, the <i>pbs</i>A gene, known for encoding heme oxygenase, had two additional copies (<i>HMOX1</i> and <i>HMOX2</i>) that were newly discovered and were reported from previously red algal nuclear genomes. Each type of heme oxygenase had a different evolutionary history and special modifications (<i>e</i>.<i>g</i>., plastid targeting signal peptide). Based on this observation, we suggest that the plastid-encoded <i>pbs</i>A contributes to the iron controlling system in iron-deprived conditions. Thus, we highlight that this functional requirement may have prevented gene loss during the long evolutionary history of red algal plastid genomes.</p></div

The Plastid Genome of the Cryptomonad <i>Teleaulax amphioxeia</i>

<div><p><i>Teleaulax amphioxeia</i> is a photosynthetic unicellular cryptophyte alga that is distributed throughout marine habitats worldwide. This alga is an important plastid donor to the dinoflagellate <i>Dinophysis caudata</i> through the ciliate <i>Mesodinium rubrum</i> in the marine food web. To better understand the genomic characteristics of <i>T</i>. <i>amphioxeia</i>, we have sequenced and analyzed its plastid genome. The plastid genome sequence of <i>T</i>. <i>amphioxeia</i> is similar to that of <i>Rhodomonas salina</i>, and they share significant synteny. This sequence exhibits less similarity to that of <i>Guillardia theta</i>, the representative plastid genome of photosynthetic cryptophytes. The gene content and order of the three photosynthetic cryptomonad plastid genomes studied is highly conserved. The plastid genome of <i>T</i>. <i>amphioxeia</i> is composed of 129,772 bp and includes 143 protein-coding genes, 2 rRNA operons and 30 tRNA sequences. The DNA polymerase III gene (<i>dna</i>X) was most likely acquired via lateral gene transfer (LGT) from a firmicute bacterium, identical to what occurred in <i>R</i>. <i>salina</i>. On the other hand, the <i>psb</i>N gene was independently encoded by the plastid genome without a reverse transcriptase gene as an intron. To clarify the phylogenetic relationships of the algae with red-algal derived plastids, phylogenetic analyses of 32 taxa were performed, including three previously sequenced cryptophyte plastid genomes containing 93 protein-coding genes. The stramenopiles were found to have branched out from the Chromista taxa (cryptophytes, haptophytes, and stramenopiles), while the cryptophytes and haptophytes were consistently grouped into sister relationships with high resolution.</p></div

tRNA sequences present in the cryptophyte plastid genome.

<p>tRNA sequences present in the cryptophyte plastid genome.</p

Overview of the red algal plastid genomes.

<p>Linearized maps of the complete <i>T</i>. <i>amphioxeia</i> plastid genome is compared with those of other cryptophytes. Color-coded syntenic blocks are shown above each genome, and gene maps are shown below each genome. The syntenic blocks above the horizontal line are on the same strand, and those below the line are on the opposite strand. The horizontal bars inside of the syntenic blocks indicate sequence conservation. The block boundaries correspond to sites at which inversion events occurred. On the gene maps, the genes above the horizontal line are transcribed from left to right, and those below the horizontal line are transcribed from right to left. The rRNA operons are shown in red.</p

List of genes in the <i>Teleaulax amphioxeia</i> plastid genome (143 total).

<p>List of genes in the <i>Teleaulax amphioxeia</i> plastid genome (143 total).</p

The distribution of four putative habitat-specific genes in the phylogenetic tree.

<p>The absence/presence of four genes (<i>pbs</i>A, <i>ycf</i>34, <i>ycf</i>35, <i>ycf4</i>6) in 127 species is visualized with habitat information. The maximum likelihood phylogenetic tree was reconstructed based on the concatenated 190 orthologous plastid gene alignment. The dataset used in this analysis is shown in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0196995#pone.0196995.s005" target="_blank">S3 Table</a>.</p

The genome maps of three Nemaliophycidae plastids and their genome structure comparison.

<p>(A) Three plastid genome maps of <i>Kumanoa americana</i>, <i>Thorea hispida</i>, and <i>Palmaria palmata</i>. (B) A simplified comparative genome structure between three species based on MAUVE and UniMoG analyses. A large inversion in <i>rps</i>6-<i>chl</i>L region was observed consistently from two different analyses.</p

Circular map of the plastid genome of the cryptophyte <i>Teleaulax amphioxeia</i>.

<p>All of the genes are transcribed in a clockwise direction. Note the dense gene arrangement and the single large intergenic region. The protein-coding genes and ribosomal RNA and transfer RNA genes are labeled inside or outside of the circle. The genes are color coded according to the functional categories listed in the index below the map.</p