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

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

Comparison of general features for 102 florideophycean plastid genomes.

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

The sequence alignment of heme oxygenase proteins.

<p>(A) The alignment of <i>pbs</i>A and its homologous proteins. The alignment shows the conserved heme oxygenases amino acid sequences in different lineages. Conserved heme binding pockets are marked as a blue asterisk. N-terminal transit peptides (green) are unique for <i>HMOX1</i> proteins, with an exceptional transit peptide of <i>pbs</i>A gene in <i>Cyanophora paradoxa</i>, which was likely transferred to the nuclear genome independently. Heme oxygenase domain (grey) and putative transmembrane domain (red) are shown. (B) <i>HMOX2</i> and <i>pbs</i>A contain putative transmembrane domain(s) (TM domain; red box). Multiple TM domains were found in <i>HMOX2</i>.</p