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 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

Characteristics of the cryptophyte plastid genome analyzed in this study.

<p>Characteristics of the cryptophyte plastid genome analyzed in this study.</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

Phylogenetic tree of SSU (18S rDNA) sequences among microorganisms genetically-close to <i>Chloromonas</i> sp.

The sequences used for analysis were acquired from the NCBI database and aligned by the ClustalW algorithm [24]. The tree was generated by the maximum likelihood (ML) method. The probabilities from maximum parsimony and distance methods (left and right values, respectively) were obtained by bootstrap analysis of 5000 repetitions.</p

Multigene phylogeny of <i>Synura</i> (Synurophyceae) and descriptions of four new species based on morphological and DNA evidence

<p>We used phylogenetic analyses based on multiple gene sequences (partial nr SSU and LSU rDNA, partial pt LSU rDNA, <i>psa</i>A and <i>rbc</i>L) from 148 strains (including three outgroups) and scale ultrastructure to examine phylogenetic relationships among species of the colonial genera <i>Synura</i> and <i>Tessellaria</i>. The phylogenetic tree based on the combined dataset was congruent with ultrastructural characteristics of the scales. <i>Synura</i> was divided into three major clades, two including species in section <i>Synura</i>, and one representing section <i>Peterseniae</i>. One clade, consisting of seven strains of <i>S. uvella</i> (section <i>Synura</i>), diverged at the base of the genus. The second clade consisted of the remaining species belonging to the section <i>Synura</i>. The third clade, containing organisms in the section <i>Peterseniae</i> and characterized by scales possessing a keel, was monophyletic with strong support values. Based on our findings, <i>S. uvella</i> needs to be in a separate section from other spine-bearing species, and we therefore propose new sectional ranks; <i>Synura, Peterseniae, Curtispinae</i> (presence of body scales with slender spines, tubular scales and caudal scales). We further propose four new species based on phylogenetic analyses and unique scale characters: <i>S. longitubularis</i> sp. nov., <i>S. sungminbooi</i> sp. nov., <i>S. soroconopea</i> sp. nov. and <i>S. lanceolata</i> sp. nov. Lastly, we propose a new genus name, <i>Neotessella</i>, to replace the invalid use of the name <i>Tessellaria</i>.</p

New Cysteine-Rich Ice-Binding Protein Secreted from Antarctic Microalga, <i>Chloromonas</i> sp.

<div><p>Many microorganisms in Antarctica survive in the cold environment there by producing ice-binding proteins (IBPs) to control the growth of ice around them. An IBP from the Antarctic freshwater microalga, <i>Chloromonas</i> sp., was identified and characterized. The length of the <i>Chloromonas</i> sp. IBP (<i>ChloroIBP</i>) gene was 3.2 kb with 12 exons, and the molecular weight of the protein deduced from the <i>ChloroIBP</i> cDNA was 34.0 kDa. Expression of the <i>ChloroIBP</i> gene was up- and down-regulated by freezing and warming conditions, respectively. Western blot analysis revealed that native ChloroIBP was secreted into the culture medium. This protein has fifteen cysteines and is extensively disulfide bonded as shown by in-gel mobility shifts between oxidizing and reducing conditions. The open-reading frame of <i>ChloroIBP</i> was cloned and over-expressed in <i>Escherichia coli</i> to investigate the IBP’s biochemical characteristics. Recombinant ChloroIBP produced as a fusion protein with thioredoxin was purified by affinity chromatography and formed single ice crystals of a dendritic shape with a thermal hysteresis activity of 0.4±0.02°C at a concentration of 5 mg/ml. <i>In silico</i> structural modeling indicated that the three-dimensional structure of ChloroIBP was that of a right-handed β-helix. Site-directed mutagenesis of <i>ChloroIBP</i> showed that a conserved region of six parallel T-X-T motifs on the β-2 face was the ice-binding region, as predicted from the model. In addition to disulfide bonding, hydrophobic interactions between inward-pointing residues on the β-1 and β-2 faces, in the region of ice-binding motifs, were crucial to maintaining the structural conformation of ice-binding site and the ice-binding activity of ChloroIBP.</p></div

Pictures of <i>Chloromonas</i> sp., and single ice crystal shapes from the extracellular fraction of <i>Chloromonas</i> sp.

(A) light micrograph showing chloroplast and flagella; (b) electron micrographs showing ultrastructural features by longitudinal and cross-section views (Cp, Chloroplast; F, Flagella; G, Golgi complex; L, Lumen; Mt, Mitochondria; N, Nucleus; S, Starch (C and D) ice crystal shapes formed by ice-binding proteins secreted from Chloromonas sp showing hexagonal morphology.</p