Cell wall chemistry and tissue structure underlie shifts in material properties of a perennial kelp

<p><i>Laminaria</i> is an abundant kelp genus in temperate nearshore ecosystems that grows with a circannual ‘stop-start’ pattern. Species of <i>Laminaria</i> play important ecological roles in kelp forests worldwide and are harvested commercially as a source of food and valuable extracts. In order to evaluate seasonal differences in tissue properties and composition, we compared the material properties, histology and cell-wall composition of overwintering blades with newly synthesized, actively growing blades from <i>Laminaria setchellii</i>. We found that overwintering blades were fortified with a thicker cortex and increased cell wall investment, leading to increased material strength. Overwintering tissues were composed of higher proportions of cellulose and fucose-containing polysaccharides (i.e. FCSPs, fucoidans) than newly formed blades and were found to possess thicker cell walls, likely to withstand the waves of winter storms. Chemical cell wall profiling revealed that significant proportions of fucose were associated with cellulose, especially in overwintering tissues, confirming the association between cellulose and some fucose-containing polysaccharides. Changes in material properties during the resting phase may allow these kelps to retain their non-growing blades through several months of winter storms. The results of this study demonstrate how one species might regulate its material properties seasonally, and at the same time shed light on the mechanisms that might control the material properties of kelps in general.</p

Maximum likelihood phylogeny of 160 concatenated red algal plastid genes.

<p>Major lineages are shaded and named to the right (Cya Cyaninidiales; Por Porphyridiales; Ban Bangiales; Flo florideophytes). The phylogeny is fully supported except for the node uniting <i>G. lanceola</i> and <i>G. tenuistipitata</i>, for which RAxML rapid boostrap (left) and PhyML SH-aLRT supports (right) are shown for trees both including Cyanidiales (above) and excluding them (below).</p

Gene content, gain and loss in red algal plastid genomes.

<p>(A) Gain and loss of genes in the florideophyte and Bangiales plastid genomes. Losses of cyanobacterial genes (blue), and gene gains (red) are mapped onto a schematic phylogeny (see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0059001#pone-0059001-g005" target="_blank">Figure 5</a>) using maximum parsimony. Note that losses may have occurred later (independently), whereas gains may have occurred earlier (loss in early-branching lineage) than inferred under this criterion. RT/mat abbreviates a reverse transcriptase/maturase ORF and the intron-bearing gene is in squared brackets. The absence of magnesium chelatase (chl), tRNA genes (trn), and unknown conserved genes (ycf) may represent outright losses rather than transfers to the nucleus in some cases. (B) Comparison of cyanobacterial gene content in red algal plastids including Cyanidiales. Venn diagram is showing number of cyanobacterial genes shared among red algal plastid genomes, which represented by bubbles. Ppu <i>Porphyra purpurea</i>, Pye <i>Pyropia yezoensis</i>, Ctu <i>Calliarthron tuberculosum</i>, Ccr <i>Chondrus crispus</i>, Gte <i>Gracilaria tenustipitata</i> var. <i>liui</i>, Gla <i>Grateloupia lanceola,</i> Cya Cyanidiales (sum of genes in <i>Cyanidium caldarium</i> and <i>Cyanidioschyzon merolae</i>).</p

Maximum likelihood phylogeny of concatenated <i>leuC</i> and <i>leuD</i> genes.

<p>Numbers at nodes indicate RAxML rapid boostrap (left) and PhyML SH-aLRT supports (right), and nodes with full support are indicated by black dots. Nucleus-encoded plastid-targeted genes are boxed in green and major lineages labelled to the right. <i>Gracilaria</i> sequences are shown in white text on black: <i>G. changii</i> has canonical nucleus-encoded <i>leuC</i> and <i>leuD</i> genes but <i>G. tenuistipitata</i> has a plastid-encoded operon that appears to have been derived by recent horizontal gene transfer from a proteobacterial source. Phylogenies of l<i>euC</i> and <i>leuD</i> are largely congruent, and can be found in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0059001#pone.0059001.s002" target="_blank">Figure S2</a>. Black “O” after species name indicates that <i>leuC/D</i> operon is present, red “O” indicates it is intervened by one (<i>Ch. flavus</i>) or two short ORFs (<i>S. termitidis</i>).</p

Conserved group II intron in florideophyte plastid <i>trnMe</i>.

<p>(A) Model of hypothetical secondary structure of the newly identified elongator methionine tRNA showing the position of the intron inserted after the third anticodon position (arrow). Residues in red differ among florideophytes. (B) Sequence alignment of the intron-encoded reverse transcriptase/maturase from five florideophyte plastid genomes with putative reverse transcriptase domains shown by dotted line boxes, the maturase domain shown by a solid line box, and conserved residues shown by asterisks (Gla <i>Grateloupia lanceola</i>; Cru <i>Cruoria</i> sp.; Gte <i>Gracilaria tenustipitata</i>; Ccr <i>Chondrus crispus</i>; Ctu <i>Calliarthron tuberculosum</i>).</p

Overview of red algal plastid genomes.

<p>Linearized maps of complete florideophyte plastid genomes compared with the bangialean <i>Porphyra</i>. For each genome, colour-coded syntenic blocks are shown above and gene maps are shown below. Syntenic blocks above the horizontal line are in the same strand while those below the line are on the opposite strand. Horizontal bars inside the syntenic blocks show sequence conservation. Block boundaries correspond to sites where inversion events occurred. In gene maps, genes above the horizontal line are transcribed left to right while those below are transcribed from right to left. Unique regions are boxed with genes in green, regions with introns are boxed with intronic segments in blue, and rRNA operons are red.</p

Assessing red algal plastid genes for phylogenetic and barcoding potential.

<p>(A) Comparison of median nonsynonymous substitution rate (dN) of protein-coding genes with interquartile range (IQR). The dN is positively correlated with the IQR (lowess local fit scatterplot, top), indicating that genes with higher evolutionary rate tend to show higher rate variations among species. When adjusted for data normality the positive correlation strength increases (log2-transformed scatterplot, bottom). (B) Summary of characteristics of individual genes. genes are binned according to their synonymous rate (vertical axis) and IQR (horizontal axis). Genes with a low IQR (right) and low dN (top) are potentially useful for higher level phylogenetic questions and distant species discrimination, whereas genes with low IQR (right) and medium-to-high dN (mid-to-bottom) are potentially useful for population studies and barcoding at subspecies level. Most promising candidate genes for phylogenies, barcoding, and population studies are in red (see text).</p

General characteristics of red algal plastid genomes¹.

1<p>All values are based on updated annotations (Materials and Methods and <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0059001#pone.0059001.s004" target="_blank">Table S1</a>).</p>2<p>Ppu = Porphyra purpurea str. Avonport (NC_000925), Pye = Pyropia yezoensis str. U-51(NC_007932), Ctu (Calliarthron tuberculosum; KC153978), Ccr (Chondrus crispus; HF562234), Gte (Calliarthron tuberculosum; KC153978), Ccr (Chondrus crispus; HF562234), Gte (Gracilaria tenuistipitata var. liui; NC_006137), Gla (Grateloupia lanceola; HM767098 and HM767138), Cca (Cyanidium caldarium str. RK1; NC_001840), Cme (Cyanidioschyzon merolae str. 10; NC_004799).</p>3<p>base pairs.</p>4<p>several bases in two stem-loop regions may be missing (see Materials and Methods).</p>5<p>GC content.</p>6<p>species-specific ORFs (not counting ORFs that are shared among multiple species).</p