Transcriptome Co-expression Network Analysis Identifies Key Genes Regulating Conchosporangia Maturation of Pyropia haitanensis

Abstract

Conchosporangia maturation is crucial for the yield of Pyropia/Porphyra. However, the molecular mechanisms underlying this process are poorly understood. In this study, we selected two strains of Pyropia haitanensis that show significant differences in conchosporangia maturation as materials to produce RNA-Seq libraries. Then, we identified key molecular pathways and genes involved in conchosporangia maturation by conducting a weighted gene co-expression network analysis. Two specific modules were identified, and included functions such as phosphorus metabolism, lipid metabolism, and the phosphatidylinositol signaling system. The hub genes that responded positively during conchosporangia maturation encoded diacylglycerol kinase (DGK) and phosphatidylinositol-3-phosphate-5-kinase, which are involved in the synthesis of phosphatidic acid, a key component of lipid metabolism. A full-length DGK sequence of P. haitanensis, designated as PhDGK1, was obtained by rapid-amplification of cDNA ends. Conserved motif and phylogenetic tree analyses showed that PhDGK1 belongs to DGK Cluster II. The transcript level of PhDGK1 increased during conchosporangia maturation in both strains, but increased earlier, and to higher levels, in the early-maturing strain than in the late-maturing strain. This pattern of gene expression was consistent with the patterns of maturity and changes in pigment contents. These results indicate that lipid metabolism plays a key role in regulating conchosporangia maturation in Pyropia spp., and that PhDGK1 might be a useful molecular marker for breeding new early-maturing strains.

Investigating the Mechanisms Underlying the Low Irradiance-Tolerance of the Economically Important Seaweed Species Pyropia haitanensis

“…The PE, PC, and APC contents in the P. haitanensis conchocelis life cycle stage gradually increase under maturation-inducing conditions (e.g., LI as well as high temperatures and phosphorous levels). This increase helps cells maintain efficient light-harvesting activities under decreased light irradiance and duration [ 27 ]. In the present study, the PE, PC, and APC contents were higher in the P. haitanensis LIT strain than in the LIS strain under control and LI conditions ( Figure 2 ).…”

“…Our previous study found that the PI signaling system is important for the perception of external stimuli and the subsequent signal transduction in P. haitanensis [ 27 , 28 , 29 ]. In the present study, LI treatment resulted in the upregulated expression of key genes associated with the PI signaling system in both P. haitanensis strains, including genes encoding PLCD, PI4KB, PIK3C3, PIP5K, and DGK ( Figure 8 ).…”

“…Lin et al (2021) cloned the P. haitanensis DGK1 gene ( PhDGK1 ) and determined that its expression increases during the conchosporangia maturation stage under LI conditions and in response to short exposures to light. The expression of PhDGK1 also increases earlier and to higher levels in the early maturing strain than in the late-maturing strain of P. haitanensis [ 27 ]. In addition to being a signaling lipid, PA is also an important intermediate in the lipid biosynthesis pathway because it is a precursor for the biosynthesis of the major phospholipid components in cell membranes [ 33 ].…”

“…Decreasing unnecessary energy consumption is critical for preventing cell damage in P. haitanensis during exposure to abiotic stress [ 27 , 52 ]. In the current study, the expression of 33 of 57 and 34 of 57 DEGs related to the TCA cycle was downregulated in the LIT and LIS strains, respectively, after 1 day of LI treatment ( Figure 7 ).…”

H2O2 drives the transition from conchocelis to conchosporangia in the red alga Pyropia haitanensis with promotion facilitated by 1-Aminocyclopropane-1-carboxylic acid

“…Interestingly, filamentous sporophytes within the shell do not undergo direct meiotic division to form gametophytes. Instead, it takes months for them to produce conchosporangial branches, and only then do mature conchosporangia release conchospores ( Lin et al., 2021 ). Moreover, the conchosporangia do not result from enlargement of the original conchocelis cells; rather, they are newly produced from the conchocelis through tip growth via swelling of the apical cells of the conchocelis branch ( Taya et al., 2022 ).…”