Transcriptomic Responses to Thermal Stress and Varied Phosphorus Conditions in Fugacium kawagutii

Abstract

Coral reef-associated Symbiodiniaceae live in tropical and oligotrophic environments and are prone to heat and nutrient stress. How their metabolic pathways respond to pulses of warming and phosphorus (P) depletion is underexplored. Here, we conducted RNA-seq analysis to investigate transcriptomic responses to thermal stress, phosphate deprivation, and organic phosphorus (OP) replacement in Fugacium kawagutii. Using dual-algorithm (edgeR and NOIseq) to remedy the problem of no replicates, we conservatively found 357 differentially expressed genes (DEGs) under heat stress, potentially regulating cell wall modulation and the transport of iron, oxygen, and major nutrients. About 396 DEGs were detected under P deprivation and 671 under OP utilization, both mostly up-regulated and potentially involved in photosystem and defensome, despite different KEGG pathway enrichments. Additionally, we identified 221 genes that showed relatively stable expression levels across all conditions (likely core genes), mostly catalytic and binding proteins. This study reveals a wide range of, and in many cases previously unrecognized, molecular mechanisms in F. kawagutii to cope with heat stress and phosphorus-deficiency stress. Their quantitative expression dynamics, however, requires further verification with triplicated experiments, and the data reported here only provide clues for generating testable hypotheses about molecular mechanisms underpinning responses and adaptation in F. kawagutii to temperature and nutrient stresses.

Genome Improvement and Core Gene Set Refinement of Fugacium kawagutii

“…The KEGG annotatable genes (451) were significantly enriched in thirteen 32 KEGG pathways (p-value cutoff = 0.05) such as ribosome, RNA transport, DNA replication, and cell cycle ( Figure 3B). We have previously identified 221 core genes in F. kawagutii exhibiting stable expression under heat stress, phosphate deprivation, glycerol-3-phosphate replacement, and nutrient replete conditions based on Fugka_Geneset_V1 as the reference gene set [33]. Among the 221 core genes, the two most highly and commonly expressed ones were 14-3-3 protein and ADP ribosylation factor, which are different from that found in the present study.…”

“…To investigate differential gene expression patterns under the different trace metal conditions, the RNA samples of F. kawagutii from nutrient-replete, -Cu, -Mn, -Ni, + 1/5 Zn, and + 1/5 Fe conditions were also separately sequenced using BGI RNA-Seq [23]. Genes commonly and highly expressed across all six treatment conditions were identified as core genes, following previously reported methods [33]. Briefly, these were genes showing expression of ≥ 90% average Transcripts Per Million (TPM) and coefficient of variation (CV) ≤ 0.08 across the six treatment conditions.…”

“…Briefly, these were genes showing expression of ≥ 90% average Transcripts Per Million (TPM) and coefficient of variation (CV) ≤ 0.08 across the six treatment conditions. Then, cores genes selected from nutrient replete and trace metal deficiencies were used to compare with the previous core gene set [33] using BLASTN with E-value ≤ 10 −5 to generate a new core gene set.…”

“…It has been postulated that highly and commonly expressed genes under different growth conditions can be classified as core genes, whereas genes showing variable expression levels in response to growth condition changes are environment responsive genes [33]. In this study, a total of 2113 annotated genes were qualified as core genes based on their high and stable expression levels under five trace metal deficiencies and nutrient replete conditions, which we designated as core gene set 1 ( Supplementary Table S8).…”

Metabolic Responses of Carotenoid and Cordycepin Biosynthetic Pathways in Cordyceps militaris under Light-Programming Exposure through Genome-Wide Transcriptional Analysis

“…Total RNA was extracted using the RNeasy mini kit (Qiagen). Equal amounts of total RNA samples extracted from three independent cultures, using each sugar as a sole carbon source, were taken and pooled together for RNA sequencing according to the other previous studies [ 17 , 18 , 19 , 20 ]. RNA quality and concentration were measured by the Agilent 2100 bioanalyzer.…”