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Series GSE245492 Query DataSets for GSE245492
Status Public on Jan 01, 2024
Title Phenotypic plasticity for improved light harvesting, in tandem with methylome repatterning in reef-building corals [Methyl-seq]
Organism Acropora palmata
Experiment type Methylation profiling by high throughput sequencing
Summary Acclimatization through phenotypic plasticity represents a more rapid response to environmental change than adaptation and is vital to optimize organisms’ performance in different conditions. Generally, animals are less phenotypically plastic than plants, but reef-building corals exhibit plant-like properties. They are light-dependent with a sessile and moddular construction that facilitates rapid morphological changes within their lifetime. We induced phenotypic changes by altering light exposure in a reciprocal transplant experiment and found that coral plasticity is a colony trait emerging from comprehensive morphological and physiological changes within the colony. Plasticity in skeletal features optimized coral light harvesting and utilization and paralleled with significant methylome and transcriptome modifications. Network-associated responses resulted in the identification of hub genes and clusters associated to the change in phenotype: inter-partner recognition and phagocytosis, soft tissue growth and biomineralization. Furthermore, we identified hub genes putatively involved in animal photoreception-phototransduction. These findings fundamentally advance our understanding of how reef-building corals repattern the methylome and adjust a phenotype, revealing an important role of light sensing by the coral animal to optimize photosynthetic performance of the symbionts.
 
Overall design To examine the phenotype to methylome association, we conducted a reciprocal transplant experiment to induce light-mediated phenotypic responses in the reef-building Elkhorn coral Acropora palmata and investigated DNA methylation and transcriptional responses potentially responsible for plasticity. Extensive biometrics revealed not only changes in coral tissue pigmentation and metabolic rates but also in skeletal morphology after five weeks. This skeletal remodeling was accompanied by intragenic methylome repatterning, discovered by signal detection with machine learning-based analysis. We further integrated differentially methylated (DMG) and expressed (DEG) gene datasets to elucidate how light responses integrate into gene regulatory networks controlling functional traits. By exploring the resulting hub genes and gene clusters, we were able to predict functional associations with observed phenotype changes and identify markers of plasticity in reef-building corals. Moreover, our results contribute to emerging evidence that epigenetics contribute to the machinery that can alter DNA structure during skeletal remodeling in metazoans.
To induce phenotypic plasticity, we performed a reciprocal transplant experiment. We sampled 3 colonies (representing 3 distinct multilocus genotypes, or genets, as detected with Standard Tools for Acroporid Genotyping STAGdb) from a depth of 2-3 m, each at least 300 m apart. We collected ~7 cm2 fragments from HL (n= 42 Upperside) and LL (n = 42 Underside) surfaces of branch surfaces keeping track of genet identification. We settled them in a reef-deployed PVC structure designed to simulate the light condition and colony position of source colonies. We placed all coral fragments in their original light condition and orientation (i.e. HL Uppersides facing up) and allowed them to heal and acclimate. Subsequently, we randomly divided HL fragments into control (Upperside Control) and treatment groups (Upperside Treatment), equal grouping was done for LL fragments (Underside Control and Underside Treatment). To induce phenotypic plasticity, coral fragments in treatment groups were flipped to the opposite light condition and position (i.e. high light fragments were flipped to a low light condition, while LL fragments were flipped to a HL position). This second acclimatory period was carried out for 5+ weeks. Four group conditions were analyzed after 13+ weeks of experiment: HL controls (n= 21 Upperside Control), HL⇾LL treatments (High Light to Low Light, n = 21, Upperside Treatment), LL controls (n= 21 Underside Control), LL⇾HL treatments (Low Light to High Light, n = 21, Underside Treatment)).
 
Contributor(s) Gomez-Campo K, Sanchez R, Martinez-Rugerio I, Yang X, Maher T, Osborne CC, Enriquez S, Baums IB, Mackenzie SA, Igelsias-Prieto R
Citation missing Has this study been published? Please login to update or notify GEO.
Submission date Oct 16, 2023
Last update date Jan 01, 2024
Contact name KELLY Johanna GOMEZ-CAMPO
E-mail(s) kellygomezcampo@gmail.com, kjg27@psu.edu
Organization name PSU
Department Biology
Lab Baums
Street address 212 Mueller Laboratory
City University Park
State/province Pennsylvania
ZIP/Postal code 16802
Country USA
 
Platforms (1)
GPL33847 Illumina HiSeq 4000 (Acropora palmata)
Samples (32)
GSM7843833 unC-185-01, methylseq
GSM7843834 unC-185-02, methylseq
GSM7843835 upT-183-01, methylseq
This SubSeries is part of SuperSeries:
GSE245494 Phenotypic plasticity for improved light harvesting, in tandem with methylome repatterning in reef-building corals
Relations
BioProject PRJNA1028603

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE245492_Bismark_Summary_NCBI.xlsx 17.6 Kb (ftp)(http) XLSX
GSE245492_RAW.tar 29.3 Gb (http)(custom) TAR (of COV, TXT)
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Raw data are available in SRA
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