| Global results of proteomics analysis of bleached and non-bleached Montipora capitata outer layer (OL) tissue and inner core (IC) intra-skeletal tissue and skeleton. (A) Venn diagram depicts number of proteins identified in each sample type, and (B) non-metric dimensional scaling (NMDS) plot of all treatments. BOL, bleached outer layer; NBOL, non-bleached outer layer; NBIC, bleached inner core; BIC, bleached inner core.

| Global results of proteomics analysis of bleached and non-bleached Montipora capitata outer layer (OL) tissue and inner core (IC) intra-skeletal tissue and skeleton. (A) Venn diagram depicts number of proteins identified in each sample type, and (B) non-metric dimensional scaling (NMDS) plot of all treatments. BOL, bleached outer layer; NBOL, non-bleached outer layer; NBIC, bleached inner core; BIC, bleached inner core.

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Coral bleaching events are increasing with such frequency and intensity that many of the world’s reef-building corals are in peril. Some corals appear to be more resilient after bleaching but the mechanisms underlying their ability to recover from bleaching and persist are not fully understood. We used shotgun proteomics to compare the proteomes of...

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... output included a protein-length corrected log-fold change analysis (base 2) and a false discovery rate (FDR)-corrected z-score based on the posterior distribution of the LFC parameter, guided by the FDR estimated by a well-known Empirical Bayes method. Differential expression was reported using a LFC ≥ | 0.5| and z-score ≥ | 2| (Supplementary File 3). Enrichment analysis of biological processes were compared between NBOL and NBIC using MetaGOmics ver. ...
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... high percentage of annotated proteins allowed for more detailed analysis of active metabolic pathways utilized in each sample type across both treatments. About 70% (1,660 proteins) of all proteins were found in every sample group and the number of unique proteins per treatment or sample type ranged from 0.5-2%, with the highest number of unique proteins observed in the OL of bleached corals ( Figure 3A). NMDS ordination of protein profiles of all sample types show a distinction between the OL and IC compartments but not between bleached and non-bleached samples for either OL or IC ( Figure 3B). ...
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... 70% (1,660 proteins) of all proteins were found in every sample group and the number of unique proteins per treatment or sample type ranged from 0.5-2%, with the highest number of unique proteins observed in the OL of bleached corals ( Figure 3A). NMDS ordination of protein profiles of all sample types show a distinction between the OL and IC compartments but not between bleached and non-bleached samples for either OL or IC ( Figure 3B). ANOSIM revealed that there was a significant difference of protein profiles among all sample types (R = 0.5701; p = 9.999e-05). ...
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... revealed that there was a significant difference of protein profiles between the OL and IC of non-bleached samples (R = 0.5936; p = 0.001). Further analysis revealed that 187 proteins were significantly more abundant in the OL and 132 proteins were more abundant in the IC (Supplementary File 3). Based on enrichment analysis, the OL of non-bleached M. capitata was enriched in biological processes involved in anatomical development, carbohydrate metabolism, cell differentiation, endocytosis, lipid metabolism, protein metabolism, RNA processing and small molecule processing ( Figure 4A and Supplementary File 4). ...
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... did not reveal a significant difference of protein profiles between OL of bleached and non-bleached corals (R = 0.05316; p = 0.159). Qspec analysis of differential abundances between the OL of bleached and non-bleached corals revealed 63 significant proteins at higher, and 28 at lower, abundance in bleached corals compared to non-bleached corals (Supplementary File 3). Biological enrichment analysis of GO terms identified that the OL of bleached corals have a higher abundance of proteins involved in carbon metabolism, lipid metabolism, nitrogen metabolism, protein metabolism, response to oxidative stress, RNA processing and cellular signaling and transport than non-bleached corals (Figures 5A, 6). ...
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... our four sample types, the most significant proteomic difference was found when comparing the OL and IC (see Figure 3B). Biological enrichment analysis of GO terms using MetaGOmics highlight how the coral OL is characterized by routine cellular activities such as metabolic processes, cellular maintenance, and growth, while the IC was significantly enriched in proteins related to structural maintenance, cell adhesion, immune and stimulus response, as well as carbon and lipid metabolism. ...