Dataset Information

Developmental Progression in the Coral Acropora digitifera Is Controlled by Differential Expression of Distinct Regulatory Gene Networks.

ABSTRACT: Corals belong to the most basal class of the Phylum Cnidaria, which is considered the sister group of bilaterian animals, and thus have become an emerging model to study the evolution of developmental mechanisms. Although cell renewal, differentiation, and maintenance of pluripotency are cellular events shared by multicellular animals, the cellular basis of these fundamental biological processes are still poorly understood. To understand how changes in gene expression regulate morphogenetic transitions at the base of the eumetazoa, we performed quantitative RNA-seq analysis duringAcropora digitifera's development. We collected embryonic, larval, and adult samples to characterize stage-specific transcription profiles, as well as broad expression patterns. Transcription profiles reconstructed development revealing two main expression clusters. The first cluster grouped blastula and gastrula and the second grouped subsequent developmental time points. Consistently, we observed clear differences in gene expression between early and late developmental transitions, with higher numbers of differentially expressed genes and fold changes around gastrulation. Furthermore, we identified three coexpression clusters that represented discrete gene expression patterns. During early transitions, transcriptional networks seemed to regulate cellular fate and morphogenesis of the larval body. In late transitions, these networks seemed to play important roles preparing planulae for switch in lifestyle and regulation of adult processes. Although developmental progression inA. digitiferais regulated to some extent by differential coexpression of well-defined gene networks, stage-specific transcription profiles appear to be independent entities. While negative regulation of transcription is predominant in early development, cell differentiation was upregulated in larval and adult stages.

SUBMITTER: Reyes-Bermudez A

PROVIDER: S-EPMC4824149 | biostudies-literature | 2016 Mar

REPOSITORIES: biostudies-literature

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Developmental Progression in the Coral Acropora digitifera Is Controlled by Differential Expression of Distinct Regulatory Gene Networks.

Reyes-Bermudez Alejandro A Villar-Briones Alejandro A Ramirez-Portilla Catalina C Hidaka Michio M Mikheyev Alexander S AS

Genome biology and evolution 20160323 3

Corals belong to the most basal class of the Phylum Cnidaria, which is considered the sister group of bilaterian animals, and thus have become an emerging model to study the evolution of developmental mechanisms. Although cell renewal, differentiation, and maintenance of pluripotency are cellular events shared by multicellular animals, the cellular basis of these fundamental biological processes are still poorly understood. To understand how changes in gene expression regulate morphogenetic tran ...[more]

PMID: 26941230

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Project description:BACKGROUND:Being critically important to the ecosystem, the stability of coral reefs is directly related to the marine and surrounding terrestrial environments. However, coral reefs are now undergoing massive and accelerating devastation due to bleaching. The fact that the breakdown of symbiosis between coral and the dinoflagellate, zooxanthellae, has been well elucidated as the main cause of bleaching, implying the establishment of symbiosis with zooxanthellae plays a crucial role in maintaining coral survival. However, the relevant molecular and cellular mechanisms have not been well studied yet. In this study, based on the deep RNA-sequencing data derived from Mohamed, A. R. et al., an integrated transcriptome analysis was performed to deeply investigate global transcriptome changes of the coral Acropora digitifera in response to infection by dinoflagellate of the genus Symbiodinium. RESULTS:The results revealed that compared to RefTranscriptome_v1.0 (A. digitifera transcriptome assembly v1.0), numerous novel transcripts and isoforms were identified, the Symbiodinium-infected coral larvae at 4?h generated the highest proportion of specific isoforms. Alternative splicing analysis showed that intron retention predominated in all alternative transcripts among six statuses. Additionally, 8117 lncRNAs were predicted via a stringent stepwise filtering pipeline. A complex lncRNAs-mRNAs network including 815 lncRNAs and 6395 mRNAs were established, in which 21 lncRNAs were differentially expressed at 4?h post infection. Functional clustering analysis for those differentially lncRNAs-coexpressed mRNAs demonstrated that several biological processes and pathways related to protein kinase activity, metabolic pathways, mitochondrion, ribosome, etc. were enriched. CONCLUSIONS:Our study not only refined A. digitifera transcriptome via identification of novel transcripts and isoforms, but also predicted a high-confidence dataset of lncRNAs. Functional study based on the construction of lncRNAs-mRNAs co-expression network has disclosed a complex lncRNA-mediated regulation in response to Symbiodinium infection exhibited in A. digitifera. Once validated, these lncRNAs could be good potential targets for treatment and prevention of bleaching in coral.

Project description:Coral reefs are suffering a major decline due to the environmental constraints imposed by climate change. Over the last 20 years, three major coral bleaching events occurred in concomitance with anomalous heatwaves, provoking a severe loss of coral cover worldwide. The conservation strategies for preserving reefs, as they are implemented now, cannot cope with global climatic shifts. Consequently, researchers are advocating for preservation networks to be set-up to reinforce coral adaptive potential. However, the main obstacle to this implementation is that studies on coral adaption are usually hard to generalize at the scale of a reef system. Here, we study the relationships between genotype frequencies and environmental characteristics of the sea (seascape genomics), in combination with connectivity analysis, to investigate the adaptive potential of a flagship coral species of the Ryukyu Archipelago (Japan). By associating genotype frequencies with descriptors of historical environmental conditions, we discovered six genomic regions hosting polymorphisms that might promote resistance against heat stress. Remarkably, annotations of genes in these regions were consistent with molecular roles associated with heat responses. Furthermore, we combined information on genetic and spatial distances between reefs to predict connectivity at a regional scale. The combination of these results portrayed the adaptive potential of this population: we were able to identify reefs carrying potential heat stress adapted genotypes and to understand how they disperse to neighbouring reefs. This information was summarized by objective, quantifiable and mappable indices covering the whole region, which can be extremely useful for future prioritization of reefs in conservation planning. This framework is transferable to any coral species on any reef system and therefore represents a valuable tool for empowering preservation efforts dedicated to the protection of coral reefs in warming oceans.

Dataset Information

Developmental Progression in the Coral Acropora digitifera Is Controlled by Differential Expression of Distinct Regulatory Gene Networks.

Publications

Developmental Progression in the Coral Acropora digitifera Is Controlled by Differential Expression of Distinct Regulatory Gene Networks.

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