Developmental Progression in the CoralAcropora digitiferaIs 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 during Acropora 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 in A. digitifera is 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.

An ancient genome duplication in the speciose reef-building coral genus, Acropora

“…To better to understand evolution of duplicated genes, gene expression analysis across five developmental stages in A. digitifera (blastula, gastrula, postgastrula, planula, and adult polyps) was carried out based on previous transcriptome data [60]. We identified 236 ohnologous pairs in A. digitifera from 883 ML phylogeny (for details see Methods) and found that these ohnologous pairs present an interesting gene expression profiling.…”

“…The Acropora species information in this study will be described in the paper (Mao et al, in revision). Information about Astreopora sp1 was described previously [7] and transcriptome data across five development stages was descried previously [60]. Protein sequences of the six species were combined together to perform all-against-all BLASTP approach to find all orthologs and paralogs among six species.…”

“…We selected 236 gene pairs of A. digitifera (ohnologous gene pairs) from 831 orthogroups. We BLASTed these ohnologous gene pairs against the gene expression data across five developmental stages [60] and these data were normalized for each developmental stage. Correlations between two ohnologous genes were performed using Pearson’s correlation in R [74].…”

The characterization of larval homology: transcriptomic insights into the origin and evolution of animal life cycles

“…Qiu et al 2015, Reyes-Bermudez et al 2016 were differentially present in each of the three annotation methods, denote highly specific regulatory information, and some of them are vertebrate-specific (e.g. the sponge has no heart, therefore an enrichment in WSP involved in heart development is either spurious or reflects gene pleiotropy between species).…”

“…For instance, the TF AP4 is present in the larval-specific gene suite (I), as it is in the coral, Acropora digitifera (Reyes-Bermudez et al 2016). This suggests that aspects of larval-specific circuitry may be conserved between these taxa.…”