Characterization of differential transcript abundance through time during Nematostella vectensis development

Abstract

BackgroundNematostella vectensis, a burrowing sea anemone, has become a popular species for the study of cnidarian development. In previous studies, the expression of a variety of genes has been characterized during N. vectensis development with in situ mRNA hybridization. This has provided detailed spatial resolution and a qualitative perspective on changes in expression. However, little is known about broad transcriptome-level patterns of gene expression through time. Here we examine the expression of N. vectensis genes through the course of development with quantitative RNA-seq. We provide an overview of changes in the transcriptome through development, and examine the maternal to zygotic transition, which has been difficult to investigate with other tools.ResultsWe measured transcript abundance in N. vectensis with RNA-seq at six time points in development: zygote (2 hours post fertilization (HPF)), early blastula (7 HPF), mid-blastula (12 HPF), gastrula (24 HPF), planula (5 days post fertilization (DPF)) and young polyp (10 DPF). The major wave of zygotic expression appears between 7–12 HPF, though some changes occur between 2–7 HPF. The most dynamic changes in transcript abundance occur between the late blastula and early gastrula stages. More transcripts are upregulated between the gastrula and planula than downregulated, and a comparatively lower number of transcripts significantly change between planula and polyp. Within the maternal to zygotic transition, we identified a subset of maternal factors that decrease early in development, and likely play a role in suppressing zygotic gene expression. Among the first genes to be expressed zygotically are genes whose proteins may be involved in the degradation of maternal RNA.ConclusionsThe approach presented here is highly complementary to prior studies on spatial patterns of gene expression, as it provides a quantitative perspective on a broad set of genes through time but lacks spatial resolution. In addition to addressing the problems identified above, our work provides an annotated matrix that other investigators can use to examine genes and developmental events that we do not examine in detail here.

Characterization of the piRNA pathway during development of the sea anemone Nematostella vectensis

“…For normalization, 5 reference genes with stable expression across development were selected as follows: we calculated the Shannon entropy for each gene (as described in 68 based on normalized transcript abundance estimates for 6 time-points of Nematostella development. 69 We then ranked the genes by entropy (indicating minimal temporal change in abundance), and from the top 20 chose 5 genes (NVE3324, NVE5273, NVE11206, NVE22425, NVE14488 from 22 ) with complete gene models and mean abundance levels spanning the expected experimental range.…”

Origin and evolution of the metazoan non-coding regulatory genome: Insights from the sponge Amphimedon queenslandica

“…S4.9C, S4.9D). Analyzing RNA-seq-based gene expression through the development of the cnidarian Nematostella vectensis (Helm et al, 2013) and previously published ChIP-seq data sets in Nematostella adult female polyps (Schwaiger et al, 2014), we obtained the same pattern (Mann-Whitney U test, P-value <2.2e-16; Fig. 4.3C).…”

Host and Symbionts in Pocillopora damicornis Larvae Display Different Transcriptomic Responses to Ocean Acidification and Warming

“…These patterns of gene expression are likely to be direct responses to temperature and pCO 2 levels and not due to a development delay under particular treatment conditions. We observed a large number of transcripts that were differentially expressed between freshly released larvae and larvae from the experimental treatments, and larval development is commonly associated with large changes in gene expression across time points (e.g., Helm et al, 2013). Without fieldcaught 24-h-old larvae for comparison, the possibility that the differential gene expression observed is the result of acclimation to laboratory conditions cannot be excluded.…”