A transcriptomic hourglass in plant embryogenesis

Abstract

Animal and plant development starts with a constituting phase called embryogenesis, which evolved independently in both lineages. Comparative anatomy of vertebrate development--based on the Meckel-Serrès law and von Baer's laws of embryology from the early nineteenth century--shows that embryos from various taxa appear different in early stages, converge to a similar form during mid-embryogenesis, and again diverge in later stages. This morphogenetic series is known as the embryonic 'hourglass', and its bottleneck of high conservation in mid-embryogenesis is referred to as the phylotypic stage. Recent analyses in zebrafish and Drosophila embryos provided convincing molecular support for the hourglass model, because during the phylotypic stage the transcriptome was dominated by ancient genes and global gene expression profiles were reported to be most conserved. Although extensively explored in animals, an embryonic hourglass has not been reported in plants, which represent the second major kingdom in the tree of life that evolved embryogenesis. Here we provide phylotranscriptomic evidence for a molecular embryonic hourglass in Arabidopsis thaliana, using two complementary approaches. This is particularly significant because the possible absence of an hourglass based on morphological features in plants suggests that morphological and molecular patterns might be uncoupled. Together with the reported developmental hourglass patterns in animals, these findings indicate convergent evolution of the molecular hourglass and a conserved logic of embryogenesis across kingdoms.

Transcription factor evolution in eukaryotes and the assembly of the regulatory toolkit in multicellular lineages

“…The theoretical basis of genomic phylostratigraphy and detailed phylostratigraphic procedures have been described previously (10,13,(57)(58)(59). Protein coding sequences for Danio rerio (25,638 genes), Drosophila melanogaster (13,413 genes), and Arabidopsis thaliana (27,148 genes) were retrieved from the Ensembl database (version 69) (60).…”

“…For example, TFs are the master regulators of embryonic development in embryophytes and metazoans (9), and analyses of their embryonic transcriptional profiles support the presence of a phylotypic stage in both lineages (10)(11)(12)(13)(14). These studies have also shown that evolutionarily younger genes tend to be expressed at earlier and later stages of development, whereas the transcriptomes of the middle stages (the phylotypic stage) are dominated by ancient genes (10,13). It remains to be investigated how the evolutionary age and the expression patterns of the different TFs shift throughout the ontogeny of these lineages and whether TF expression profiles correlate with the general transcriptome profiles.…”

Evolutionarily Conserved Alternative Splicing Across Monocots

“…SASTs . 150 bp (50 codons) were used in KaKs analysis, and KaKs ratios of those SASTs alignments with Ka , 0.5, Ks , 5, and Ka/Ks , 2 were retained for further analysis (Quint et al 2012). Since these filtering processes resulted in , 100 SAST alignments associated with AltTE events, we focused only IntronR, ExonS, AltA, and AltD events for this analysis.…”

Fast-evolving microRNAs are highly expressed in the early embryo of Drosophila virilis

“…The functional relevance of nonconserved microRNAs is the subject of much debate, as they are often reported to be expressed at low levels or during restricted stages of development (Berezikov 2006;Chen and Rajewsky 2007;Liang and Li 2009;Meunier et al 2012;Roux et al 2012). Despite a general positive correlation between sequence conservation and expression, conservation of the protein-coding transcriptome is not uniform across different stages of development (Davis et al 2005;HazkaniCovo et al 2005;Cruickshank and Wade 2008;Roux and Robinson-Rechavi 2008;Domazet-Lošo and Tautz 2010;Kalinka et al 2010;Irie and Kuratani 2011;Kalinka and Tomancak 2012;Quint et al 2012). For example, the protein-coding transcriptome of adult animals has been shown to be less conserved than that of the embryo in both invertebrates and vertebrates (Domazet-Lošo and Tautz 2010).…”