Conserved, divergent and heterochronic gene expression during Brachypodium and Arabidopsis embryo development

Abstract

Key message Developmental and transcriptomic analysis of Brachypodium embryogenesis and comparison with Arabidopsis identifies conserved and divergent phases of embryogenesis and reveals widespread heterochrony of developmental gene expression. Abstract Embryogenesis, transforming the zygote into the mature embryo, represents a fundamental process for all flowering plants. Current knowledge of cell specification and differentiation during plant embryogenesis is largely based on studies of the dicot model plant Arabidopsis thaliana. However, the major crops are monocots and the transcriptional programs associated with the differentiation processes during embryogenesis in this clade were largely unknown. Here, we combined analysis of cell division patterns with development of a temporal transcriptomic resource during embryogenesis of the monocot model plant Brachypodium distachyon. We found that early divisions of the Brachypodium embryo were highly regular, while later stages were marked by less stereotypic patterns. Comparative transcriptomic analysis between Brachypodium and Arabidopsis revealed that early and late embryogenesis shared a common transcriptional program, whereas mid-embryogenesis was divergent between species. Analysis of orthology groups revealed widespread heterochronic expression of potential developmental regulators between the species. Interestingly, Brachypodium genes tend to be expressed at earlier stages than Arabidopsis counterparts, which suggests that embryo patterning may occur early during Brachypodium embryogenesis. Detailed investigation of auxin-related genes shows that the capacity to synthesize, transport and respond to auxin is established early in the embryo. However, while early PIN1 polarity could be confirmed, it is unclear if an active response is mounted. This study presents a resource for studying Brachypodium and grass embryogenesis and shows that divergent angiosperms share a conserved genetic program that is marked by heterochronic gene expression.

Evolutionary divergence in embryo and seed coat development of U’s Triangle Brassica species illustrated by a spatiotemporal transcriptome atlas

“…In this study, the distribution of genes expressed in specific stages of development, along with the observed hourglass pattern of gene expression, support greater ontogenetic divergence in early and late stages of seed development among the six Brassica species examined. The significance of these observations, together with those made in recent transcriptome and global alternative splicing landscape studies of embryo development in Arabidopsis, Brachypodium and wheat (Quint et al ., 2012; Gao et al ., 2021; Hao et al ., 2021) emphasize the importance of characterizing and comparing BPs in early and late stages of seed development in the Brassica genus for uncovering the evolutionary significance of seed diversity.…”

The wild grass Brachypodium distachyon as a developmental model system

“…Likely, we would have missed the central role of SoPIN1 in organ initiation if we relied on A. thaliana as the sole model for flowering plants. Some of the auxin-related reporter lines have recently been used to analyze auxin transport and signalling during grass embryogenesis in B. distachyon (Hao et al, 2021). In addition, stage-specific embryonic transcriptomes have been generated and identified common and diverged genetic programs during embryogenesis in B. distachyon and A. thaliana (Hao et al, 2021).…”

Single-cell transcriptome reveals the redifferentiation trajectories of the early stage of de novo shoot regeneration in Arabidopsis thaliana

“…3c), and the finding was consistent with the fact that the regenerating callus would eventually form the shoot. Among the 39 genes in pattern 1, some genes have been confirmed as key factors for shoot pro-meristem formation, such as cytokinin receptor genes AHK4, WOX4 , and PIN1 44,45 (Fig. 3d).…”