Search

SUMMARY: The developmental transition from a fertilized ovule to a dispersed diaspore (seed or fruit) involves complex differentiation processes of the ovule's integuments leading to the diversity in mature seed coat structures in angiosperms. In this study, comparative imaging and transcriptome analysis were combined to investigate the morph‐specific developmental differences during outer seed coat differentiation and mucilage production in Aethionema arabicum, the Brassicaceae model for diaspore dimorphism. One of the intriguing adaptations of this species is the production and dispersal of morphologically distinct, mucilaginous and non‐mucilaginous diaspores from the same plant (dimorphism). The dehiscent fruit morph programme producing multiple mucilaginous seed diaspores was used as the default trait combination, similar to Arabidopsis thaliana, and was compared with the indehiscent fruit morph programme leading to non‐mucilaginous diaspores. Synchrotron‐based radiation X‐ray tomographic microscopy revealed a co‐ordinated framework of morph‐specific early changes in internal anatomy of developing A. arabicum gynoecia including seed abortion in the indehiscent programme and mucilage production by the mucilaginous seed coat. The associated comparative analysis of the gene expression patterns revealed that the unique seed coat dimorphism of Ae. arabicum provides an excellent model system for comparative study of the control of epidermal cell differentiation and mucilage biosynthesis by the mucilage transcription factor cascade and their downstream cell wall and mucilage remodelling genes. Elucidating the underlying molecular framework of the dimorphic diaspore syndrome is key to understanding differential regulation of bet‐hedging survival strategies in challenging environments, timely in the face of global climatic change. Significance Statement: The crucifer Aethionema arabicum is an excellent model system for the comparative analysis of dimorphic diaspore (fruit and seed) development and its underpinning molecular mechanisms. Morph‐specific expression of transcription factor cascades drive distinct cell‐wall remodelling protein expression patterns to provide morph‐specific pathways of seed coat epidermis development and differentiation in mucilage production. This diaspore dimorphism is a blend of phenotypic plasticity and bet‐hedging, which evolved as an adaptation to climatic change and variable environments. [ABSTRACT FROM AUTHOR]

SUMMARY: Aethionema arabicum is an important model plant for Brassicaceae trait evolution, particularly of seed (development, regulation, germination, dormancy) and fruit (development, dehiscence mechanisms) characters. Its genome assembly was recently improved but the gene annotation was not updated. Here, we improved the Ae. arabicum gene annotation using 294 RNA‐seq libraries and 136 307 full‐length PacBio Iso‐seq transcripts, increasing BUSCO completeness by 11.6% and featuring 5606 additional genes. Analysis of orthologs showed a lower number of genes in Ae. arabicum than in other Brassicaceae, which could be partially explained by loss of homeologs derived from the At‐α polyploidization event and by a lower occurrence of tandem duplications after divergence of Aethionema from the other Brassicaceae. Benchmarking of MADS‐box genes identified orthologs of FUL and AGL79 not found in previous versions. Analysis of full‐length transcripts related to ABA‐mediated seed dormancy discovered a conserved isoform of PIF6‐β and antisense transcripts in ABI3, ABI4 and DOG1, among other cases found of different alternative splicing between Turkey and Cyprus ecotypes. The presented data allow alternative splicing mining and proposition of numerous hypotheses to research evolution and functional genomics. Annotation data and sequences are available at the Ae. arabicum DB (https://plantcode.online.uni‐marburg.de/aetar_db). Significance Statement: Improved gene annotation of Aethionema arabicum using long‐read transcript sequencing provides a plethora of full‐length isoforms and an important resource for Brassicaceae evolution studies. [ABSTRACT FROM AUTHOR]