Aethionema arabicum genome annotation using PacBio full‐length transcripts provides a valuable resource for seed dormancy and Brassicaceae evolution research

Abstract

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).

Comparative transcriptomics identifies the transcription factors BRANCHED1 and TCP4, as well as the microRNA miR166 as candidate genes involved in the evolutionary transition from dehiscent to indehiscent fruits in Lepidium

“…Benchmarking of Universal Single-Copy Orthologs (BUSCO) analysis revealed that the transcriptome assemblies of the two species contain more than 94% of the eudicotyledonous "near-universal single-copy orthologs". This number is similar to or more than that for transcriptome assemblies of other Brassicaceae (Chandler et al 2020;Yao et al 2020;Fernandez-Pozo et al 2021). Furthermore, we found members of all 16 miRNA families that were found to have originated before the emergence of eudicots and conserved in eudicots (Montes et al 2014).…”

A tale of two morphs: developmental patterns and mechanisms of seed coat differentiation in the dimorphic diaspore model Aethionema arabicum (Brassicaceae)

“…While the multiple‐seeded DEH fruits are predominantly produced on main flowering branches, single‐seeded IND fruits in contrast are favoured on higher‐order side branches (Lenser et al , 2018). The strict dimorphism, together with available genome and transcriptome sequences (Fernandez‐Pozo et al , 2021; Nguyen et al , 2019) (Wilhelmsson et al , 2019), make Ae. arabicum an excellent model system for investigating the mechanisms of diaspore dimorphism.…”

Phytochromes mediate germination inhibition under red, far-red, and white light in Aethionema arabicum

“…S2). The mutation in koy-1 has removed the AearHO1 promoter region between -90 and -414 bp upstream of the start codon, including the transcriptional start site identified by transcriptome analysis in the wild type (Fernandez-Pozo et al, 2021) and several binding sites for transcription factors (Fig. 2B,E).…”

“…species, closely related to the classical model Arabidopsis thaliana, and the highly improved gene annotation in a relatively small genome(Fernandez-Pozo et al, 2021) recommend A. arabicum as an attractive novel model to investigate the complex regulation of seed germination in response to light. We created the first mutant collection for A. arabicum to perform a forward genetic screen for lack of white light-inhibited germination.…”