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).

BIOSS Centre for Biological Signaling Studies University of Freiburg Freiburg Germany

Biosystematics Group Wageningen University Wageningen The Netherlands

Gregor Mendel Institute of Molecular Plant Biology Austrian Academy of Sciences Vienna BioCenter Vienna Austria

Laboratory of Growth Regulators Centre of the Region Haná for Biotechnological and Agricultural Research Palacký University and Institute of Experimental Botany Academy of Sciences of the Czech Republic Olomouc Czech Republic

LOEWE Center for Synthetic Microbiology University of Marburg Marburg Germany

Matthias Schleiden Institute Genetics Friedrich Schiller University Jena Jena Germany

Plant Cell Biology Department of Biology University of Marburg Marburg Germany

School of Biological Sciences Royal Holloway University of London Egham Surrey UK

Université Paris Saclay INRAE URGI Versailles 78026 France

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