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

Noe Fernandez-Pozo*, Timo Metz, Jake O. Chandler, Lydia Gramzow, Zsuzsanna Mérai, Florian Maumus, Ortrun Mittelsten Scheid, Günter Theißen, M.E. Schranz, Gerhard Leubner-Metzger, Stefan A. Rensing

*Corresponding author for this work

Research output: Contribution to journalArticleAcademicpeer-review

Abstract

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).

Original languageEnglish
Number of pages19
JournalPlant Journal
DOIs
Publication statusE-pub ahead of print - 16 Jan 2021

Keywords

  • Aethionema arabicum
  • alternative splicing
  • Brassicaceae evolution
  • genome annotation
  • Iso-seq
  • seed germination
  • transcription factors

Fingerprint Dive into the research topics of 'Aethionema arabicum genome annotation using PacBio full-length transcripts provides a valuable resource for seed dormancy and Brassicaceae evolution research'. Together they form a unique fingerprint.

Cite this