Aethionema arabicum genome annotation using PacBio full‐length transcripts provides a valuable resource for seed dormancy and Brassicaceae evolution research - INRAE - Institut national de recherche pour l’agriculture, l’alimentation et l’environnement Access content directly
Journal Articles Plant Journal Year : 2021

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

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 Isoseq 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-a 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 fulllength transcripts related to ABA-mediated seed dormancy discovered a conserved isoform of PIF6-b 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).
Fichier principal
Vignette du fichier
2021_Fernandez-Pozo_The Plant Journal.pdf (1.31 Mo) Télécharger le fichier
Origin : Publisher files allowed on an open archive
Licence : CC BY - Attribution

Dates and versions

hal-03135342 , version 1 (31-01-2023)

Licence

Attribution

Identifiers

Cite

Noe Fernandez‐pozo, Timo Metz, Jake Chandler, Lydia Gramzow, Zsuzsanna Mérai, et al.. Aethionema arabicum genome annotation using PacBio full‐length transcripts provides a valuable resource for seed dormancy and Brassicaceae evolution research. Plant Journal, 2021, pp.1-19. ⟨10.1111/tpj.15161⟩. ⟨hal-03135342⟩
73 View
32 Download

Altmetric

Share

Gmail Facebook X LinkedIn More