Improving the Annotation of Arabidopsis lyrata Using RNA-Seq Data

PLoS One. 2015 Sep 18;10(9):e0137391. doi: 10.1371/journal.pone.0137391. eCollection 2015.


Gene model annotations are important community resources that ensure comparability and reproducibility of analyses and are typically the first step for functional annotation of genomic regions. Without up-to-date genome annotations, genome sequences cannot be used to maximum advantage. It is therefore essential to regularly update gene annotations by integrating the latest information to guarantee that reference annotations can remain a common basis for various types of analyses. Here, we report an improvement of the Arabidopsis lyrata gene annotation using extensive RNA-seq data. This new annotation consists of 31,132 protein coding gene models in addition to 2,089 genes with high similarity to transposable elements. Overall, ~87% of the gene models are corroborated by evidence of expression and 2,235 of these models feature multiple transcripts. Our updated gene annotation corrects hundreds of incorrectly split or merged gene models in the original annotation, and as a result the identification of alternative splicing events and differential isoform usage are vastly improved.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Alternative Splicing
  • Arabidopsis / genetics*
  • Arabidopsis Proteins / genetics*
  • Brassicaceae / genetics
  • DNA Transposable Elements
  • Genes, Plant
  • Models, Genetic
  • Molecular Sequence Annotation* / methods
  • Transcriptome


  • Arabidopsis Proteins
  • DNA Transposable Elements

Associated data

  • BioProject/PRJEB6701

Grant support

This work was funded by German Research Foundation ( grant AP1829-2 to AP. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.