title: Improving the Annotation of Arabidopsis lyrata Using RNA-Seq Data.
abstract: 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.
authors.affiliation: Department of Plant Developmental Biology, Max Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, 50829, Cologne, Germany.
authors.forename: Vimal
authors.initials: V
authors.lastname: Rawat
authors.affiliation: Department of Plant Breeding and Genetics, Max Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, 50829, Cologne, Germany; Department of Genetics, Cairo University, 12613, Giza, Egypt.
authors.forename: Ahmed
authors.initials: A
authors.lastname: Abdelsamad
authors.affiliation: Department of Plant Breeding and Genetics, Max Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, 50829, Cologne, Germany.
authors.forename: Björn
authors.initials: B
authors.lastname: Pietzenuk
authors.affiliation: Department for Molecular Biology, Max Planck Institute for Developmental Biology, Spemannstrasse 35-39, 72076, Tübingen, Germany.
authors.forename: Danelle K
authors.initials: DK
authors.lastname: Seymour
authors.affiliation: Department for Molecular Biology, Max Planck Institute for Developmental Biology, Spemannstrasse 35-39, 72076, Tübingen, Germany.
authors.forename: Daniel
authors.initials: D
authors.lastname: Koenig
authors.affiliation: Department for Molecular Biology, Max Planck Institute for Developmental Biology, Spemannstrasse 35-39, 72076, Tübingen, Germany.
authors.forename: Detlef
authors.initials: D
authors.lastname: Weigel
authors.affiliation: Department of Plant Breeding and Genetics, Max Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, 50829, Cologne, Germany.
authors.forename: Ales
authors.initials: A
authors.lastname: Pecinka
authors.affiliation: Department of Plant Developmental Biology, Max Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, 50829, Cologne, Germany.
authors.forename: Korbinian
authors.initials: K
authors.lastname: Schneeberger
mesh_terms: D017398:Alternative Splicing; D017360:Arabidopsis / Q000235:genetics*; D029681:Arabidopsis Proteins / Q000235:genetics*; D019607:Brassicaceae / Q000235:genetics; D004251:DNA Transposable Elements; D017343:Genes, Plant; D008957:Models, Genetic; D058977:Molecular Sequence Annotation / Q000379:methods; D059467:Transcriptome
chemical_list: D029681:Arabidopsis Proteins; D004251:DNA Transposable Elements