Exploiting single-molecule transcript sequencing for eukaryotic gene prediction.
We develop a method to predict and validate gene models using PacBio single-molecule, real-time (SMRT) cDNA reads. Ninety-eight percent of full-insert SMRT reads span complete open reading frames. Gene model validation using SMRT reads is developed as automated process. Optimized training and prediction settings and mRNA-seq noise reduction of assisting Illumina reads results in increased gene prediction sensitivity and precision. Additionally, we present an improved gene set for sugar beet (Beta vulgaris) and the first genome-wide gene set for spinach (Spinacia oleracea). The workflow and guidelines are a valuable resource to obtain comprehensive gene sets for newly sequenced genomes of non-model eukaryotes.
Max Planck Institute for Molecular Genetics, Berlin, Germany.|Centre for Genomic Regulation (CRG), Barcelona, Spain.|Universitat Pompeu Fabra (UPF), Barcelona, Spain.
André E
AE
Minoche
Max Planck Institute for Molecular Genetics, Berlin, Germany.|Centre for Genomic Regulation (CRG), Barcelona, Spain.|Universitat Pompeu Fabra (UPF), Barcelona, Spain.|University of Natural Resources and Life Sciences (BOKU), Muthgasse 18, 1190, Vienna, Austria.
Juliane C
JC
Dohm
Department of Biology/Center for Biotechnology, Bielefeld University, 33615, Bielefeld, Germany.
Jessica
J
Schneider
Department of Biology/Center for Biotechnology, Bielefeld University, 33615, Bielefeld, Germany.
Daniela
D
Holtgräwe
Department of Biology/Center for Biotechnology, Bielefeld University, 33615, Bielefeld, Germany.
Prisca
P
Viehöver
Centre for Genomic Regulation (CRG), Barcelona, Spain.|Universitat Pompeu Fabra (UPF), Barcelona, Spain.
Magda
M
Montfort
Department of Biology/Center for Biotechnology, Bielefeld University, 33615, Bielefeld, Germany.
Thomas Rosleff
TR
Sörensen
Department of Biology/Center for Biotechnology, Bielefeld University, 33615, Bielefeld, Germany. bernd.weisshaar@uni-bielefeld.de.
Bernd
B
Weisshaar
Max Planck Institute for Molecular Genetics, Berlin, Germany. heinz.himmelbauer@boku.ac.at.|Centre for Genomic Regulation (CRG), Barcelona, Spain. heinz.himmelbauer@boku.ac.at.|Universitat Pompeu Fabra (UPF), Barcelona, Spain. heinz.himmelbauer@boku.ac.at.|University of Natural Resources and Life Sciences (BOKU), Muthgasse 18, 1190, Vienna, Austria. heinz.himmelbauer@boku.ac.at.
Heinz
H
Himmelbauer
D027461:Beta vulgaris / Q000235:genetics; D018076:DNA, Complementary / Q000737:chemistry; D020869:Gene Expression Profiling / Q000379:methods*; D017343:Genes, Plant; D008969:Molecular Sequence Data; D017423:Sequence Analysis, RNA / Q000379:methods*; D018724:Spinacia oleracea / Q000235:genetics
D018076:DNA, Complementary