Journal
GENOME BIOLOGY
Volume 16, Issue -, Pages -Publisher
BIOMED CENTRAL LTD
DOI: 10.1186/s13059-015-0729-7
Keywords
Eukaryotic gene prediction; Single-molecule real-time sequencing; mRNA-seq; Caryophyllales; Sugar beet; Spinach; Non-model species; Genome annotation
Funding
- Ministry of Education and Science (BMBF) [FKZ 0315962A, FKZ 0315962B]
- Bielefeld University
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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.
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