Abstract
The number of fully sequenced genomes of yeasts is dramatically increasing but both structural and functional annotation quality are usually neglected, as most frequently based on automatic annotation transfer tools from reference genomes. RNA sequencing technologies offer the possibility to better characterize yeast transcriptomes and to correct or improve the prediction of mRNA, ncRNA, or miscellaneous RNA. We describe a computational approach to enhance structural annotation of yeast genomes based on RNA-Seq data exploitation. The proposed pipeline is primarily based on read mapping with TopHat2. Mapping outputs are then used for various applications such as: (1) validation of exon–exon junctions of predicted transcripts, (2) definition of new transcribed features, (3) prediction of 3' UTR, and (4) identification of extra features absent from the genome assembly. We strongly encourage curators to proceed to a manual validation and editing of the reference genome. Releasing genomes with high-quality annotation is an important issue, as they will be considered as references for further predictions.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
Similar content being viewed by others
References
Eilbeck K, Moore B, Holt C et al (2009) Quantitative measures for the management and comparison of annotated genomes. BMC Bioinformatics 10:67
Guida A, Lindstädt C, Maguire SL et al (2011) Using RNA-seq to determine the transcriptional landscape and the hypoxic response of the pathogenic yeast Candida parapsilosis. BMC Genomics 12:628
Dujon B, Sherman D, Fischer G et al (2004) Genome evolution in yeasts. Nature 430:35–44
Morin N, Calcas X, Devillers H et al (2014) Draft genome sequence of Rhodosporidium toruloides CECT1137, an oleaginous yeast of biotechnological interest. Genome Announc 2:e00641–14
Andrews S. FastQC: a quality control tool for high throughput sequence data http://www.bioinformatics.babraham.ac.uk/projects/fastqc/. Accessed 6 Feb 2015
Bolger AM, Lohse M, Usadel B (2014) Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30:2114–2120
Langmead B, Salzberg SL (2012) Fast gapped-read alignment with Bowtie 2. Nat Methods 9:357–359
Kim D, Pertea G, Trapnell C et al (2013) TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions. Genome Biol 14:R36
Trapnell C, Roberts A, Goff L et al (2012) Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks. Nat Protoc 7:562–578
Grabherr MG, Haas BJ, Yassour M et al (2011) Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nat Biotechnol 29:644–652
Li B, Dewey CN (2011) RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome. BMC Bioinformatics 12:323
Li H, Handsaker B, Wysoker A et al (2009) The sequence alignment/map format and SAMtools. Bioinformatics 25:2078–2079
Camacho C, Coulouris G, Avagyan V et al (2009) BLAST+: architecture and applications. BMC Bioinformatics 10:421
Rutherford K, Parkhill J, Crook J et al (2000) Artemis: sequence visualization and annotation. Bioinformatics 16:944–945
Stajich JE, Block D, Boulez K et al (2002) The Bioperl Toolkit: Perl modules for the life sciences. Genome Res 12:1611–1618
Core Team R (2013) R: a language and environment for statistical computing. R Foundation for Statistical Computing, Vienna
Engström PG, Steijger T, Sipos B et al (2013) Systematic evaluation of spliced alignment programs for RNA-seq data. Nat Methods 10:1185–1191
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2016 Springer Science+Business Media New York
About this protocol
Cite this protocol
Devillers, H., Morin, N., Neuvéglise, C. (2016). Enhancing Structural Annotation of Yeast Genomes with RNA-Seq Data. In: Devaux, F. (eds) Yeast Functional Genomics. Methods in Molecular Biology, vol 1361. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-3079-1_2
Download citation
DOI: https://doi.org/10.1007/978-1-4939-3079-1_2
Publisher Name: Humana Press, New York, NY
Print ISBN: 978-1-4939-3078-4
Online ISBN: 978-1-4939-3079-1
eBook Packages: Springer Protocols