title: Improved annotation with de novo transcriptome assembly in four social amoeba species.
abstract: Annotation of gene models and transcripts is a fundamental step in genome sequencing projects. Often this is performed with automated prediction pipelines, which can miss complex and atypical genes or transcripts. RNA sequencing (RNA-seq) data can aid the annotation with empirical data. Here we present de novo transcriptome assemblies generated from RNA-seq data in four Dictyostelid species: D. discoideum, P. pallidum, D. fasciculatum and D. lacteum. The assemblies were incorporated with existing gene models to determine corrections and improvement on a whole-genome scale. This is the first time this has been performed in these eukaryotic species.
  
  
  
  An initial de novo transcriptome assembly was generated by Trinity for each species and then refined with Program to Assemble Spliced Alignments (PASA). The completeness and quality were assessed with the Benchmarking Universal Single-Copy Orthologs (BUSCO) and Transrate tools at each stage of the assemblies. The final datasets of 11,315-12,849 transcripts contained 5,610-7,712 updates and corrections to >50% of existing gene models including changes to hundreds or thousands of protein products. Putative novel genes are also identified and alternative splice isoforms were observed for the first time in P. pallidum, D. lacteum and D. fasciculatum.
  
  
  
  In taking a whole transcriptome approach to genome annotation with empirical data we have been able to enrich the annotations of four existing genome sequencing projects. In doing so we have identified updates to the majority of the gene annotations across all four species under study and found putative novel genes and transcripts which could be worthy for follow-up. The new transcriptome data we present here will be a valuable resource for genome curators in the Dictyostelia and we propose this effective methodology for use in other genome annotation projects.
authors.affiliation: Computational Biology, School of Life Sciences, University of Dundee, Dow Street, Dundee, UK.|Cell and Development Biology, School of Life Sciences, University of Dundee, Dow Street, Dundee, UK.
authors.forename: Reema
authors.initials: R
authors.lastname: Singh
authors.affiliation: Cell and Development Biology, School of Life Sciences, University of Dundee, Dow Street, Dundee, UK.
authors.forename: Hajara M
authors.initials: HM
authors.lastname: Lawal
authors.affiliation: Cell and Development Biology, School of Life Sciences, University of Dundee, Dow Street, Dundee, UK.
authors.forename: Christina
authors.initials: C
authors.lastname: Schilde
authors.affiliation: Institute of Biochemistry I, Medical Faculty, University of Cologne, D-50931, Cologne, Germany.|Leibniz Institute of Freshwater Ecology and Inland Fisheries (IGB), Müggelseedamm 301, D-12587, Berlin, Germany.
authors.forename: Gernot
authors.initials: G
authors.lastname: Glöckner
authors.affiliation: Computational Biology, School of Life Sciences, University of Dundee, Dow Street, Dundee, UK.
authors.forename: Geoffrey J
authors.initials: GJ
authors.lastname: Barton
authors.affiliation: Cell and Development Biology, School of Life Sciences, University of Dundee, Dow Street, Dundee, UK.
authors.forename: Pauline
authors.initials: P
authors.lastname: Schaap
authors.affiliation: Computational Biology, School of Life Sciences, University of Dundee, Dow Street, Dundee, UK. c.cole@dundee.ac.uk.
authors.forename: Christian
authors.identifier: 0000-0002-2560-2484
authors.initials: C
authors.lastname: Cole
mesh_terms: D000656:Amoeba / Q000145:classification / Q000235:genetics*; D003001:Cloning, Molecular; D019295:Computational Biology / Q000379:methods; D020869:Gene Expression Profiling; D016678:Genome; D023281:Genomics / Q000379:methods; D059014:High-Throughput Nucleotide Sequencing; D058977:Molecular Sequence Annotation; D015203:Reproducibility of Results; D059467:Transcriptome
keywords: De novo; Dictyostelia; RNA-seq; Social amoeba; Transcriptome assembly