title: Concerted action of the new Genomic Peptide Finder and AUGUSTUS allows for automated proteogenomic annotation of the Chlamydomonas reinhardtii genome.
abstract: The use and development of post-genomic tools naturally depends on large-scale genome sequencing projects. The usefulness of post-genomic applications is dependent on the accuracy of genome annotations, for which the correct identification of intron-exon borders in complex genomes of eukaryotic organisms is often an error-prone task. Although automated algorithms for predicting intron-exon structures are available, supporting exon evidence is necessary to achieve comprehensive genome annotation. Besides cDNA and EST support, peptides identified via MS/MS can be used as extrinsic evidence in a proteogenomic approach. We describe an improved version of the Genomic Peptide Finder (GPF), which aligns de novo predicted amino acid sequences to the genomic DNA sequence of an organism while correcting for peptide sequencing errors and accounting for the possibility of splicing. We have coupled GPF and the gene finding program AUGUSTUS in a way that provides automatic structural annotations of the Chlamydomonas reinhardtii genome, using highly unbiased GPF evidence. A comparison of the AUGUSTUS gene set incorporating GPF evidence to the standard JGI FM4 (Filtered Models 4) gene set reveals 932 GPF peptides that are not contained in the Filtered Models 4 gene set. Furthermore, the GPF evidence improved the AUGUSTUS gene models by altering 65 gene models and adding three previously unidentified genes.
authors: Institute of Plant Biology and Biotechnology, University of Münster, Münster, Germany.
authors: Michael
authors: M
authors: Specht
authors: Mario
authors: M
authors: Stanke
authors: Mia
authors: M
authors: Terashima
authors: Bianca
authors: B
authors: Naumann-Busch
authors: Ingrid
authors: I
authors: Janssen
authors: Ricarda
authors: R
authors: Höhner
authors: Erik F Y
authors: EF
authors: Hom
authors: Chun
authors: C
authors: Liang
authors: Michael
authors: M
authors: Hippler
mesh_terms: D000465:Algorithms; D000595:Amino Acid Sequence; D001483:Base Sequence; D016825:Chlamydomonas reinhardtii / Q000235:genetics* / Q000378:metabolism*; D019295:Computational Biology / Q000379:methods*; D030541:Databases, Genetic; D005091:Exons / Q000235:genetics; D018745:Genome, Plant / Q000235:genetics; D023281:Genomics / Q000379:methods*; D007438:Introns / Q000235:genetics; D013058:Mass Spectrometry; D008969:Molecular Sequence Data; D010455:Peptides / Q000032:analysis / Q000235:genetics; D010940:Plant Proteins / Q000032:analysis / Q000235:genetics; D040901:Proteomics / Q000379:methods*; D022821:RNA Splice Sites / Q000235:genetics; D017386:Sequence Homology, Amino Acid; D012984:Software
chemical_list: D010455:Peptides; D010940:Plant Proteins; D022821:RNA Splice Sites