title: Ustilago maydis transcript features identified through full-length cDNA analysis.
abstract: Ustilago maydis is the model for investigating basidiomycete biotrophic plant pathogens. To further the annotation of its genome, 12,943 full-length cDNA sequences were used to construct databases for the promoter and untranslated regions of U. maydis genes. A subset of clones was sequenced to determine full cDNA sequences. These and the original ESTs were assembled into contigs representing 3,058, or 45%, of the predicted U. maydis genes. The new sequencing allowed the confirmation of 2,842 gene models, 690 of which contain an intron. The use of full-length cDNA clone sequences ensured that untranslated regions were physically linked to the open reading frames (ORFs), not merely aligned upstream of the start of transcription. Identified sequence features include: (1) over 500 potential short upstream ORFs, (2) 95 gene models that require further annotation, (3) one new potential ORF, (4) varying GC content in different gene regions, (5) a WebLogo motif for the start of translation, (6) the correlation of UTR length with transcript representation in cDNA libraries and with gene function categories, (7) a relationship between natural antisense transcripts and UTR length that differs from that of Saccharomyces cerevisiae, (8) a potential relationship between DNA replication and the control of transcription, and (9) new insights regarding mechanisms for the control of transcription and mRNA maturation in U. maydis.
authors.affiliation: Environmental and Life Sciences Graduate Program, Trent University, Peterborough, ON K9J 7B8, Canada.
authors.forename: Colleen E
authors.initials: CE
authors.lastname: Doyle
authors.forename: Michael E
authors.initials: ME
authors.lastname: Donaldson
authors.forename: Erin N
authors.initials: EN
authors.lastname: Morrison
authors.forename: Barry J
authors.initials: BJ
authors.lastname: Saville
mesh_terms: D001483:Base Sequence; D018076:DNA, Complementary / Q000235:genetics*; D030541:Databases, Genetic; D020224:Expressed Sequence Tags; D005800:Genes, Fungal / Q000235:genetics; D016681:Genome, Fungal; D007438:Introns; D008969:Molecular Sequence Data; D016366:Open Reading Frames; D014588:Ustilago / Q000235:genetics*
chemical_list: D018076:DNA, Complementary