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.

Transcriptome analysis of smut fungi reveals widespread intergenic transcription and conserved antisense transcript expression

“…In identifying potential effector proteins, it is critical to correctly delineate 5’UTRs. The 5’ UTR data presented here is consistent with earlier 5’ UTR determinations from full-length cDNA analyses [14]; however, it is possible that the data set is still not comprehensive. If this was the case then some starts of transcription may have been missed and this would mean that some effector genes may not have been recognized.…”

“…Earlier expressed-sequence tag (EST) library investigations [10–13] identified novel protein-coding genes, cell-type-specific gene expression profiles, and alternative splicing. They also improved existing gene structure annotations and determined 5’ and 3’ UTR lengths [10, 14]. Together, these transcriptome-focused analyses substantially improved the initial annotation of protein-coding genes in U. maydis , providing an improved dataset for functional analysis.…”

Ustilago maydis natural antisense transcript expression alters mRNA stability and pathogenesis

“…Annotation of the U. maydis genome established this fungus as the model for basidiomycete biotrophic plant pathogenesis (Kämper et al ., ). Analyses of U. maydis cDNA libraries confirmed and corrected gene models, and led to the identification of natural antisense transcripts (NATs) to 247 non‐redundant ORFs (Ho et al ., ; Doyle et al ., ; Morrison et al ., ). In the current study, cDNAs representing NATs were fully sequenced, enabling their annotation.…”

Global analyses of Ceratocystis cacaofunesta mitochondria: from genome to proteome

“…The S. cerevisiae mitochondrial proteome contains an estimated 1,000 proteins, of which 851 were identified using proteomic assays [34]. In N. crassa , proteomic studies have led to the identification of 438 mitochondrial proteins [35]. Proteomics has previously been used to illuminate central processes in phytopathogenic fungi [36,37].…”