Ustilago maydis transcript features identified through full-length cDNA analysis
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- 作者：Colleen E. Doyle (1)
Michael E. Donaldson (1)
Erin N. Morrison (1)
Barry J. Saville (12) barrysaville@trentu.ca - 关键词：Ustilago maydis – ; Transcript structure – ; Full ; length cDNA sequencing – ; Untranslated regions – ; Promoter regions – ; Poly(A) addition signals – ; uORFs – ; Gene model annotation
- 刊名：Molecular Genetics and Genomics
- 出版时间：August 2011
- 出版年：2011
- 期刊代码：180_1617-4615
- 类别：bio
- 卷：286
- 期：2
- 页码：143-159
- 数据来源：sp
摘要
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.