Ustilago maydis transcript features identified through full-length cDNA analysis
Ustilago maydis transcript features identified through full-length cDNA analysis
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DOI：
10.1007/s00438-011-0634-z
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发表时间：
2011-08-01
影响因子：
3.1
通讯作者：
Saville, Barry J.
中科院分区：
文献类型：
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作者：
Doyle, Colleen E.;Donaldson, Michael E.;Saville, Barry J.
玉米黑粉菌是研究担子菌类生物营养型植物病原菌的模式菌。为了进一步注释其基因组，我们利用12，943个全长cDNA序列构建了U.玉米的基因对克隆的子集进行测序以确定完整的cDNA序列。这些和原始的EST被组装成重叠群，占预测U的3，058，或45%。玉米的基因新的测序允许确认2，842个基因模型，其中690个包含内含子。全长cDNA克隆序列的使用确保了非翻译区与开放阅读框（ORF）物理连接，而不仅仅是在转录起始点的上游对齐。鉴定的序列特征包括：（1）超过500个潜在的短上游ORF，（2）95个需要进一步注释的基因模型，（3）一个新的潜在ORF，（4）不同基因区域中不同的GC含量，（5）用于翻译起始的WebLogo基序，（6）UTR长度与cDNA文库中的转录本表达和基因功能类别的相关性，（7）天然反义转录物和UTR长度之间的关系，不同于酿酒酵母的UTR长度，（8）DNA复制和转录控制之间的潜在关系，和（9）关于U.玉米粉
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.