Reinvestigation of the Saccharomyces cerevisiae genome annotation by comparison to the genome of a related fungus: Ashbya gossypii.
Reinvestigation of the Saccharomyces cerevisiae genome annotation by comparison to the genome of a related fungus: Ashbya gossypii.
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DOI：
10.1186/gb-2003-4-7-r45
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发表时间：
2003
期刊：
影响因子：
12.3
通讯作者：
Philippsen, Peter
中科院分区：
文献类型：
--
作者：
Brachat, Sophie;Dietrich, Fred S;Voegeli, Sylvia;Zhang, Zhihong;Stuart, Larissa;Lerch, Anita;Gates, Krista;Gaffney, Tom;Philippsen, Peter
虽然，S.尽管酿酒酵母基因组被认为是最精确测序和注释的真核生物基因组之一，但与棉阿舒囊霉（Ashbya gossypii）（一种进化上相关的真菌）的完整序列和同线基因图谱的比较仍然有很大的益处。最近测序的丝状真菌Ashbya gossypii的基因组显示显着的相似性，芽殖酵母酿酒酵母的同源性和同线性（基因顺序的保护）的水平。因此，重新研究S.酿酒酵母基因组中的同线区域，导致改进的注释。我们已经确定了23个新的S。酿酒酵母开放阅读框（ORF）作为A. gossypii基因;除了一个之外，所有同源物都存在于包括人类在内的其他真核生物中。其他比较鉴定了13个被忽略的内含子，并提出了69个潜在的序列校正，导致ORF延伸或ORF融合，与同线A的同源性提高。棉的同源物在拟议的更正中，25项已通过重新排序进行了测试和确认。此外，近1,000个S.酿酒酵母ORF，目前注释为假设的，发现于A. gossypii在同线位置，因此可以被认为是真实的基因。最后，我们建议超过400 S。酿酒酵母的ORF与S.在酿酒酵母中没有检测到同源物。棉应被视为假的。虽然，S.酿酒酵母基因组被正确地认为是最准确的测序和注释的真核生物基因组之一，我们已经表明，它仍然受益于比较的完整序列和同线基因图的A. gossypii，一种进化上相关的真菌。这种类型的方法将有力地支持更复杂的基因组，如人类和小鼠基因组的注释。
Although, the S. cerevisiae genome is rightly considered as one of the most accurately sequenced and annotated eukaryotic genomes, it still benefits substantially from comparison to the completed sequence and syntenic gene map of Ashbya gossypii, an evolutionarily related fungus. The recently sequenced genome of the filamentous fungus Ashbya gossypii revealed remarkable similarities to that of the budding yeast Saccharomyces cerevisiae both at the level of homology and synteny (conservation of gene order). Thus, it became possible to reinvestigate the S. cerevisiae genome in the syntenic regions leading to an improved annotation. We have identified 23 novel S. cerevisiae open reading frames (ORFs) as syntenic homologs of A. gossypii genes; for all but one, homologs are present in other eukaryotes including humans. Other comparisons identified 13 overlooked introns and suggested 69 potential sequence corrections resulting in ORF extensions or ORF fusions with improved homology to the syntenic A. gossypii homologs. Of the proposed corrections, 25 were tested and confirmed by resequencing. In addition, homologs of nearly 1,000 S. cerevisiae ORFs, presently annotated as hypothetical, were found in A. gossypii at syntenic positions and can therefore be considered as authentic genes. Finally, we suggest that over 400 S. cerevisiae ORFs that overlap other ORFs in S. cerevisiae and for which no homolog can be detected in A. gossypii should be regarded as spurious. Although, the S. cerevisiae genome is rightly considered as one of the most accurately sequenced and annotated eukaryotic genomes, we have shown that it still benefits substantially from comparison to the completed sequence and syntenic gene map of A. gossypii, an evolutionarily related fungus. This type of approach will strongly support the annotation of more complex genomes such as the human and murine genomes.