Augmented Annotation of the Schizosaccharomyces pombe Genome Reveals Additional Genes Required for Growth and Viability
Augmented Annotation of the Schizosaccharomyces pombe Genome Reveals Additional Genes Required for Growth and Viability
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DOI：
10.1534/genetics.110.123497
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发表时间：
2011-04-01
期刊：
影响因子：
3.3
通讯作者：
Miller, Crispin J.
中科院分区：
文献类型：
--
作者：
Bitton, Danny A.;Wood, Valerie;Miller, Crispin J.
基因组注释是计算预测和实验证据的综合。众所周知，小基因很难检测，因为用于识别它们的模式通常与偶然发生的事件无法区分，导致仅通过计算机分析识别的蛋白质编码基因的长度存在任意截止阈值。我们报告了对粟酒裂殖酵母基因组的系统重新评估，忽略了阈值。将完整的六帧翻译与蛋白质组数据集、Pfam 域数据库和其他六种真菌的基因组进行了比较。鉴定出 39 个新位点。 RTPCR 和 RNA-Seq 确认了 38 个位点的转录； 59 和 39 RACE 描述了 33 个新的基因结构。 14 个转录物的表达水平在减数分裂过程中发生波动。 10 个基因的翻译证据、支持 35 个预测的进化保护数据以及 ORF 删除后的不同表型（一种必需表型、四种缓慢生长表型、两种延迟分裂表型）表明所有 39 个预测都编码功能蛋白。粟酒裂殖酵母作为模式生物的流行表明，这种增强的注释将引起分子和细胞生物学的不同领域的兴趣，而该方法的通用性表明其广泛适用于其他基因组。
Genome annotation is a synthesis of computational prediction and experimental evidence. Small genes are notoriously difficult to detect because the patterns used to identify them are often indistinguishable from chance occurrences, leading to an arbitrary cutoff threshold for the length of a protein-coding gene identified solely by in silico analysis. We report a systematic reappraisal of the Schizosaccharomyces pombe genome that ignores thresholds. A complete six-frame translation was compared to a proteome data set, the Pfam domain database, and the genomes of six other fungi. Thirty-nine novel loci were identified. RTPCR and RNA-Seq confirmed transcription at 38 loci; 33 novel gene structures were delineated by 59 and 39 RACE. Expression levels of 14 transcripts fluctuated during meiosis. Translational evidence for 10 genes, evolutionary conservation data supporting 35 predictions, and distinct phenotypes upon ORF deletion (one essential, four slow-growth, two delayed-division phenotypes) suggest that all 39 predictions encode functional proteins. The popularity of S. pombe as a model organism suggests that this augmented annotation will be of interest in diverse areas of molecular and cellular biology, while the generality of the approach suggests widespread applicability to other genomes.