A large number of novel coding small open reading frames in the intergenic regions of the Arabidopsis thaliana genome are transcribed and/or under purifying selection
A large number of novel coding small open reading frames in the intergenic regions of the Arabidopsis thaliana genome are transcribed and/or under purifying selection
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DOI：
10.1101/gr.5836207
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发表时间：
2007-05-01
期刊：
影响因子：
7
通讯作者：
Shiu, Shin-Han
中科院分区：
文献类型：
--
作者：
Hanada, Kousuke;Zhang, Xu;Shiu, Shin-Han
大规模cDNA测序项目和平铺阵列研究揭示了许多未注释基因的存在。对于蛋白质编码基因，由于预测算法的保守性，小的编码序列可能无法被基因发现者识别。在这项研究中，我们通过一种简单的基因寻找方法（编码指数，CI），基于在大多数编码序列中发现的核苷酸组成偏差，确定了具有高编码潜力的小开放阅读框（sorf）。将该方法应用于18个拟南芥和84个酵母sORF基因，在蛋白水平上有表达的证据，预测准确率为100%。在拟南螺旋体基因组中，我们鉴定出7159个sorf可能是编码序列（编码sorf）， CI测量为1%的假阳性率。为了确定这些编码sORF是否是功能基因的一部分，我们评估了每个编码sORF的转录或进化保护证据。在5%的假阳性率下，我们发现2996个编码sorf可能在拟南拟南植物平铺阵列数据的至少一种实验条件下表达。此外，利用完整或部分基因组序列分析了拟南芥sORF在拟南芥内部或与5种植物之间的进化保守性。在3997个易于识别同源序列的编码sorf中，2376个以1%的假阳性率进行了纯化选择。在剔除与已知转座因子相似的编码sorf和可能缺失已知基因外显子的sorf后，剩余的3241个编码sorf可能属于拟南拟南植物基因组中新的编码基因，这些sorf要么有转录证据，要么有纯化选择证据。
Large-scale cDNA sequencing projects and tiling array studies have revealed the presence of many unannotated genes. For protein coding genes, small coding sequences may not be identified by gene finders because of the conservative nature of prediction algorithms. In this study, we identified small open reading frames (sORFs) with high coding potential by a simple gene finding method (Coding Index, CI) based on the nucleotide composition bias found in most coding sequences. Applying this method to 18 Arabidopsis thaliana and 84 yeast sORF genes with evidence of expression at the protein level gives 100% accurate prediction. In the A. thaliana genome, we identified 7159 sORFs that are likely coding sequences (coding sORFs) with the CI measure at the 1% false-positive rate. To determine if these coding sORFs are parts of functional genes, we evaluated each coding sORF for evidence of transcription or evolutionary conservation. At the 5% false-positive rate, we found that 2996 coding sORFs are likely expressed in at least one experimental condition of the A. thaliana tiling array data. In addition, the evolutionary conservation of each A. thaliana sORF was examined within A. thaliana or between A. thaliana and five plants with complete or partial genome sequences. In 3997 coding sORFs with readily identifiable homologous sequences, 2376 are subject to purifying selection at the 1% false-positive rate. After eliminating coding sORFs with similarity to known transposable elements and those that are likely missing exons of known genes, the remaining 3241 coding sORFs with either evidence of transcription or purifying selection likely belong to novel coding genes in the A. thaliana genome.