Consistency of gene starts among Burkholderia genomes
Consistency of gene starts among Burkholderia genomes
复制标题
DOI：
10.1186/1471-2164-12-125
复制
发表时间：
2011-02-22
期刊：
影响因子：
4.4
通讯作者：
Wall, Michael E.
中科院分区：
文献类型：
--
作者：
Dunbar, John;Cohn, Judith D.;Wall, Michael E.
背景：同源基因间翻译起始位点位置的进化差异会对功能产生重大影响。分化可以改变编码蛋白的翻译速率、降解速率、亚细胞位置和功能。结果：现有的基因库基因图谱显示，伯克霍尔德菌基因组存在广泛的分化——53%基于基因库基因图谱的同源集具有不一致的基因起始位点。然而，大多数不一致似乎是基因调用错误。进化分歧是对只有17%的同源集合最合理的解释。修正Genbank基因图谱中可能的错误使起始不一致的同源集的百分比降低了68%，使可提取的上游基因间区域的同源集的百分比提高了32%，增加了基因间区域和预测蛋白的序列相似性，并增加了可识别信号肽的蛋白数量。结论：我们的发现突出了比较基因组学中一个新出现的问题：基因预测的个位数误差可能导致两位数百分比的不一致同源集。这项工作展示了一种简单的方法来评估和提高基因图谱的质量。
Background: Evolutionary divergence in the position of the translational start site among orthologous genes can have significant functional impacts. Divergence can alter the translation rate, degradation rate, subcellular location, and function of the encoded proteins.Results: Existing Genbank gene maps for Burkholderia genomes suggest that extensive divergence has occurred-53% of ortholog sets based on Genbank gene maps had inconsistent gene start sites. However, most of these inconsistencies appear to be gene-calling errors. Evolutionary divergence was the most plausible explanation for only 17% of the ortholog sets. Correcting probable errors in the Genbank gene maps decreased the percentage of ortholog sets with inconsistent starts by 68%, increased the percentage of ortholog sets with extractable upstream intergenic regions by 32%, increased the sequence similarity of intergenic regions and predicted proteins, and increased the number of proteins with identifiable signal peptides.Conclusions: Our findings highlight an emerging problem in comparative genomics: single-digit percent errors in gene predictions can lead to double-digit percentages of inconsistent ortholog sets. The work demonstrates a simple approach to evaluate and improve the quality of gene maps.