[论文解读] How and where to look for tRNAs in Metazoan mitochondrial genomes, and what you might find when you get there

David A. Morrison|arXiv (Cornell University)|Jan 21, 2010

Genomics and Phylogenetic Studies参考文献 46被引用 7

一句话总结

本研究通过比较分析ARWEN与DOGMA程序在后生动物线粒体基因组中tRNA检测的表现，发现没有单一工具能捕获所有tRNA基因，因为其存在互补性的假阴性。研究揭示了公共数据库中广泛存在的注释错误，并支持关于双重功能基因组区域及缺乏D-和T-环结构的tRNA的新假说。

ABSTRACT

The ability to locate and annotate mitochondrial genes is an important practical issue, given the rapidly increasing number of mitogenomes appearing in the public databases. Unfortunately, tRNA genes in Metazoan mitochondria have proved to be problematic because they often vary in number (genes missing or duplicated) and also in the secondary structure of the transcribed tRNAs (T or D arms missing). I have performed a series of comparative analyses of the tRNA genes of a broad range of Metazoan mitogenomes in order to address this issue. I conclude that no single computer program is necessarily capable of finding all of the tRNA genes in any given mitogenome, and that use of both the ARWEN and DOGMA programs is sometimes necessary because they produce complementary false negatives. There are apparently a very large number of erroneous annotations in the databased mitogenome sequences, including missed genes, wrongly annotated locations, false complements, and inconsistent criteria for assigning the 5' and 3' boundaries; and I have listed many of these. The extent of overlap between genes is often greatly exaggerated due to inconsistent annotations, although notable overlaps involving tRNAs are apparently real. Finally, three novel hypotheses were examined and found to have support from the comparative analyses: (1) some organisms have mitogenomic locations that simultaneously code for multiple tRNAs; (2) some organisms have mitogenomic locations that simultaneously code for tRNAs and proteins (but not rRNAs); and (3) one group of nematodes has several genes that code for tRNAs lacking both the D and T arms.

研究动机与目标

• 解决公共线粒体基因组数据库中tRNA基因注释不一致和不准确的问题。
• 评估现有计算工具（ARWEN与DOGMA）在后生动物线粒体基因组中tRNA检测的可靠性与局限性。
• 识别tRNA注释中的系统性错误，包括遗漏基因、边界错误及错误互补序列。
• 研究新型基因组排列的生物学合理性，例如编码于重叠或双重功能区域的tRNA。
• 评估特定线虫类群中是否存在缺乏D-臂和T-臂结构的tRNA。

提出的方法

• 在广泛的后生动物线粒体基因组中进行比较分析，以评估tRNA基因检测的准确性。
• 使用ARWEN与DOGMA程序预测tRNA基因，并比较其输出结果以识别互补性的假阴性。
• 分析预测tRNA的二级结构，检测D-或T-环的缺失，特别是在线虫中。
• 评估基因之间的基因组重叠，重点关注tRNA的位置与边界，以评估注释的一致性。
• 将预测的tRNA位置与已发表的注释进行交叉比对，以识别差异，如5′/3′边界错误与错误互补序列。
• 验证三项新假说：(1) 单一位点编码双重tRNA，(2) tRNA与蛋白质共定位，(3) 线虫中存在同时缺乏D-臂与T-臂结构的tRNA。

实验结果

研究问题

• RQ1 为何当前的tRNA检测工具（如ARWEN与DOGMA）无法在后生动物线粒体基因组中识别出所有tRNA基因？
• RQ2 公共数据库中tRNA基因注释的不准确程度如何？最普遍的错误类型是什么？
• RQ3 后生动物线粒体基因组中是否存在同时编码多个tRNA或tRNA与蛋白质的基因组区域？
• RQ4 后生动物线粒体中是否存在缺乏D-臂与T-臂结构的tRNA基因？若存在，出现在哪些分类群中？
• RQ5 不一致的边界分配与互补注释如何影响线粒体基因组中基因重叠的解释？

主要发现

• 在后生动物线粒体基因组中，没有单一的tRNA检测程序（ARWEN或DOGMA）能识别出所有tRNA基因，因为两者存在互补性的假阴性。
• 公共数据库中大量tRNA注释存在错误，包括遗漏基因、5′/3′边界错误、错误互补序列，以及边界分配标准不一致。
• 由于注释不一致，基因重叠常被夸大，尽管部分tRNA相关的重叠在生物学上是真实的。
• 本研究为某些后生动物类群中同时编码多个tRNA的基因组区域的存在提供了支持。
• 证据支持在特定线虫类群中存在缺乏D-和T-臂结构的tRNA基因。
• 本研究识别并列出了多个线粒体基因组中的具体注释错误，强调了人工校对与自动化预测交叉验证的必要性。