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首页> 美国卫生研究院文献>PLoS Clinical Trials >Strategies to Avoid Wrongly Labelled Genomes Using as Example the Detected Wrong Taxonomic Affiliation for Aeromonas Genomes in the GenBank Database
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Strategies to Avoid Wrongly Labelled Genomes Using as Example the Detected Wrong Taxonomic Affiliation for Aeromonas Genomes in the GenBank Database

机译：避免使用错误标记的基因组的策略例如以GenBank数据库中检测到的气单胞菌基因组的错误分类从属关系为例

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Around 27,000 prokaryote genomes are presently deposited in the Genome database of GenBank at the National Center for Biotechnology Information (NCBI) and this number is exponentially growing. However, it is not known how many of these genomes correspond correctly to their designated taxon. The taxonomic affiliation of 44 Aeromonas genomes (only five of these are type strains) deposited at the NCBI was determined by a multilocus phylogenetic analysis (MLPA) and by pairwise average nucleotide identity (ANI). Discordant results in relation to taxa assignation were found for 14 (35.9%) of the 39 non-type strain genomes on the basis of both the MLPA and ANI results. Data presented in this study also demonstrated that if the genome of the type strain is not available, a genome of the same species correctly identified can be used as a reference for ANI calculations. Of the three ANI calculating tools compared (ANI calculator, EzGenome and JSpecies), EzGenome and JSpecies provided very similar results. However, the ANI calculator provided higher intra- and inter-species values than the other two tools (differences within the ranges 0.06–0.82% and 0.92–3.38%, respectively). Nevertheless each of these tools produced the same species classification for the studied Aeromonas genomes. To avoid possible misinterpretations with the ANI calculator, particularly when values are at the borderline of the 95% cutoff, one of the other calculation tools (EzGenome or JSpecies) should be used in combination. It is recommended that once a genome sequence is obtained the correct taxonomic affiliation is verified using ANI or a MLPA before it is submitted to the NCBI and that researchers should amend the existing taxonomic errors present in databases.
机译：目前，大约有27,000个原核生物基因组被保存在美国国家生物技术信息中心（NCBI）的GenBank的基因组数据库中，并且这个数字呈指数增长。但是，尚不清楚这些基因组中有多少正确地与其指定的分类单元相对应。通过多基因组系统发育分析（MLPA）和成对平均核苷酸同一性（ANI）确定了存放在NCBI上的44种气单胞菌基因组的分类学隶属关系（其中只有五个是类型菌株）。根据MLPA和ANI结果，在39个非类型菌株基因组中发现了14个（35.9％）与分类单元分配相关的不一致结果。这项研究中提供的数据还表明，如果无法获得该类型菌株的基因组，则可以正确识别出相同物种的基因组作为ANI计算的参考。在比较的三种ANI计算工具（ANI计算器，EzGenome和JSpecies）中，EzGenome和JSpecies提供了非常相似的结果。但是，ANI计算器提供的物种内和物种间值高于其他两个工具（差异分别在0.06-0.82％和0.92-3.38％之间）。然而，对于所研究的气单胞菌基因组，每种工具都产生了相同的物种分类。为避免使用ANI计算器可能造成的误解，尤其是当值位于95％临界值的边界时，应结合使用其他一种计算工具（EzGenome或JSpecies）。建议在获得基因组序列后，使用ANI或MLPA验证正确的分类学隶属关系，然后再将其提交给NCBI，研究人员应修改数据库中存在的现有分类学错误。

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