Gene fragmentation in bacterial draft genomes: extent, consequences and mitigation.
Gene fragmentation in bacterial draft genomes: extent, consequences and mitigation.
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DOI：
10.1186/1471-2164-13-14
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发表时间：
2012-01-10
期刊：
影响因子：
4.4
通讯作者：
Currie CR
中科院分区：
文献类型：
--
作者：
Klassen JL;Currie CR
基因组测序方面正在进行的技术进步使细菌基因组能够以越来越低的成本进行测序。然而，几乎所有这些新技术都会降低基因组质量，主要是因为它们相对较短的阅读长度无法连接某些基因组区域，例如那些包含重复序列的区域。预测的开放阅读框架(ORF)的片段化是这种质量下降的一个可能的后果。在这项研究中，我们量化了草案微生物基因组中的ORF片段及其对注释效率的影响，并提出了一个解决方案来改善这一问题。GenBank对草稿质量基因组的调查显示，在一些基因组中，片断的ORF占预测ORF的80%，并且片段化的增加与基因组组装质量的降低相关。在对25个链霉菌基因组的更全面的分析中，片段尤其丰富在某些具有重复的多模块结构的蛋白质类别中，如聚酮合成酶、非核糖体多肽合成酶和丝氨酸/苏氨酸激酶。总体而言，基因组片段化增加与假阴性Pfam和COG注释率增加以及假阳性KEGG注释率增加相关。利用片段ORF在相关基因组中的同源序列连接片断ORF，可以改善KEGG的假阳性注释率。虽然这一策略成功地连接了某些基因组中46%的总ORF片段，但其敏感性似乎在很大程度上取决于对特定分类群可变基因组的采样深度。草案中的微生物基因组包含许多开放阅读框架片段。如果这些基因对应于相同的基因，它们特别有可能混淆比较基因含量分析。鉴于我们的发现，以及微生物草稿高质量基因组数量的快速增加，我们认为，在设计比较基因组项目时，考虑到基因片断及其相关的偏见是重要的。
Ongoing technological advances in genome sequencing are allowing bacterial genomes to be sequenced at ever-lower cost. However, nearly all of these new techniques concomitantly decrease genome quality, primarily due to the inability of their relatively short read lengths to bridge certain genomic regions, e.g., those containing repeats. Fragmentation of predicted open reading frames (ORFs) is one possible consequence of this decreased quality. In this study we quantify ORF fragmentation in draft microbial genomes and its effect on annotation efficacy, and we propose a solution to ameliorate this problem. A survey of draft-quality genomes in GenBank revealed that fragmented ORFs comprised > 80% of the predicted ORFs in some genomes, and that increased fragmentation correlated with decreased genome assembly quality. In a more thorough analysis of 25 Streptomyces genomes, fragmentation was especially enriched in some protein classes with repeating, multi-modular structures such as polyketide synthases, non-ribosomal peptide synthetases and serine/threonine kinases. Overall, increased genome fragmentation correlated with increased false-negative Pfam and COG annotation rates and increased false-positive KEGG annotation rates. The false-positive KEGG annotation rate could be ameliorated by linking fragmented ORFs using their orthologs in related genomes. Whereas this strategy successfully linked up to 46% of the total ORF fragments in some genomes, its sensitivity appeared to depend heavily on the depth of sampling of a particular taxon's variable genome. Draft microbial genomes contain many ORF fragments. Where these correspond to the same gene they have particular potential to confound comparative gene content analyses. Given our findings, and the rapid increase in the number of microbial draft quality genomes, we suggest that accounting for gene fragmentation and its associated biases is important when designing comparative genomic projects.
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DOI：
10.1093/bioinformatics/btq365
发表时间：
2010-09-15
期刊：
Bioinformatics (Oxford, England)
影响因子：
--
作者：
Balzer S;Malde K;Lanzén A;Sharma A;Jonassen I
通讯作者：
Jonassen I
影响因子：
3.2
作者：
Konstantinidis, KT;Tiedje, JM
通讯作者：
Tiedje, JM
影响因子：
3.2
作者：
Ohnishi, Yasuo;Ishikawa, Jun;Horinouchi, Sueharu
通讯作者：
Horinouchi, Sueharu
影响因子：
3.2
作者：
Song, Ju Yeon;Jeong, Haeyoung;Kim, Jihyun F.
通讯作者：
Kim, Jihyun F.
影响因子：
3.2
作者：
Fan, Longjiang;Liu, Yun;Cai, Daguang
通讯作者：
Cai, Daguang