Additive methods for genomic signatures.
Additive methods for genomic signatures.
复制标题
DOI：
10.1186/s12859-016-1157-8
复制
发表时间：
2016-08-22
影响因子：
3
通讯作者：
Solis-Reyes S
中科院分区：
文献类型：
--
作者：
Karamichalis R;Kari L;Konstantinidis S;Kopecki S;Solis-Reyes S
探索基因组序列的混沌游戏表示（CGR）作为“基因组签名”（物种和基因组特异性）的潜力的研究表明，同一生物体的细胞核和细胞器DNA序列的CGR模式可能非常不同。虽然线粒体DNA序列的CGR可以充当基因组签名的假设对于NCBI GenBank序列数据库中可获得的所有测序的线粒体基因组的快照进行了验证，但据我们所知，迄今为止还不存在对核DNA序列的CGR的如此广泛的分析。我们分析了一个广泛的数据集，总计1.45千兆碱基对，来自42种不同生物体的核/类核基因组序列（nDNA），涵盖了所有主要的生命王国。我们的计算实验表明，两种不同来源的nDNA的CGR签名并不总是可以区分的，特别是如果它们来自密切相关的物种，如H。sapiens和P. troglodytes或E. coli和E. fergusonii。为了解决这个问题，我们提出了DNA序列集合的加性DNA签名的一般概念。一个特殊的例子，复合DNA签名，结合了来自nDNA片段和细胞器（线粒体，叶绿体或质粒）基因组的信息。我们证明，在这个数据集中，来自两种不同生物体的复合DNA签名在所有情况下都可以区分，包括那些使用CGR签名的nDNA失败或不确定的情况。另一个例子，组装的DNA签名，结合了来自许多短DNA亚片段的信息（例如，100个碱基对），以产生其签名。我们表明，组装的DNA签名具有相同的区分能力作为一个传统的计算CGR签名，而使用较短的连续序列和潜在的序列信息较少。我们的研究结果表明，虽然nDNA的CGR签名不能总是发挥基因组签名的作用，但复合和组装的DNA签名（单独或组合）可能会被替代。可以使用这样的附加签名，例如，当无法获得高质量测序数据时，使用原始未组装的下一代测序（NGS）读取数据，或补充通过其他物种鉴定或分类方法获得的信息。本文的在线版本（doi：10.1186/s12859-016-1157-8）包含补充材料，可供授权用户使用。
Studies exploring the potential of Chaos Game Representations (CGR) of genomic sequences to act as “genomic signatures” (to be species- and genome-specific) showed that CGR patterns of nuclear and organellar DNA sequences of the same organism can be very different. While the hypothesis that CGRs of mitochondrial DNA sequences can act as genomic signatures was validated for a snapshot of all sequenced mitochondrial genomes available in the NCBI GenBank sequence database, to our knowledge no such extensive analysis of CGRs of nuclear DNA sequences exists to date. We analyzed an extensive dataset, totalling 1.45 gigabase pairs, of nuclear/nucleoid genomic sequences (nDNA) from 42 different organisms, spanning all major kingdoms of life. Our computational experiments indicate that CGR signatures of nDNA of two different origins cannot always be differentiated, especially if they originate from closely-related species such as H. sapiens and P. troglodytes or E. coli and E. fergusonii. To address this issue, we propose the general concept of additive DNA signature of a set (collection) of DNA sequences. One particular instance, the composite DNA signature, combines information from nDNA fragments and organellar (mitochondrial, chloroplast, or plasmid) genomes. We demonstrate that, in this dataset, composite DNA signatures originating from two different organisms can be differentiated in all cases, including those where the use of CGR signatures of nDNA failed or was inconclusive. Another instance, the assembled DNA signature, combines information from many short DNA subfragments (e.g., 100 basepairs) of a given DNA fragment, to produce its signature. We show that an assembled DNA signature has the same distinguishing power as a conventionally computed CGR signature, while using shorter contiguous sequences and potentially less sequence information. Our results suggest that, while CGR signatures of nDNA cannot always play the role of genomic signatures, composite and assembled DNA signatures (separately or in combination) could potentially be used instead. Such additive signatures could be used, e.g., with raw unassembled next-generation sequencing (NGS) read data, when high-quality sequencing data is not available, or to complement information obtained by other methods of species identification or classification. The online version of this article (doi:10.1186/s12859-016-1157-8) contains supplementary material, which is available to authorized users.