The convergence of cytogenetics and rearrangement-based models for ancestral genome reconstruction
The convergence of cytogenetics and rearrangement-based models for ancestral genome reconstruction
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DOI：
10.1101/gr.4631806
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发表时间：
2006-03-01
期刊：
影响因子：
7
通讯作者：
Pevzner, PA
中科院分区：
文献类型：
--
作者：
Bourque, G;Tesler, G;Pevzner, PA
Froenicke等人（2006年）提出了这样一个问题：“分子细胞遗传学和生物信息学是否表明祖先哺乳动物基因组的不同模型？他们的评论似乎暗示，当涉及到对祖先哺乳动物基因组的研究时，细胞遗传学比“生物信息学”优越上级。但是，比较细胞遗传学和其他方法来推导祖先基因组结构，（类似于Bourque和Pevzner 2002年开发的MGR）（80多个细胞遗传学图谱与4个远亲测序基因组）并没有说明这些方法的优点和缺点;相反，它间接评估输入数据集的质量。在这种情况下，Froenicke等（2006）的主要结论相当于这样的陈述：当涉及低分辨率祖先结构时，80+细胞遗传学图谱导致比四个不同基因组更确定的重建。我们从未在我们的出版物中反对这一点，甚至主张使用辐射杂交作图（作为细胞遗传学和测序数据之间分辨率的权衡）来扩大分析基因组的数量（Murphy et al. 2003，2005）。事实上，随着更多的分类单元采样，仅用7个基因组的基于参考的重建（Murphy et al. 2005）已经与细胞遗传学重建高度一致。在我们证实这种收敛性之前，我们澄清了弱关联的概念，这是在Bourque et al.（2005）中使用的，以提醒读者，一些邻接在祖先中是未解决的。Froenicke等人（2006）发现的差异都涉及弱关联，并且指向误解而不是矛盾。最后，我们强调了基于重排的方法所独有的一些重要优势，例如检测较小基因组片段的能力，处理快速进化的谱系，以及定位祖先中的保守片段。
Froenicke et al. (2006) asked the question "Are molecular cytogenetics and bioinformatics suggesting diverging models of ancestral mammalian genomes?" Their commentary seems to imply that cytogenetics is superior to "bioinformatics" when it comes to studies of ancestral mammalian genomes. But, comparing cytogenetics with other approaches to deriving ancestral genomic architectures (like MGR developed by Bourque and Pevzner 2002) on two very different data sets (80+ cytogenetic maps vs. four distantly related sequenced genomes) does not say much about the merits and demerits of the approaches; instead, it indirectly evaluates the quality of the input data sets.In this context, the main conclusion of Froenicke et al. (2006) amounts to the statement that 80+ cytogenetic maps lead to a more definitive reconstruction than four divergent genomes when it comes to low-resolution ancestral architectures. We never argued against this point in our publications and even advocated for the use of radiation hybrid mapping (as a trade-off in resolution between cytogenetic and sequencing data) to extend the number of analyzed genomes (Murphy et al. 2003, 2005). Indeed, with more taxon sampling, a rearrangement-based reconstruction with just seven genomes (Murphy et al. 2005) is already highly consistent with the cytogenetics reconstruction. Before we substantiate this convergence, we clarify the notion of weak associations, which was used in Bourque et al. (2005) to alert the reader that some of the adjacencies were left as unresolved in the ancestor. The discrepancies identified by Froenicke et al. (2006) all involve weak associations and point toward a misunderstanding more than a contradiction.Finally, we underline some of the important strengths exclusive to rearrangement-based approaches, such as the ability to detect smaller genomic segments, to handle fast evolving lineages, and to orient conserved segments in the ancestors.