Comprehensive mutation identification in an evolved bacterial cooperator and its cheating ancestor
Comprehensive mutation identification in an evolved bacterial cooperator and its cheating ancestor
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DOI：
10.1073/pnas.0510740103
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发表时间：
2006-05-23
影响因子：
11.1
通讯作者：
Schuster, Stephan C.
中科院分区：
文献类型：
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作者：
Velicer, Gregory J.;Raddatz, Guenter;Schuster, Stephan C.
精确描述进化谱系的突变历史对于理解进化过程至关重要，然而突变鉴定一直受到传统技术的限制。我们试图在实验进化的合作性细菌黄粘球菌谱系中确定所有积累的突变，这种细菌通过社会性多细胞发育过程来响应饥饿而构建子实体。这个世系在社会表型上经历了两次主要的转变：从祖先的合作者到社会缺陷的骗子，从骗子到重新进化出社会和发展能力的竞争优势的合作者。利用最近的“合成测序”技术对进化的优势合作菌（菌株“PX”）的9.14 mb基因组进行了测序，测序覆盖率接近19倍，部分测序采用毛细管技术（约45%）。结果数据显示，经过两个阶段的实验进化，与PX的实验室祖先相比，有15个单核苷酸突变，但没有证据表明存在重复、转位或多碱基缺失。除了焦磷酸测序发现的突变外，毛细管测序没有发现任何突变，导致所有突变都被发现的可能性很大。在先前由Sanger方法测序的参考菌株中发现了7个错误，以及参考菌株的两个不同实验室库存之间的5个突变差异。在菌株PX中发现了一个负责恢复发育的突变，而在实验进化的前一阶段发生了14个突变。这些结果提供了洞察两个大的适应性转变在社会细菌的遗传基础。
Precise characterization of the mutation histories of evolutionary lineages is crucial for understanding the evolutionary process, yet mutation identification has been constrained by traditional techniques. We sought to identify all accumulated mutations in an experimentally evolved lineage of the cooperative bacterium Myxococcus xanthus, which constructs fruiting bodies by a process of social multicellular development in response to starvation. This lineage had undergone two major transitions in social phenotype: from an ancestral cooperator to a socially defective cheater, and from the cheater to a competitively dominant cooperator that re-evolved social and developmental proficiency. The 9.14-Mb genome of the evolved, dominant cooperator (strain "PX") was sequenced to approximate to 19-fold coverage by using recent "sequencing-by-synthesis" technology and partially sequenced (approximate to 45%) by using capillary technology. The resulting data revealed 15 single-nucleotide mutations relative to the laboratory ancestor of PX after the two phases of experimental evolution but no evidence of duplications, transpositions, or multiple-base deletions. No mutations were identified by capillary sequencing beyond those found by pyrosequencing, resulting in a high probability that all mutations were discovered. Seven errors in the reference strain previously sequenced by the Sanger approach were revealed, as were five mutational differences between two distinct laboratory stocks of the reference strain. A single mutation responsible for the restoration of development in strain PX was identified, whereas 14 mutations occurred during the prior phase of experimental evolution. These results provide insight into the genetic basis of two large adaptive transitions in a social bacterium.