The development of three long universal nuclear protein-coding locus markers and their application to osteichthyan phylogenetics with nested PCR.
The development of three long universal nuclear protein-coding locus markers and their application to osteichthyan phylogenetics with nested PCR.
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三个长通用核蛋白编码位点标记的开发及其在巢式 PCR 骨鱼系统发育学中的应用
DOI：
10.1371/journal.pone.0039256
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发表时间：
2012
期刊：
影响因子：
3.7
通讯作者：
Zhang P
中科院分区：
文献类型：
--
作者：
Shen XX;Liang D;Zhang P
通用核蛋白编码位点（NPCL）标记适用于不同的分类群，并显示出良好的系统发育辨别力，在分子系统发育研究中具有广泛的应用。例如，RAG1（NPCL 的代表性标记）已成功用于在所有主要骨鱼类群内进行系统发育推断。然而，此类具有广泛工作范围和高系统发育性能的标记仍然稀缺。有必要开发与 RAG1 类似的更通用的 NPCL 标记用于骨鱼系统发育。我们基于单拷贝核基因（KIAA1239、SACS 和 TTN）开发了三个长通用 NPCL 标记（每个 >1.6 kb），这些基因具有较大的外显子并表现出适当的进化速率。然后，我们将它们的系统发育效用与参考标记 RAG1 在 47 个有颌脊椎动物物种中的系统发育效用进行了比较。与 RAG1 相比，三个长通用标记中的每一个都产生了相似的拓扑和分支支持，所有这些都与目前公认的骨鱼系统发育一致。为了直观地比较它们的系统发育性能，我们还估计了四个长通用 NPCL 标记中每一个的系统发育信息 (PI) 概况。 PI曲线表明SACS在整个时间尺度上表现最好，而RAG1、KIAA1239和TTN表现出相似的系统发育表现。此外，我们还比较了巢式 PCR 和标准 PCR 在扩增 NPCL 标记片段时的成功情况。巢式PCR的扩增成功率和效率明显高于标准PCR。我们的工作清楚地证明了巢式PCR在系统发育研究中相对于传统PCR的优越性，并利用巢式PCR策略开发了三个长通用NPCL标记（KIAA1239、SACS和TTN）。这三个标记在骨鱼系统发育学中表现出很高的系统发育实用性，可广泛用作不同分类水平的骨鱼系统发育问题的先导基因。
Universal nuclear protein-coding locus (NPCL) markers that are applicable across diverse taxa and show good phylogenetic discrimination have broad applications in molecular phylogenetic studies. For example, RAG1, a representative NPCL marker, has been successfully used to make phylogenetic inferences within all major osteichthyan groups. However, such markers with broad working range and high phylogenetic performance are still scarce. It is necessary to develop more universal NPCL markers comparable to RAG1 for osteichthyan phylogenetics. We developed three long universal NPCL markers (>1.6 kb each) based on single-copy nuclear genes (KIAA1239, SACS and TTN) that possess large exons and exhibit the appropriate evolutionary rates. We then compared their phylogenetic utilities with that of the reference marker RAG1 in 47 jawed vertebrate species. In comparison with RAG1, each of the three long universal markers yielded similar topologies and branch supports, all in congruence with the currently accepted osteichthyan phylogeny. To compare their phylogenetic performance visually, we also estimated the phylogenetic informativeness (PI) profile for each of the four long universal NPCL markers. The PI curves indicated that SACS performed best over the whole timescale, while RAG1, KIAA1239 and TTN exhibited similar phylogenetic performances. In addition, we compared the success of nested PCR and standard PCR when amplifying NPCL marker fragments. The amplification success rate and efficiency of the nested PCR were overwhelmingly higher than those of standard PCR. Our work clearly demonstrates the superiority of nested PCR over the conventional PCR in phylogenetic studies and develops three long universal NPCL markers (KIAA1239, SACS and TTN) with the nested PCR strategy. The three markers exhibit high phylogenetic utilities in osteichthyan phylogenetics and can be widely used as pilot genes for phylogenetic questions of osteichthyans at different taxonomic levels.
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