Multiple genome alignments facilitate development of NPCL markers: a case study of tetrapod phylogeny focusing on the position of turtles.
Multiple genome alignments facilitate development of NPCL markers: a case study of tetrapod phylogeny focusing on the position of turtles.
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DOI：
10.1093/molbev/msr148
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发表时间：
2011-12
影响因子：
10.7
通讯作者：
Xing‐Xing Shen;Dan Liang;Jun-Zhi Wen;Peng Zhang
中科院分区：
文献类型：
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作者：
Xing‐Xing Shen;Dan Liang;Jun-Zhi Wen;Peng Zhang
近年来，基因组资源的日益丰富为开发系统发育标记提供了机会。在基因组学时代，从基因组数据中的大量基因中搜索候选标记的有效方法特别需要。在这里，而不是使用传统的方法比较基因组的两个远亲类群开发保守的引物，我们利用多个基因组比对资源从加州大学-圣克鲁兹基因组浏览器，并提出了一个简单而直接的生物信息学方法来自动筛选候选核蛋白编码位点（NPCL）标记。我们在四足动物中测试了我们的方案，并在16种不同的四足动物分类群中成功获得了21个新的NPCL标记，聚合酶链反应扩增成功率很高（大多超过80%）。这21个新开发的标记与两个参考基因（RAG 1和线粒体12 S-16 S）一起被用来推断四足动物的更高层次的关系，重点是海龟的争议位置。最大似然（ML）和贝叶斯分析的串联数据结合23个标记（21，137 bp）产生相同的树，ML自助值超过95%，贝叶斯后验概率等于1.0的大多数节点。没有数据连接的情况下，使用程序BEST的树种树估计产生类似的结果。在所有的分析中，海龟都被有力地恢复为初龙类（鸟类和鳄鱼）的姐妹群。拼接数据的刀切分析表明，稳健地解决海龟的位置所需的最小序列长度为13-14 kb。基于大的23个基因的数据集和良好解决的树，我们还估计了进化的时间尺度与流行的贝叶斯方法MultiDivTime的四足动物。大多数四足动物的估计年龄与《生命的时间表》一书中总结的先前测年研究的平均估计相似。
In recent years, the increasing availability of genomic resources has provided an opportunity to develop phylogenetic markers for phylogenomics. Efficient methods to search for candidate markers from the huge number of genes within genomic data are particularly needed in the era of phylogenomics. Here, rather than using the traditional approach of comparing genomes of two distantly related taxa to develop conserved primers, we take advantage of the multiple genome alignment resources from the the University of California-San Cruz Genome Browser and present a simple and straightforward bioinformatic approach to automatically screen for candidate nuclear protein-coding locus (NPCL) markers. We tested our protocol in tetrapods and successfully obtained 21 new NPCL markers with high success rates of polymerase chain reaction amplification (mostly over 80%) in 16 diverse tetrapod taxa. These 21 newly developed markers together with two reference genes (RAG1 and mitochondrial 12S-16S) are used to infer the higher level relationships of tetrapods, with emphasis on the debated position of turtles. Both maximum likelihood (ML) and Bayesian analyses on the concatenated data combining the 23 markers (21,137 bp) yield the same tree, with ML bootstrap values over 95% and Bayesian posterior probability equaling 1.0 for most nodes. Species tree estimation using the program BEST without data concatenation produces similar results. In all analyses, turtles are robustly recovered as the sister group of Archosauria (birds and crocodilians). The jackknife analysis on the concatenated data showed that the minimum sequence length needed to robustly resolve the position of turtles is 13-14 kb. Based on the large 23-gene data set and the well-resolved tree, we also estimated evolutionary timescales for tetrapods with the popular Bayesian method MultiDivTime. Most of the estimated ages among tetrapods are similar to the average estimates of the previous dating studies summarized by the book The Timetree of Life.