A comprehensive analysis of bilaterian mitochondrial genomes and phylogeny
A comprehensive analysis of bilaterian mitochondrial genomes and phylogeny
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DOI：
10.1016/j.ympev.2013.05.002
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发表时间：
2013-11-01
影响因子：
4.1
通讯作者：
Struck, Torsten H.
中科院分区：
文献类型：
--
作者：
Bernt, Matthias;Bleidorn, Christoph;Struck, Torsten H.
目前 NCBI RefSeq 中存在约 2800 个后生动物线粒体基因组，其中三分之二属于脊椎动物。后生动物系统发育最近受到大规模 EST 方法（系统基因组学）的挑战，稳定了经典节点，同时支持新的姐妹群假设。在深度系统发育分析中使用线粒体数据经常受到批评，因为核苷酸替换率高、类群之间氨基酸替换率差异大以及核苷酸频率偏差。尽管如此，线粒体基因组数据可能仍然有希望，因为它允许更大的分类单元采样，同时提供更少量的序列信息。我们基于线粒体基因组数据对两侧对称动物关系进行了最全面的分析。分析的数据集包含 650 多个线粒体基因组，这些基因组被选择来代表系统发育和序列多样性的深刻样本。结果基于对 NCBI RefSeq 数据库的线粒体基因组序列进行完整重新注释而获得的高质量氨基酸比对。然而，这些结果未能支持许多其他无可争议的高级类群，如软体动物、六足动物、节肢动物，并且受到线虫类、扁形动物和其他一些类群极长分支的影响。为了确定误导性系统发育信号的来源，我们讨论了与线粒体基因组数据集相关的几个问题，例如核苷酸和氨基酸景观以及基因重排与长分支的强相关性。 (C) 2013 Elsevier Inc. 保留所有权利。
About 2800 mitochondrial genomes of Metazoa are present in NCBI RefSeq today, two thirds belonging to vertebrates. Metazoan phylogeny was recently challenged by large scale EST approaches (phylogenomics), stabilizing classical nodes while simultaneously supporting new sister group hypotheses. The use of mitochondrial data in deep phylogeny analyses was often criticized because of high substitution rates on nucleotides, large differences in amino acid substitution rate between taxa, and biases in nucleotide frequencies. Nevertheless, mitochondrial genome data might still be promising as it allows for a larger taxon sampling, while presenting a smaller amount of sequence information. We present the most comprehensive analysis of bilaterian relationships based on mitochondrial genome data. The analyzed data set comprises more than 650 mitochondrial genomes that have been chosen to represent a profound sample of the phylogenetic as well as sequence diversity. The results are based on high quality amino acid alignments obtained from a complete reannotation of the mitogenomic sequences from NCBI RefSeq database. However, the results failed to give support for many otherwise undisputed high-ranking taxa, like Mollusca, Hexapoda, Arthropoda, and suffer from extreme long branches of Nematoda, Platyhelminthes, and some other taxa. In order to identify the sources of misleading phylogenetic signals, we discuss several problems associated with mitochondrial genome data sets, e.g. the nucleotide and amino acid landscapes and a strong correlation of gene rearrangements with long branches. (C) 2013 Elsevier Inc. All rights reserved.