Using ultraconserved elements to reconstruct the termite tree of life
Using ultraconserved elements to reconstruct the termite tree of life
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DOI：
10.1101/2021.12.09.472027
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发表时间：
2021-12
期刊：
影响因子：
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通讯作者：
S. Hellemans;Menglin Wang;Nonno Hasegawa;J. Šobotník;R. Scheffrahn;T. Bourguignon
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文献类型：
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作者：
S. Hellemans;Menglin Wang;Nonno Hasegawa;J. Šobotník;R. Scheffrahn;T. Bourguignon
白蚁的系统发育历史已经使用线粒体基因组和转录组进行了研究。然而，这两组标记物都有特定的局限性。线粒体基因组代表一个单一的遗传标记，可能会产生系统发育树呈现不一致的物种树，和转录组只能从保存完好的样品。相比之下，超保守元件（UCE）包括许多独立的标记，可以从保存不良的样品中检索。在这里，我们设计了针对50，616个UCE位点的白蚁特异性诱饵。我们在42个白蚁样本和3个隐尾虫样本上测试了我们的UCE诱饵集，为此我们生成了低覆盖率的高度片段化的基因组组装体，并成功地在计算机上提取了每个样本3，426至42，860个非重复的UCE。我们的最大似然系统发育树，使用从75%以上的样本中检索到的5，934个UCE位点重建，与基于转录组的同源性一致，表明我们的UCE诱饵集是可靠的和遗传信息。结合非破坏性DNA提取方案，我们的UCE诱饵集提供了基于保存较差的标本（如旧博物馆样本）进行白蚁全球分类修订所需的工具。Termite UCE数据库维护于：https://github.com/oist/TER-UCE-DB/。
The phylogenetic history of termites has been investigated using mitochondrial genomes and transcriptomes. However, both sets of markers have specific limitations. Mitochondrial genomes represent a single genetic marker likely to yield phylogenetic trees presenting incongruences with species trees, and transcriptomes can only be obtained from well-preserved samples. In contrast, ultraconserved elements (UCEs) include a great many independent markers that can be retrieved from poorly preserved samples. Here, we designed termite-specific baits targeting 50,616 UCE loci. We tested our UCE bait set on 42 samples of termites and three samples of Cryptocercus, for which we generated low-coverage highly-fragmented genome assemblies and successfully extracted in silico between 3,426 to 42,860 non-duplicated UCEs per sample. Our maximum likelihood phylogenetic tree, reconstructed using the 5,934 UCE loci retrieved from upward of 75% of samples, was congruent with transcriptome-based phylogenies, demonstrating that our UCE bait set is reliable and phylogenetically informative. Combined with non-destructive DNA extraction protocols, our UCE bait set provides the tool needed to carry out a global taxonomic revision of termites based on poorly preserved specimens such as old museum samples. The Termite UCE database is maintained at: https://github.com/oist/TER-UCE-DB/.