Okinawa Institute of Science & Technology Graduate University, 1919-1 Tancha, Onna-son, Okinawa 904-0495, Japan.
Okinawa Institute of Science & Technology Graduate University, 1919-1 Tancha, Onna-son, Okinawa 904-0495, Japan.
Mol Phylogenet Evol. 2022 Aug;173:107520. doi: 10.1016/j.ympev.2022.107520. Epub 2022 May 13.
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/.
已使用线粒体基因组和转录组研究了白蚁的系统发育历史。然而，这两种标记物都有其特定的局限性。线粒体基因组代表了一个单一的遗传标记，可能会产生与物种树不一致的系统发育树，而转录组只能从保存完好的样本中获得。相比之下，超保守元件 (UCE) 包含许多可以从保存不佳的样本中检索到的独立标记。在这里，我们设计了针对 50616 个 UCE 基因座的白蚁特异性诱饵。我们在 42 个白蚁样本和 3 个 Cryptocercus 样本上测试了我们的 UCE 诱饵组，我们为这些样本生成了低覆盖率的高度碎片化基因组组装，并成功地从每个样本的 3426 到 42860 个非重复 UCE 中提取了计算机模拟数据。我们使用从超过 75%的样本中获取的 5934 个 UCE 基因座重建的最大似然系统发育树与基于转录组的系统发育树一致，表明我们的 UCE 诱饵组是可靠的，并且具有系统发育信息。结合非破坏性 DNA 提取协议，我们的 UCE 诱饵组为基于保存不佳的标本（如旧博物馆标本）对白蚁进行全球分类修订提供了所需的工具。白蚁 UCE 数据库维护在：https://github.com/oist/TER-UCE-DB/。
