Illinois Natural History Survey, Prairie Research Institute, University of Illinois, 1816 South Oak Street, Champaign, IL 61820 USA.
Curr Opin Insect Sci. 2019 Dec;36:111-117. doi: 10.1016/j.cois.2019.08.002. Epub 2019 Aug 13.
Next-generation sequencing technologies provide a substantial increase in the size of molecular phylogenetic datasets that can be obtained for studies of insect systematics. Several new genome reduction approaches are leveraging these technologies to generate large phylogenomic datasets: targeted amplicon sequencing, target capture, and transcriptome sequencing. Although cost effective, these approaches provide limited data for questions outside of phylogenetics. For many groups of insects, sequencing the entire genome at modest coverage is feasible. Using these genomic reads, an automated Target Restricted Assembly Method (aTRAM) can use the results of blast searches to assemble thousands of single copy ortholog genes across a group of interest. These locally assembled genes can then be compiled into very large phylogenomic datasets. These genomic libraries have the advantage in that they also contain reads from the mitochondrial genome and symbiont genomes, as well the entire insect genome, and can be leveraged for additional studies beyond phylogenetics.
下一代测序技术为昆虫系统学研究提供了大量可获得的分子系统发育数据集，使这些数据集的大小有了显著的增加。几种新的基因组简化方法正在利用这些技术来生成大型基因组数据集：靶向扩增子测序、目标捕获和转录组测序。虽然这些方法具有成本效益，但它们提供的数据对于系统发育以外的问题有限。对于许多昆虫群体来说，以适度的覆盖率对整个基因组进行测序是可行的。使用这些基因组读取，自动化目标限制组装方法 (aTRAM) 可以利用blast 搜索的结果在感兴趣的一组中组装数千个单拷贝直系同源基因。然后，可以将这些局部组装的基因编译成非常大的基因组数据集。这些基因组文库的优势在于，它们还包含来自线粒体基因组和共生体基因组的读取，以及整个昆虫基因组，可以用于除系统发育学以外的其他研究。
