Hyb-Seq：植物系统基因组学中目标富集与基因组浅测序的结合
Hyb-Seq: Combining target enrichment and genome skimming for plant phylogenomics.
机构信息
Department of Botany and Plant Pathology, Oregon State University, 2082 Cordley Hall, Corvallis, Oregon 97331 USA.
Pacific Northwest Research Station, USDA Forest Service, 3200 SW Jefferson Way, Corvallis, Oregon 97331 USA.
出版信息
Appl Plant Sci. 2014 Aug 29;2(9). doi: 10.3732/apps.1400042. eCollection 2014 Sep.
PREMISE OF THE STUDY
Hyb-Seq, the combination of target enrichment and genome skimming, allows simultaneous data collection for low-copy nuclear genes and high-copy genomic targets for plant systematics and evolution studies. •
METHODS AND RESULTS
Genome and transcriptome assemblies for milkweed (Asclepias syriaca) were used to design enrichment probes for 3385 exons from 768 genes (>1.6 Mbp) followed by Illumina sequencing of enriched libraries. Hyb-Seq of 12 individuals (10 Asclepias species and two related genera) resulted in at least partial assembly of 92.6% of exons and 99.7% of genes and an average assembly length >2 Mbp. Importantly, complete plastomes and nuclear ribosomal DNA cistrons were assembled using off-target reads. Phylogenomic analyses demonstrated signal conflict between genomes. •
CONCLUSIONS
The Hyb-Seq approach enables targeted sequencing of thousands of low-copy nuclear exons and flanking regions, as well as genome skimming of high-copy repeats and organellar genomes, to efficiently produce genome-scale data sets for phylogenomics.
研究前提
Hyb-Seq 是目标富集和基因组浅测序的结合，允许同时收集植物系统发育和进化研究中的低拷贝核基因和高拷贝基因组靶标数据。
方法和结果
使用乳草（Asclepias syriaca）的基因组和转录组组装来设计 768 个基因的 3385 个外显子的富集探针（>1.6 Mbp），然后对富集文库进行 Illumina 测序。对 12 个个体（10 种乳草属物种和两个相关属）进行 Hyb-Seq 后，至少有 92.6%的外显子和 99.7%的基因得到了部分组装，平均组装长度>2 Mbp。重要的是，使用非目标读取可以组装完整的质体基因组和核核糖体 DNA 顺反子。系统基因组分析表明基因组之间存在信号冲突。
结论
Hyb-Seq 方法能够靶向测序数千个低拷贝核外显子和侧翼区域，以及对高拷贝重复和细胞器基因组进行基因组浅测序，从而高效地产生用于系统基因组学的基因组规模数据集。
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