针叶树是生态和经济上重要的种子植物群,可以为陆地植物的进化提供重要的见解。分子系统遗传学已发展成为进化研究中的重要方法,尽管使用来自多个核基因的大规模数据的针叶树研究相对较少。靶标富集测序(靶标捕获,外显子捕获,或Hyb-Seq)已发展成为现代系统基因组研究的关键方法。然而,直到现在,没有专门针对整个针叶树枝的诱饵。REMcon是一种目标序列捕获探针,旨在用于针对c的针叶树的家庭和物种水平的系统发育研究。100个单拷贝核基因座。我们使用69个物种测试了REMcon探针集,包括六个家庭的44个针叶树属和其他四个裸子植物类群,评估靶标捕获的效率,以有效地生成针叶树之间的可比DNA序列数据。目标基因座的回收率高,with,平均而言,94%的靶向区域在具有高读段覆盖率的样品中恢复。对这些数据的系统发育分析产生了支持良好的拓扑结构,这与当前对针叶树之间关系的理解是一致的。REMcon诱饵集将有助于为任何针叶树谱系一致地生成相对大规模的核数据集。
Conifers are an ecologically and economically important seed plant group that can provide significant insights into the evolution of land plants. Molecular phylogenetics has developed as an important approach in evolutionary studies, although there have been relatively few studies of
conifers that employ large-scale data sourced from multiple nuclear genes. Target enrichment sequencing (target capture, exon capture, or Hyb-Seq) has developed as a key approach in modern phylogenomic studies. However, until now, there has been no bait set that specifically targets the entire conifer clade. REMcon is a target sequence capture probe set intended for family- and species-level phylogenetic studies of
conifers that target c. 100 single-copy nuclear loci. We tested the REMcon probe set using 69 species, including 44 conifer genera across six families and four other gymnosperm taxa, to evaluate the efficiency of target capture to efficiently generate comparable DNA sequence data across
conifers. The recovery of target loci was high, with, on average, 94% of the targeted regions recovered across samples with high read coverage. A phylogenetic analysis of these data produced a well-supported topology that is consistent with the current understanding of relationships among
conifers. The REMcon bait set will be useful in generating relatively large-scale nuclear data sets consistently for any conifer lineage.