Eserman Lauren A, Thomas Shawn K, Coffey Emily E D, Leebens-Mack James H
Department of Conservation and Research Atlanta Botanical Garden Atlanta Georgia 30309 USA.
Division of Biological Sciences University of Missouri Columbia Missouri 65211 USA.
Appl Plant Sci. 2021 May 17;9(7):e11416. doi: 10.1002/aps3.11416. eCollection 2021 Jul.
Understanding relationships among orchid species and populations is of critical importance for orchid conservation. Target sequence capture has become a standard method for extracting hundreds of orthologous loci for phylogenomics. Up-front cost and time associated with design of bait sets makes this method prohibitively expensive for many researchers. Therefore, we designed a target capture kit to reliably sequence hundreds of orthologous loci across orchid lineages.
We designed an Orchidaceae target capture bait set for 963 single-copy genes identified in published orchid genome sequences. The bait set was tested on 28 orchid species, with representatives of the subfamilies Cypripedioideae, Orchidoideae, and Epidendroideae.
Between 1,518,041 and 87,946,590 paired-end 150-base reads were generated for target-enriched genomic libraries. We assembled an average of 812 genes per library for Epidendroideae species and a mean of 501 genes for species in the subfamilies Orchidoideae and Cypripedioideae. Furthermore, libraries had on average 107 of the 254 genes that are included in the Angiosperms353 bait set, allowing for direct comparison of studies using either bait set.
The Orchidaceae963 kit will enable greater accessibility and utility of next-generation sequencing for orchid systematics, population genetics, and identification in the illegal orchid trade.
了解兰花物种和种群之间的关系对于兰花保护至关重要。目标序列捕获已成为一种从数百个直系同源基因座中提取用于系统发育基因组学的标准方法。与诱饵集设计相关的前期成本和时间使得该方法对许多研究人员来说过于昂贵。因此，我们设计了一种目标捕获试剂盒，以可靠地对兰花谱系中的数百个直系同源基因座进行测序。
我们针对已发表的兰花基因组序列中鉴定出的963个单拷贝基因设计了一种兰科目标捕获诱饵集。该诱饵集在28种兰花上进行了测试，这些兰花代表了杓兰亚科、兰亚科和树兰亚科。
针对目标富集的基因组文库生成了1,518,041至87,946,590对150碱基的双端读数。我们为树兰亚科物种的每个文库平均组装了812个基因，为兰亚科和杓兰亚科的物种平均组装了501个基因。此外，文库平均包含被子植物353诱饵集中254个基因中的107个，从而可以直接比较使用这两种诱饵集的研究。
兰科963试剂盒将使下一代测序在兰花系统学、种群遗传学以及非法兰花贸易鉴定中更易于获取和应用。
