The field of systematics is experiencing a new molecular revolution driven by the increased availability of high-throughput sequencing technologies. As these techniques become more affordable, the increased genomic resources have increasingly far-reaching implications for our understanding of the Tree of Life. With c. 2000 species, Carex (Cyperaceae) is one of the five largest genera of angiosperms and one of the two largest among monocots, but the phylogenetic relationships between the main lineages are still poorly understood. We designed a Cyperaceae-specific HybSeq bait kit using transcriptomic data of Carex siderosticta and Cyperus papyrus. We identified 554 low-copy nuclear orthologous loci, targeting a total length of c. 1 Mbp. Our Cyperaceae-specific kit shared loci with a recently published angiosperm-specific Anchored Hybrid Enrichment kit, which enabled us to include and compile data from different sources. We used our Cyperaceae kit to sequence 88 Carex spp., including samples of all the five major clades in the genus. For the first time, we present a phylogenetic tree of Carex based on hundreds of loci (308 nuclear exon matrices, 543 nuclear intron matrices and 66 plastid exon matrices), demonstrating that there are six strongly supported main lineages in Carex: the Siderostictae, Schoenoxiphium, Unispicate, Uncinia, Vignea and Core Carex clades. Based on our results, we suggest a revised subgeneric treatment and provide lists of the species belonging to each of the subgenera. Our results will inform future biogeographic, taxonomic, molecular dating and evolutionary studies in Carex and provide the step towards a revised classification that seems likely to stand the test of time.

中文翻译：

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HybSeq 主干系统发育树支持的 Carex (Cyperaceae) 亚属的新分类

随着高通量测序技术的普及，系统学领域正在经历一场新的分子革命。随着这些技术变得越来越便宜，增加的基因组资源对我们理解生命之树的影响越来越深远。与 c。2000 种，苔草科 (Cyperaceae) 是被子植物的五个最大属之一，也是单子叶植物中最大的两个属之一，但主要谱系之间的系统发育关系仍知之甚少。我们使用 Carex siderosticta 和 Cyperus papyrus 的转录组数据设计了莎草科特定的 HybSeq 诱饵套件。我们确定了 554 个低拷贝核直向同源基因座，目标总长度为 c。1 兆字节。我们的莎草科特定试剂盒与最近发布的被子植物特定锚定杂交富集试剂盒共享位点，这使我们能够包括和编译来自不同来源的数据。我们使用我们的莎草科试剂盒对 88 个 Carex spp. 进行了测序，包括该属中所有五个主要进化枝的样本。我们首次提出了基于数百个基因座（308 个核外显子矩阵、543 个核内含子矩阵和 66 个质体外显子矩阵）的 Carex 系统发育树，表明 Carex 中有六个强烈支持的主要谱系：Siderostictae、Schoenoxiphium 、Uncinia、Uncinia、Vignea 和 Core Carex 进化枝。根据我们的结果，我们建议修改亚属处理并提供属于每个亚属的物种列表。我们的结果将为未来的生物地理学、分类学、