Data from: Phylogenomics in Cactaceae: a case study using the chollas sensu lato (Cylindropuntieae, Opuntioideae) reveals a common pattern out of the Chihuahuan/Sonoran Deserts

PREMISE OF THE STUDY: Although numerous phylogenetic studies have been conducted in Cactaceae, whole plastome datasets have not been employed. We used the chollas to develop a plastome dataset for phylogeny reconstruction to test species relationships, biogeography, clade age and morphological evolution. METHODS: We developed a plastome dataset for most known diploid members of the chollas, 42 taxa, as well as for other members of Cylindropuntieae. Paired-end, raw reads from genome skimming were referenced-mapped onto a de novo plastome assembly of one species of cholla, Cylindropuntia bigelovii, which were used to build our plastome dataset that was analyzed using various methods. KEY RESULTS: Our plastome dataset resolved the phylogeny of the chollas, including most inter- and intraspecific relationships. Tribe Cylindropuntieae arose during the early Miocene in southern South America, ca. 18 mya, and is supported as sister to the South American clade Tephrocacteae. The (Micropuntia (Cylindropuntia + Grusonia)) clade most likely originated in the Chihuahuan Desert region around 16 mya, and then migrated into other North American desert regions. Key morphological characters for recognizing traditional taxonomic series (e.g., spiny fruit) in Cylindropuntia are mostly homoplasious. CONCLUSIONS: This study provides the first comprehensive plastome phylogeny for any clade within Cactaceae. Although widespread throughout western North American deserts, the most recent common ancestor of the chollas s.l. likely arose in the Chihuahuan Desert region during the mid-Miocene, with much of their species diversity arising in the early to mid-Pliocene, showing a strikingly similar pattern to other western North American Desert groups.

研究背景：尽管针对仙人掌科（Cactaceae）已开展了大量系统发育研究，但尚未有研究采用全质体基因组（plastome）数据集。本研究以团扇仙人掌类（chollas）为研究对象，构建质体基因组数据集用于系统发育重建，以检验类群间亲缘关系、生物地理学特征、支系（clade）分化时间及形态演化规律。
研究方法：本研究为绝大多数已知的二倍体团扇仙人掌类类群（共42个分类单元）以及圆柱仙人掌族（Cylindropuntieae）的其他成员构建了质体基因组数据集。将基因组浅层测序（genome skimming）获得的双端原始测序读段，参照1个团扇仙人掌物种——大果团扇仙人掌（Cylindropuntia bigelovii）的从头组装质体基因组进行参考比对，以此构建质体基因组数据集，并采用多种分析方法对其进行解析。
主要结果：本研究构建的质体基因组数据集解析了团扇仙人掌类的系统发育关系，涵盖了绝大多数种间及种内亲缘关系。圆柱仙人掌族起源于南美洲南部的中新世早期，距今约1800万年，该族被支持为刺戟仙人掌族（Tephrocacteae）的姊妹支系。（微团扇属（Micropuntia）（团扇属（Cylindropuntia）+ 格里仙人掌属（Grusonia）））支系最可能起源于奇瓦瓦沙漠区域，距今约1600万年，随后迁徙至北美其他荒漠区域。用于识别团扇属（Cylindropuntia）传统分类组的关键形态性状（如具刺果实）大多具有同塑现象（即非同源相似）。
结论：本研究为仙人掌科内的任一演化支系提供了首个全面的质体基因组系统发育研究。尽管广义团扇仙人掌类（chollas s.l.）广泛分布于北美西部荒漠，但其最近共同祖先很可能起源于中新世中期的奇瓦瓦沙漠区域，多数物种多样性形成于上新世早中期，这一演化模式与北美西部荒漠的其他类群极为相似。