Rapid allopolyploid radiation of moonwort ferns (Botrychium ; Ophioglossaceae) revealed by PacBio sequencing of homologous and homeologous nuclear regions

Polyploidy is a major speciation process in vascular plants, and is postulated to be particularly important in shaping the diversity of extant ferns. However, limitations in the availability of bi-parental markers for ferns have greatly limited phylogenetic investigation of polyploidy in this group. With a large number of allopolyploid species, the genus Botrychium is a classic example in ferns where recurrent polyploidy is postulated to have driven frequent speciation events. Here, we use PacBio sequencing and the PURC bioinformatics pipeline to capture all homeologous or allelic copies of four long (∼1kb) low-copy nuclear regions from a sample of 45 specimens (25 diploids and 20 polyploids) representing 37 Botrychium taxa, and three outgroups. This sample includes most currently recognized Botrychium species in Europe and North America, and the majority of our specimens were genotyped with co-dominant nuclear allozymes to ensure species identification. We analyzed the sequence data us...

多倍体（Polyploidy）是维管植物（vascular plants）物种形成的主要过程，且被推测在塑造现存蕨类植物多样性方面尤为重要。然而，蕨类植物双亲标记（bi-parental markers）的可获得性受限，极大地制约了该类群多倍体的系统发育研究。瓶尔小草属（Botrychium）包含大量异源多倍体物种（allopolyploid species），是蕨类植物中被推测由反复多倍化驱动频繁物种形成事件的经典案例。本研究采用PacBio测序技术及PURC生物信息学流程，从代表37个瓶尔小草属分类群的45份样本（25份二倍体、20份多倍体）及3个外类群中，捕获了4个长约1kb的低拷贝核区域（low-copy nuclear regions）的所有部分同源序列（homeologous）或等位基因拷贝（allelic copies）。该样本涵盖了欧洲及北美地区目前已确认的大部分瓶尔小草属物种，且我们对多数样本采用共显性核同工酶（co-dominant nuclear allozymes）进行基因分型，以确保物种鉴定的准确性。我们对序列数据进行了分析