Ferns are the second most diverse group of land plants after angiosperms. Extant species occupy a wide range of habitats and contribute significantly to ecosystem functioning. Despite the importance of ferns, most taxa are poorly covered by genomic resources and within-species studies based on high-resolution markers are entirely lacking. The genus Botrychium belongs to the family Ophioglossaceae, which includes species with very large genomes and chromosome numbers (e.g., Ophioglossum reticulatum 2n = 1520). The genus has a cosmopolitan distribution with 35 species, half of which are polyploids. Here, we establish a transcriptome for Botrychium lunaria (L.) Sw., a diploid species with an extremely large genome of about ~19.0–23.7 Gb. We assembled 25,677 high-quality transcripts with an average length of 1,333 bp based on deep RNA-sequencing of a single individual. We sequenced 11 additional transcriptomes of individuals from two populations in Switzerland, including the population of the reference individual. Based on read mapping to reference transcript sequences, we identified 374,463 single nucleotide polymorphisms (SNPs) segregating among individuals for an average density of 14 SNPs per kilobase. We found that all 12 transcriptomes were most likely from diploid individuals. The transcriptome-wide markers provided unprecedented resolution of the population genetic structure, revealing substantial variation in heterozygosity among individuals. We also constructed a phylogenomic tree of 92 taxa representing all fern orders to ascertain the placement of the genus Botrychium. High-quality transcriptomic resources and SNP sets constitute powerful population genomic resources to investigate the ecology, and evolution of fern populations.

中文翻译：

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Botrychium lunaria ferns 的全转录组 SNP 能够对倍性和种群结构进行细粒度分析

蕨类植物是仅次于被子植物的第二大种类多样的陆地植物。现存物种占据了广泛的栖息地，并对生态系统功能做出了重大贡献。尽管蕨类植物很重要，但大多数分类群很少被基因组资源覆盖，并且完全缺乏基于高分辨率标记的种内研究。Botrychium属属于蛇舌草科，其中包括具有非常大的基因组和染色体数目的物种（例如，Ophioglossum reticulatum 2 n  = 1520）。该属世界性分布，有35种，其中一半是多倍体。在这里，我们建立了Botrychium lunaria的转录组(L.) Sw.，一种二倍体物种，基因组非常大，约为 19.0–23.7 Gb。我们基于单个个体的深度 RNA 测序组装了 25,677 个平均长度为 1,333 bp 的高质量转录本。我们对来自瑞士两个群体（包括参考个体的群体）的另外 11 个转录组进行了测序。基于到参考转录序列的读取映射，我们确定了 374,463 个单核苷酸多态性 (SNP)，这些单核苷酸多态性 (SNP) 在个体之间分离，平均密度为每千碱基 14 个 SNP。我们发现所有 12 个转录组最有可能来自二倍体个体。转录组范围的标记提供了前所未有的群体遗传结构分辨率，揭示了个体间杂合性的巨大差异。葡萄孢属。高质量的转录组资源和 SNP 集构成了强大的种群基因组资源，用于研究蕨类种群的生态和进化。