Extreme haplotype variation in the desiccation-tolerant clubmoss Selaginella lepidophylla

Robert Vanburen,Patrick Edger,Doug Bryant,Jeremy Pardo,Ching Man Wai,Todd P Michael,Shujun Ou,Todd C Mockler,Ning Jiang

doi:10.1038/s41467-017-02546-5

Abstract

Plant genome size varies by four orders of magnitude, and most of this variation stems from dynamic changes in repetitive DNA content. Here we report the small 109 Mb genome of Selaginella lepidophylla, a clubmoss with extreme desiccation tolerance. Single-molecule sequencing enables accurate haplotype assembly of a single heterozygous S. lepidophylla plant, revealing extensive structural variation. We observe numerous haplotype-specific deletions consisting of largely repetitive and heavily methylated sequences, with enrichment in young Gypsy LTR retrotransposons. Such elements are active but rapidly deleted, suggesting “bloat and purge” to maintain a small genome size. Unlike all other land plant lineages, Selaginella has no evidence of a whole-genome duplication event in its evolutionary history, but instead shows unique tandem gene duplication patterns reflecting adaptation to extreme drying. Gene expression changes during desiccation in S. lepidophylla mirror patterns observed across angiosperm resurrection plants.

Highlights

Plant genome size varies by four orders of magnitude, and most of this variation stems from dynamic changes in repetitive DNA content
Desiccation tolerance is widespread in non-seed plants such as mosses, ferns, and lycophytes[3, 4], but is uncommon in angiosperms
High-quality genomes for several angiosperm resurrection plants have shed light on the molecular basis of desiccation tolerance[2, 5, 6], but the sparse genomic resources for non-seed plants has hindered progress toward understanding the origin of this trait

Summary

Introduction

Plant genome size varies by four orders of magnitude, and most of this variation stems from dynamic changes in repetitive DNA content. The majority (96%) of core eukaryotic BUSCOs16 were identified in the gene set, supporting the completeness of the genome assembly and quality of the annotation (Supplementary Table 3). The proportion of young LTR elements is higher in S. lepidophylla than other high-quality plant genomes (Supplementary Figure 5).

Results

Conclusion