Extreme haplotype variation in the desiccation-tolerant clubmoss Selaginella lepidophylla

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

*Corresponding author for this work

Research output: Contribution to journalArticle

27 Scopus citations

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.

Original languageEnglish (US)
Article number13
JournalNature communications
Volume9
Issue number1
DOIs
StatePublished - Dec 1 2018
Externally publishedYes

ASJC Scopus subject areas

  • Chemistry(all)
  • Biochemistry, Genetics and Molecular Biology(all)
  • Physics and Astronomy(all)

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    Vanburen, R., Wai, C. M., Ou, S., Pardo, J., Bryant, D., Jiang, N., Mockler, T. C., Edger, P., & Michael, T. P. (2018). Extreme haplotype variation in the desiccation-tolerant clubmoss Selaginella lepidophylla. Nature communications, 9(1), [13]. https://doi.org/10.1038/s41467-017-02546-5