Plant evolution and environmental adaptation unveiled by long-read whole-genome sequencing of Spirodela

Dong An, Yong Zhou, Changsheng Li, Qiao Xiao, Tao Wang, Yating Zhang, Yongrui Wu, Yubin Li, Dai Yin Chao, Joachim Messing, Wenqin Wang

Research output: Contribution to journalArticlepeer-review

24 Scopus citations

Abstract

Aquatic plants have to adapt to the environments distinct from where land plants grow. A critical aspect of adaptation is the dynamics of sequence repeats, not resolved in older sequencing platforms due to incomplete and fragmented genome assemblies from short reads. Therefore, we used PacBio long-read sequencing of the Spirodela polyrhiza genome, reaching a 44-fold increase of contiguity with an N50 (a median of contig lengths) of 831 kb and filling 95.4% of gaps left from the previous version. Reconstruction of repeat regions indicates that sequentially nested long terminal repeat (LTR) retrotranspositions occur early in monocot evolution, featured with both prokaryote-like gene-rich regions and eukaryotic repeat islands. Protein-coding genes are reduced to 18,708 gene models supported by 492,435 high-quality full-length PacBio complementary DNA (cDNA) sequences. Different from land plants, the primitive architecture of Spirodela’s adventitious roots and lack of lateral roots and root hairs are consistent with dispensable functions of nutrient absorption. Disease-resistant genes encoding antimicrobial peptides and dirigent proteins are expanded by tandem duplications. Remarkably, disease-resistant genes are not only amplified, but also highly expressed, consistent with low levels of 24-nucleotide (nt) small interfering RNA (siRNA) that silence the immune system of land plants, thereby protecting Spirodela against a wide spectrum of pathogens and pests. The long-read sequence information not only sheds light on plant evolution and adaptation to the environment, but also facilitates applications in bioenergy and phytoremediation.

Original languageEnglish (US)
Pages (from-to)18893-18899
Number of pages7
JournalProceedings of the National Academy of Sciences of the United States of America
Volume116
Issue number38
DOIs
StatePublished - Sep 17 2019

All Science Journal Classification (ASJC) codes

  • General

Keywords

  • Aquatic adaptation
  • Disease resistance
  • Long reads
  • Root evolution
  • Tandem duplication

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