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New Mechanism on Plants Evolution and Adaptation Revealed by Wang Wenqin’s Team

September 06, 2019      Author: School of Agriculture and Biology

On September 3, 2019, the PNAS (Proceedings of the National Academy of Sciences of the United States of America) published online a paper entitled Plant evolution and environmental adaptation unveiled by long-read whole-genome sequencing of Spirodela. The paper reveals the latest research findings of Wang Wenqin's research team, SJTU. With the third generation of PacBio single-molecule sequencing technology, a Spirodela polyrhiza genome of high quality was observed and thus the functions of Spirodela's roots and new mechanism on aquatic plants evolution and environmental adaptation were revealed.

The research was carried out by Wang Wenqin's research team of SJTU and academician Joachim Messing's research team of Waksman Institute of Microbiology, Rutgers University. Post doctor An Dong of SJTU and post doctor. Zhou Yong of the Institute of Plant Physiology and Ecology CAS (IPP for short) were the first authors. Post doctor Li Changsheng, graduate student Xiao Qiao, Wang Tao, and Zhang Yating also participated in the work. The project was funded by National Natural Science Foundation of China. Other supporters include Wu Yongrui and Chao Daiyin's research teams from IPP, and researcher Li Yubin from Biotechnology Research Institute ,CAAS.

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.

Link of the paper:https://www.pnas.org/content/early/2019/09/03/1910401116

 

Translated by Liu Yixuan             Reviewed by Wang Bingyu