Chromosome-level genome assembly of Niphotrichum japonicum provides new insights into heat stress responses in mosses

Frontiers in Plant Science

Plant Science

Tao Peng¹  Shanshan Dong²  Li Zhang²  Qin Zuo²  Xuping Zhou³  Yang Liu⁴  Yuqing Cai⁵  Yuying Zeng⁵ 

[1] Colleage of Life Sciences, Guizhou Normal University, Guiyang, China;Laboratory of Southern Subtropical Plant Diversity, Fairy Lake Botanical Garden, Shenzhen & Chinese Academy of Sciences, Shenzhen, China;Laboratory of Southern Subtropical Plant Diversity, Fairy Lake Botanical Garden, Shenzhen & Chinese Academy of Sciences, Shenzhen, China;Colleage of Life Sciences, Guizhou Normal University, Guiyang, China;Laboratory of Southern Subtropical Plant Diversity, Fairy Lake Botanical Garden, Shenzhen & Chinese Academy of Sciences, Shenzhen, China;State Key Laboratory of Agricultural Genomics, BGI Research, Shenzhen, China;State Key Laboratory of Agricultural Genomics, BGI Research, Shenzhen, China;College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China;

关键词: moss;    genome assembly;    heat stress;    structural cluster;    Niphotrichum japonicum;   

DOI  :  10.3389/fpls.2023.1271357

 received in 2023-08-02, accepted in 2023-09-25,  发布年份 2023

来源: Frontiers

【 摘 要 】

With a diversity of approximately 22,000 species, bryophytes (hornworts, liverworts, and mosses) represent a major and diverse lineage of land plants. Bryophytes can thrive in many extreme environments as they can endure the stresses of drought, heat, and cold. The moss Niphotrichum japonicum (Grimmiaceae, Grimmiales) can subsist for extended periods under heat and drought conditions, providing a good candidate for studying the genetic basis underlying such high resilience. Here, we de novo assembled the genome of N. japonicum using Nanopore long reads combined with Hi-C scaffolding technology to anchor the 191.61 Mb assembly into 14 pseudochromosomes. The genome structure of N. japonicum’s autosomes is mostly conserved and highly syntenic, in contrast to the sparse and disordered genes present in its sex chromosome. Comparative genomic analysis revealed the presence of 10,019 genes exclusively in N. japonicum. These genes may contribute to the species-specific resilience, as demonstrated by the gene ontology (GO) enrichment. Transcriptome analysis showed that 37.44% (including 3,107 unique genes) of the total annotated genes (26,898) exhibited differential expression as a result of heat-induced stress, and the mechanisms that respond to heat stress are generally conserved across plants. These include the upregulation of HSPs, LEAs, and reactive oxygen species (ROS) scavenging genes, and the downregulation of PPR genes. N. japonicum also appears to have distinctive thermal mechanisms, including species-specific expansion and upregulation of the Self-incomp_S1 gene family, functional divergence of duplicated genes, structural clusters of upregulated genes, and expression piggybacking of hub genes. Overall, our study highlights both shared and species-specific heat tolerance strategies in N. japonicum, providing valuable insights into the heat tolerance mechanism and the evolution of resilient plants.

【 授权许可】

Unknown   
Copyright © 2023 Zhou, Peng, Zeng, Cai, Zuo, Zhang, Dong and Liu