AUTHOR=Zhou Xuping , Peng Tao , Zeng Yuying , Cai Yuqing , Zuo Qin , Zhang Li , Dong Shanshan , Liu Yang 

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

JOURNAL=Frontiers in Plant Science

VOLUME=14

YEAR=2023

URL=https://www.frontiersin.org/journals/plant-science/articles/10.3389/fpls.2023.1271357

DOI=10.3389/fpls.2023.1271357

ISSN=1664-462X

ABSTRACT=<p>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 <italic>Niphotrichum japonicum</italic> (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 <italic>de novo</italic> assembled the genome of <italic>N. japonicum</italic> using Nanopore long reads combined with Hi-C scaffolding technology to anchor the 191.61 Mb assembly into 14 pseudochromosomes. The genome structure of <italic>N. japonicum</italic>’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 <italic>N. japonicum</italic>. 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 <italic>HSP</italic>s, <italic>LEA</italic>s, and reactive oxygen species (ROS) scavenging genes, and the downregulation of <italic>PPR</italic> genes. <italic>N. japonicum</italic> 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 <italic>N. japonicum</italic>, providing valuable insights into the heat tolerance mechanism and the evolution of resilient plants.</p>