| Bryophytes(hornworts,liverworts and mosses)originated around470 million years ago,and as pioneer plants,bryophytes need to cope with a range of environmental challenges such as dryness,UV radiation and greater temperature variation,they may have developed effective stress resistance mechanisms.Temperature is an important factor affecting the normal growth and development of plants,and high temperatures can cause many adverse effects on plants,including inhibiting seed germination,altering growth and development,and reducing crop yield and quality.Moreover,this damage is expected to increase in the absence of effective adaptation and genetic improvement in the context of global warming.Racomitrium japonicum,which can survive under long-term high temperature and dry conditions,is a superior resource for studying stress resistance genes.However,little is known about the molecular mechanisms of resistance due to the lack of a high-quality reference genome.In this study,we sequenced and assembled the chromosome-level genome of R.japonicum and studied its response to heat stress(42°C)to obtain heat tolerance genes for transfer to crops.The main contributions of this research are as follows:(1)The genome size of R.japonicum is 191.61 Mb,the smallest moss genome to date.It contains 14 chromosomes,with a contig N50 of6.60 Mb and a scaffold N50 of 14.23 Mb.It encodes 26,898protein-coding genes,has a BUSCO completeness of 97.00%,and has a much higher proportion of transposable elements on its sex chromosomes than on its autosomes,but a much lower gene density than on its autosomes.R.japonicum has undergone only one whole genome duplication(WGD),shared with Physcomitrium patens,and its ancestral karyotype consists of seven chromosomes.Among published moss genomes,R.japonicum has no synteny with Sphagnum and has the strongest synteny with Ceratodon purpureus GG1.(2)Approximately 25.20% of the R.japonicum genome consists of duplicated genes,with tandem duplicates and proximal duplicates having more relaxed purifying selection and a higher proportion of up-regulated genes in response to heat stress.(3)No expansion of other gene families occurred in R.japonicum except for the plant self-incompatibility protein S1 gene family,of which15 members were differentially expressed under heat stress.R.japonicum contained 63 heat shock protein(HSP)families,which were up-regulated mainly at 1 and 3 h of heat stress and then began to decline,with the HSP20 subfamily showing the strongest response.The number of late embryogenesis abundant proteins(41)in R.japonicum was higher than in P.patens(35),but comparable to that of the desert moss Syntrichia caninervis(40),of which 11 members were up-regulated in response to heat stress.(4)Under heat treatment at 42°C,10,070 differentially expressed genes were identified in R.japonicum,including 3,819 up-regulated genes and 6,253 down-regulated genes.And structural clusters were identified in the up-regulated genes,which may have a potential cell economy for R.japonicum under heat stress.Weighted gene co-expression network analysis identified 122 hub genes in R.japonicum in response to heat stress,of which 35.25% belonged to neighbouring genes consisting of 2-3 genes.In conclusion,this study has successfully assembled a high-quality chromosome-level genome of R.japonicum,analysed the role of duplicated genes,revealed the structural clusters of genes up-regulated under heat stress,and identified the hub genes involved in heat stress,providing an excellent genetic resource for studying heat tolerance. |
