Figure - available from: Frontiers in Plant Science
This content is subject to copyright.
Genomic structure of the Antarctic moss Pohlia nutans. (A) Photo of P. nutans under normal condition. (B) The landscape of genome assembly and annotation of P. nutans. Tracks from outside to inside correspond to: a, GC content; b, contigs density; c, gene density; d, repeat density; e, LTR/Gypsy content; f, LTR/Copia content; g, DNA/CMC-EnSpm; and h, syntonic relationship. (C) The genome size, gene content, and repeat content of four bryophyte genomes (the Antarctic moss P. nutans, the moss model plant Physcomitrella patens, the liverwort model plant Marchantia polymorpha, the hornwort model plant Anthoceros angustus).
Source publication
The Antarctic continent has extreme natural environment and fragile ecosystem. Mosses are one of the dominant floras in the Antarctic continent. However, their genomic features and adaptation processes to extreme environments remain poorly understood. Here, we assembled the high-quality genome sequence of the Antarctic moss (Pohlia nutans) with 698...
Citations
... They are known as the "pioneer plants" of nature and the key members of the Earth's "epidermis". They can adapt to extreme environments such as drought, cold, and strong light (Cao et al. 2014;Gao et al. 2017;Liu et al. 2022cLiu et al. , 2022aLiu et al. , 2022bLi et al. 2022). Many mosses are the typical "resurrection plant" that they can tolerate Yue Liu and Daqing Zhang have contributed equally to this work. ...
Key message
Desiccation-tolerant process of xerophytic moss Pogonatum inflexum were identified through de novo transcriptome assembly , morphological structure and physiology analysis.
Abstract
Pogonatum inflexum (Lindb.) Lac. is a typical xerophytic moss and have been widely used in gardening and micro-landscape. However, the mechanisms underlying desiccation tolerance are still unclear. In this study, morphological, physiological and trancriptomic analyses of P. inflexum to tolerate desiccation were carried out. Our results indicate that P. inflexum increase osmoregulation substances, shut down photosynthesis, and alter the content of membrane lipid fatty acids in response to desiccation, and the genes involved in these biological processes were changes in expression after desiccation. 12 h is the threshold for P. inflexum to tolerate desiccation and its photosynthesis has not been damaged within 12 h of desiccation and can still recover after rewater. We also proved that the gametocyte of P. inflexum has the ability to absorb and transport water, and contains lignin-synthesis genes in response to tolerant desiccation. Our findings not only explain the mechanisms of P. inflexum during desiccation, but also provide some attractive candidate genes for genetic breeding.
... Mb; Yu et al., 2022), Fontinalis antipyretica (385.2 Mb; Yu et al., 2020), Calohypnum plumiforme (434 Mb;Mao et al., 2020), and the very large Bryidae moss Pohlia nutans (698.20 Mbp; Liu et al., 2022). However, the genome of a fourth pleurocarpous moss, Hypnum curvifolium, is estimated to be smaller than that of S. ruralis, at (which was not certified by peer review) is the author/funder. ...
Water scarcity poses a significant threat to ecosystems in the face of global climate change. Syntrichia ruralis , a dryland moss known for its desiccation tolerance, provides valuable insights into surviving water-limited conditions. In this study, the genome of S. ruralis was sequenced and assembled into 12 chromosomes encompassing 21,169 protein-coding genes. Additionally, 3,199 unplaced scaffolds were identified as non-nuclear and symbiont DNA. Transposable elements (TEs) constitute 51.24% of the genome. Notably, chromosome 12, the largest in size due to its high TE load, was identified as the putative sex chromosome. Comparative analysis with the closely related Syntrichia caninervis genome reveals significant large-scale synteny yet some rearrangements, as well as the occurrence of older duplication events that are shared by both. Desiccation and drought tolerance associated gene families, such as early light-inducible proteins (ELIPs) and late embryogenesis abundant (LEA) proteins, were characterized. In addition to a subset of LEA genes being species-specific, a comparative transcriptomic analysis revealed that some shared LEA genes respond differently to dehydration in these two species. Many ELIPs (9 out of 30) are the product of tandem duplication events. As expected, our analyses revealed the importance of the phytohormone abscisic acid (ABA) in the desiccation response of S. ruralis . A significant number of ABA responsive genes were found to be regulated by S. ruralis orthologs of ABA insensitive 3 (ABI3) and abscisic acid responsive element binding factor 2 (AREB2). Markedly, an uncharacterized, but deeply conserved MYB transcription factor, appears to act as a negative regulator of AREB2 in S. ruralis . Interestingly, we determined that the orthologous MYB TF is also involved in an ABA-dependent stress response in the model flowering plant A. thaliana . In sum, the new genomic resources from this emerging model moss offer new insights into the evolution of desiccation tolerance in land plants.
... They can grow in deserts and alpine environments, but also in less stressful habitats such as rock faces, tree trunks and the forest floor (Dey and De, 2012;Proctor et al., 2007). Full genome sequences are available from nine species of mosses, namely, Physcomitrium patens (Rensing et al., 2008), Sphagnum fallax (Shaw et al., 2016), Pleurozium schreberi (Pederson et al., 2019), Ceratodon purpureus (Carey et al., 2020), Syntrichia caninervis (Silva et al., 2020), Pohlia nutans (Liu et al., 2022), Rhytidiadelphus loreus (BioProject PRJEB56418, 2022), Sphagnum magellanicum (BioProject PRJNA242127, 2022) and Thuidium tamariscinum (Bio-Project PRJEB56419, 2022). Analysis of the NCBI and Phytozome databases detected 84 PODs from Physcomitrium patens, 4 PODs from Pohlia nutans and 64 PODs from S. fallax. ...
Class III peroxidases (POD: EC 1.11.1.7) are classical secretory plant peroxidases belonging to a large multi-gene family with diverse functions. Members of the POD family have been well-studied and characterized in many plants, including three species of bryophytes, but not from the moss Dicranum scoparium Hedw. Ecologically , D. scoparium is a very important species, which has a widespread distribution throughout the Hol-arctic. Here we present the first comprehensive report on the POD gene family in D. scoparium, identifying 22 genes encoding PODs (DsPODs), two of which were cloned for verification. All genes were deposited to Gen-Bank under the third-party annotation (Accession numbers TPA: BK061169 À BK061190). Here, we present an in silico study of the physicochemical properties of these proteins. Analyses of conserved domains and subcellular localization suggested that DsPODs have classical peroxidase domain structure; they are secre-tory proteins and most of them are extracellular. Eight DsPODs highly homologous to Class III peroxidases from the mosses Pohlia nutans and Physcomitrium patens were further microcharacterized. All eight DsPODs possess a haem ligand and active sites necessary for enzymatic activity; they also contained sites for post-translational modifications. Prediction of secondary structure indicated that these proteins mainly consist of a-helices and random coils. Experiments involving the reverse transcription quantitative real-time polymer-ase chain reaction (RT-qPCR) showed that DsPOD1, DsPOD2, DsPOD6, and DsPOD8 are differentially upregu-lated in response to stress. The stresses applied here included CdCl 2 , paraquat, unfavorable temperatures, and a hydration-desiccation-rehydration cycle. Our results indicate that Class III PODs contribute to the abi-otic stress tolerance of D. scoparium, and specific DsPOD genes may play diverse roles in the response of the moss to stress.
... Similar to the B. argenteum genome, both of the hypnalean moss genomes, H. curvifolium and E. seductrix, also had 11 chromosomes. The P. nutans genome was characterized by a recent WGD to encompass 23 chromosomes, where two-fold syntenic chromosomal counterparts could be observed 10 . ...
... In this scenario, two hypotheses might arise: it is possible that the P. nutans genome was contaminated or incorporated sporophyte materials that included both U and V chromosomes; or the subgenome donors for the recent WGD were from female and a male gametophytes, and an economic hermaphroditic reproductive system could have been established 28 . This later scenario could perhaps have been bene cial for survival in the Antarctic environment, and would also suggest that the sex-linked maker gene had not yet eroded in the fractionation process given that the WGD event is pretty "young" with a K S peak around 0.11 10 . We speculate that the latter might be the case because our analyses indicated the breakage of an ancestral chromosome that generated chromosomes 20 and 21, homologous to separate segments of the chr. ...
The UV chromosomal sex-determination system primarily found in bryophytes, together with the XY and ZW chromosomal sex-determination systems, constitute the three principal types of chromosomal sex determination systems in nature. In this report, the genome of the moss Bryum argenteum was sequenced and assembled into 11 chromosomes containing 17,721 protein coding genes. A giant female U sex chromosome demonstrated conspicuously lower gene density, higher repeat coverage, and higher GC content compared to the ten autosomes. By further characterizing the sex-chromosomes and sex-linked genes in seven chromosomal-scale Bryopsida genomes, lower gene densities and distinct GC contents were revealed to be common in all moss sex chromosomes, likely resulting from degeneration. Weaker purifying selection, as evidenced by lower codon usage preference in sex-linked genes, was shared in most but not all Bryopsida mosses. Retained genomic syntenies between U/V sex chromosomes and ancestral Bryopsida chromosome 4 provided new evidence to support an autosomal origin for sex chromosomes. The seven ancestral Bryopsida chromosomes were reconstructed to decipher and depict chromosomal evolution; Dicranidae and Bryidae mosses demonstrated one and three chromosomal fusions and evolved 13 and 11 ancestral chromosomes, respectively. Ancient whole genome duplications characterized many plant lineages including the psi polyploidy event that occurred in the early diversification of Bryopsida. By aligning the modern chromosomes to the seven reconstructed ancestral chromosomes, genomic synteny-guided phylogenomic analyses provided strong evidence for the ancestral psi event shared by Dicranidae, Bryidae and P. patens . Furthermore, ancestral chromosomal projections and a phylogenomic resolution of Bryopsida subgenomes revealed distinct and lineage-specific chromosomal loss patterns in Dicranidae and Bryidae following the psi event. Our reconstructions reinforced the evolutionary significance and phylogenetic timing of the psi event and provided systemic insights into the sex and chromosomal evolution in mosses.
... We generated the clean data by eliminating adapter sequences, reads containing poly-N and low-quality reads from the raw data, using the FastQC tools [77]. Clean reads were then aligned to the P. nutans reference genome [78] using HISAT2 [31]. Using StringTie [79], the lncRNA transcriptome was assembled based on the reads mapped to the P. nutans reference genome [78]. ...
... Clean reads were then aligned to the P. nutans reference genome [78] using HISAT2 [31]. Using StringTie [79], the lncRNA transcriptome was assembled based on the reads mapped to the P. nutans reference genome [78]. The GffCompare tool was used to annotate the assembled transcripts. ...
Antarctic organisms are consistently suffering from multiple environmental pressures, especially the strong UV radiation caused by the loss of the ozone layer. The mosses and lichens dominate the vegetation of the Antarctic continent, which grow and propagate in these harsh environments. However, the molecular mechanisms and related regulatory networks of these Antarctic plants against UV-B radiation are largely unknown. Here, we used an integrated multi-omics approach to study the regulatory mechanism of long non-coding RNAs (lncRNAs) of an Antarctic moss (Pohlia nutans) in response to UV-B radiation. We identified a total of 5729 lncRNA sequences by transcriptome sequencing, including 1459 differentially expressed lncRNAs (DELs). Through functional annotation, we found that the target genes of DELs were significantly enriched in plant-pathogen interaction and the flavonoid synthesis pathway. In addition, a total of 451 metabolites were detected by metabonomic analysis, and 97 differentially change metabolites (DCMs) were found. Flavonoids account for 20% of the total significantly up-regulated metabolites. In addition, the comprehensive transcriptome and metabolome analyses revealed the co-expression pattern of DELs and DCMs of flavonoids. Our results provide insights into the regulatory network of lncRNA under UV-B radiation and the adaptation of Antarctic moss to the polar environments.
... In land plants, flavonoids serve as signal molecules and antioxidants under stress conditions and have prominent roles regulating plant growth and development [48,49]. Flavonoids, such as flavonols and anthocyanins, emerged sequentially as land plants evolved from aquatic to terrestrial environments, facilitating their adaptation to harsh conditions [19]. However, the molecular process of flavonoid biosynthesis in bryophytes and basal land plants is largely unknown [50]. ...
... In the present study, flavonoids, including flavanols, flavanones, flavones, and flavonols, accounted for 7.25% of the total compounds in P. nutans (Table S1). Under stress conditions, bryophytes can synthesize early colorless UV-B ultraviolet-absorbing substances rather than the down-stream products, such as anthocyanins [19,51]. Flavone and flavonol biosynthesis, however, belong to the early metabolites of flavonoid pathway, and they are catalysed by enzymes of different branching pathways into anthocyanins [52]. ...
... The high-quality clean reads were then retrieved and used for following analyses. Firstly, the clean reads were aligned to the reference genome of P. nutans [19], using HISAT program v2.1.0 to generate a bam format file with index information [63]. ...
12-oxo-phytodienoic acid (OPDA) is a biosynthetic precursor of jasmonic acid and triggers multiple biological processes from plant development to stress responses. However, the OPDA signaling and relevant regulatory networks were largely unknown in basal land plants. Using an integrated multi-omics technique, we investigated the global features in metabolites and transcriptional profiles of an Antarctic moss (Pohlia nutans) in response to OPDA treatment. We detected 676 metabolites based on the widely targeted metabolomics approach. A total of 82 significantly changed metabolites were observed, including fatty acids, flavonoids, phenolic acids, amino acids and derivatives, and alkaloids. In addition, the transcriptome sequencing was conducted to uncover the global transcriptional profiles. The representative differentially expressed genes were summarized into functions including Ca2+ signaling, abscisic acid signaling, jasmonate signaling, lipid and fatty acid biosynthesis, transcription factors, antioxidant enzymes, and detoxification proteins. The integrated multi-omics analysis revealed that the pathways of jasmonate and ABA signaling, lipid and fatty acid biosynthesis, and flavonoid biosynthesis might dominate the molecular responses to OPDA. Taken together, these observations provide insights into the molecular evolution of jasmonate signaling and the adaptation mechanisms of Antarctic moss to terrestrial habitats.
... Differentially expressed genes related to fatty acid pathway Previously, we have found that several gene families were expanded which participated in biosynthesis of metabolites such as fatty acid elongation and alpha-Linolenic acid metabolism (Liu et al., 2022). Here, we found that the content of verylong-chain fatty acids (VLCFAs) increased significantly under cold stress in metabolome analysis. ...
Antarctica is the coldest, driest, and most windy continent on earth. The major terrestrial vegetation consists of cryptogams (mosses and lichens) and two vascular plant species. However, the molecular mechanism of cold tolerance and relevant regulatory networks were largely unknown in these Antarctic plants. Here, we investigated the global alterations in metabolites and regulatory pathways of an Antarctic moss (Pohlia nutans) under cold stress using an integrated multi-omics approach. We found that proline content and several antioxidant enzyme activities were significantly increased in P. nutans under cold stress, but the contents of chlorophyll and total flavonoids were markedly decreased. A total of 559 metabolites were detected using ultra high-performance liquid chromatography/electrospray ionization tandem mass spectrometry (HPLC-ESI-MS/MS). We observed 39 and 71 differentially changed metabolites (DCMs) after 24 h and 60 h cold stress, indicating that several major pathways were differentially activated for producing fatty acids, alkaloids, flavonoids, terpenoids, and phenolic acids. In addition, the quantitative transcriptome sequencing was conducted to uncover the global transcriptional profiles of P. nutans under cold stress. The representative differentially expressed genes (DEGs) were identified and summarized to the function including Ca²⁺ signaling, ABA signaling, jasmonate signaling, fatty acids biosynthesis, flavonoid biosynthesis, and other biological processes. The integrated dataset analyses of metabolome and transcriptome revealed that jasmonate signaling, auxin signaling, very-long-chain fatty acids and flavonoid biosynthesis pathways might contribute to P. nutans acclimating to cold stress. Overall, these observations provide insight into Antarctic moss adaptations to polar habitats and the impact of global climate change on Antarctic plants.
... The clean reads were generated and used for the following analysis. Firstly, we performed the alignment program for mapping sequencing reads to the reference genome of P. nutans (Liu et al., 2022). This process was conducted by HISAT2 program, generating a bam format file with index information (Kim et al., 2019). ...
Most regions of the Antarctic continent are experiencing increased dryness due to global climate change. Mosses and lichens are the dominant vegetation of the ice-free areas of Antarctica. However, the molecular mechanisms of these Antarctic plants adapting to drought stress are less documented. Here, transcriptome and metabolome analyses were employed to reveal the responses of an Antarctic moss (Pohlia nutans subsp. LIU) to drought stress. We found that drought stress made the gametophytes turn yellow and curled, and enhanced the contents of malondialdehyde and proline, and the activities of antioxidant enzymes. Totally, 2,451 differentially expressed genes (DEGs) were uncovered under drought treatment. The representative DEGs are mainly involved in ROS-scavenging and detoxification, flavonoid metabolism pathway, plant hormone signaling pathway, lipids metabolism pathway, transcription factors and signal-related genes. Meanwhile, a total of 354 differentially changed metabolites (DCMs) were detected in the metabolome analysis. Flavonoids and lipids were the most abundant metabolites and they accounted for 41.53% of the significantly changed metabolites. In addition, integrated transcriptome and metabolome analyses revealed co-expression patterns of flavonoid and long-chain fatty acid biosynthesis genes and their metabolites. Finally, qPCR analysis demonstrated that the expression levels of stress-related genes were significantly increased. These genes included those involved in ABA signaling pathway (NCED3, PP2C, PYL, and SnAK2), jasmonate signaling pathway (AOC, AOS, JAZ, and OPR), flavonoid pathway (CHS, F3’,5’H, F3H, FLS, FNS, and UFGT), antioxidant and detoxifying functions (POD, GSH-Px, Prx and DTX), and transcription factors (ERF and DREB). In summary, we speculated that P. nutans were highly dependent on ABA and jasmonate signaling pathways, ROS scavenging, flavonoids and fatty acid metabolism in response to drought stress. These findings present an important knowledge for assessing the impact of coastal climate change on Antarctic basal plants.
Desiccation is typically fatal, but a small number of land plants have evolved vegetative desiccation tolerance (VDT), allowing them to dry without dying through a process called anhydrobiosis. Advances in sequencing technologies have enabled the investigation of genomes for desiccation-tolerant plants over the past decade. However, a dedicated and integrated database for these valuable genomic resources has been lacking. Our prolonged interest in VDT plant genomes motivated us to create the “Drying without Dying” database, which contains a total of 16 VDT-related plant genomes (including ten mosses) and incorporates 10 genomes that are closely related to VDT plants. The database features bioinformatic tools, such as blast and homologous cluster search, sequence retrieval, GO term and metabolic pathway enrichment statistics, expression profiling, co-expression network extraction, and JBrowser exploration for each genome. To demonstrate its utility we conducted tailored PFAM family statistical analyses, and we discovered that the drought-responsive ABA transporter AWPM-19 family is significantly tandemly duplicated in all bryophytes but rarely so in tracheophytes. Transcriptomic investigations also revealed that response patterns following desiccation diverged between bryophytes and angiosperms. Combined, the analyses provided genomic and transcriptomic evidence supporting a possible divergence and lineage-specific evolution of VDT in plants. The database can be accessed at http://desiccation.novogene.com. We expect this initial release of the “Drying without Dying” plant genome database will facilitate future discovery of VDT genetic resources.
