The Antarctic Moss Pohlia nutans Genome Provides Insights Into the Evolution of Bryophytes and the Adaptation to Extreme Terrestrial Habitats

Liu, Shenghao; Fang, Shuo; Cong, Bin; Li, Tingting; Zhang, Zhaohui; Zhao, Linlin; Zhang, Pengying

doi:10.3389/fpls.2022.920138

Cited by 12 publications

(16 citation statements)

References 94 publications

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“…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 ).…”

Section: Methodsmentioning

confidence: 99%

Integrated transcriptome and metabolome analyses reveal the adaptation of Antarctic moss Pohlia nutans to drought stress

Fang

Zhang

et al. 2022

Front. Plant Sci.

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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.

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Section: Methodsmentioning

confidence: 99%

Integrated transcriptome and metabolome analyses reveal the adaptation of Antarctic moss Pohlia nutans to drought stress

Fang

Zhang

et al. 2022

Front. Plant Sci.

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“…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 very-long-chain fatty acids (VLCFAs) increased significantly under cold stress in metabolome analysis.…”

Section: Resultsmentioning

confidence: 99%

Metabolic profiling and gene expression analyses provide insights into cold adaptation of an Antarctic moss Pohlia nutans

Liu

Fang

et al. 2022

Front. Plant Sci.

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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.

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“…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 ].…”

Section: Discussionmentioning

confidence: 99%

“…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 ].…”

Section: Discussionmentioning

confidence: 99%

“…However, the signal transduction and the endogenous responses involved in OPDA signaling remain elusive in bryophytes [ 18 ]. Scientists have sequenced and released several genomes of bryophytes, such as P. patens , M. polymorpha , Anthoceros angustus , Ceratodon purpureus , and Pohlia nutans [ 11 , 19 , 20 , 21 ]. These new genomes and transcriptome sequencing projects provide abundant supports for evolutionary analysis of hormone signaling.…”

Section: Introductionmentioning

confidence: 99%

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Insights into the Jasmonate Signaling in Basal Land Plant Revealed by the Multi-Omics Analysis of an Antarctic Moss Pohlia nutans Treated with OPDA

Liu

Li²,

Zhang³

et al. 2022

IJMS

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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.

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The Antarctic Moss Pohlia nutans Genome Provides Insights Into the Evolution of Bryophytes and the Adaptation to Extreme Terrestrial Habitats

Cited by 12 publications

References 94 publications

Integrated transcriptome and metabolome analyses reveal the adaptation of Antarctic moss Pohlia nutans to drought stress

Integrated transcriptome and metabolome analyses reveal the adaptation of Antarctic moss Pohlia nutans to drought stress

Metabolic profiling and gene expression analyses provide insights into cold adaptation of an Antarctic moss Pohlia nutans

Insights into the Jasmonate Signaling in Basal Land Plant Revealed by the Multi-Omics Analysis of an Antarctic Moss Pohlia nutans Treated with OPDA

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