Dynamics of chromatin accessibility and genome wide control of desiccation tolerance in the resurrection plant Haberlea rhodopensis
Abstract Background Drought is one of the main consequences of global climate change and this problem is expected to intensify in the future. Resurrection plants evolved the ability to withstand the negative impact of long periods of almost complete desiccation and to recover at rewatering. In this...
| Main Authors: | , , , , |
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BMC
2023-12-01
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| Series: | BMC Plant Biology |
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| Online Access: | https://doi.org/10.1186/s12870-023-04673-2 |
| _version_ | 1797377101097074688 |
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| author | Petko Mladenov Xiaohua Wang Zhaolin Yang Dimitar Djilianov Xin Deng |
| author_facet | Petko Mladenov Xiaohua Wang Zhaolin Yang Dimitar Djilianov Xin Deng |
| author_sort | Petko Mladenov |
| collection | DOAJ |
| description | Abstract Background Drought is one of the main consequences of global climate change and this problem is expected to intensify in the future. Resurrection plants evolved the ability to withstand the negative impact of long periods of almost complete desiccation and to recover at rewatering. In this respect, many physiological, transcriptomic, proteomic and genomic investigations have been performed in recent years, however, few epigenetic control studies have been performed on these valuable desiccation-tolerant plants so far. Results In the present study, for the first time for resurrection plants we provide evidences about the differential chromatin accessibility of Haberlea rhodopensis during desiccation stress by ATAC-seq (Assay for Transposase Accessible Chromatin with high-throughput sequencing). Based on gene similarity between species, we used the available genome of the closely related resurrection plant Dorcoceras hygrometricum to identify approximately nine hundred transposase hypersensitive sites (THSs) in H. rhodopensis. The majority of them corresponds to proximal and distal regulatory elements of different genes involved in photosynthesis, carbon metabolism, synthesis of secondary metabolites, cell signalling and transcriptional regulation, cell growth, cell wall, stomata conditioning, chaperons, oxidative stress, autophagy and others. Various types of binding motifs recognized by several families of transcription factors have been enriched from the THSs found in different stages of drought. Further, we used the previously published RNA-seq data from H. rhodopensis to evaluate the expression of transcription factors putatively interacting with the enriched motifs, and the potential correlation between the identified THS and the expression of their corresponding genes. Conclusions These results provide a blueprint for investigating the epigenetic regulation of desiccation tolerance in resurrection plant H. rhodopensis and comparative genomics between resurrection and non-resurrection species with available genome information. |
| first_indexed | 2024-03-08T19:48:06Z |
| format | Article |
| id | doaj.art-298f27a64ee040ce9e352e28590b2ce0 |
| institution | Directory Open Access Journal |
| issn | 1471-2229 |
| language | English |
| last_indexed | 2024-03-08T19:48:06Z |
| publishDate | 2023-12-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Plant Biology |
| spelling | doaj.art-298f27a64ee040ce9e352e28590b2ce02023-12-24T12:13:39ZengBMCBMC Plant Biology1471-22292023-12-0123111710.1186/s12870-023-04673-2Dynamics of chromatin accessibility and genome wide control of desiccation tolerance in the resurrection plant Haberlea rhodopensisPetko Mladenov0Xiaohua Wang1Zhaolin Yang2Dimitar Djilianov3Xin Deng4State Key Laboratory of Plant Diversity and Specialty Crops, Institute of Botany, Chinese Academy of SciencesState Key Laboratory of Plant Diversity and Specialty Crops, Institute of Botany, Chinese Academy of SciencesState Key Laboratory of Plant Diversity and Specialty Crops, Institute of Botany, Chinese Academy of SciencesAgricultural AcademyState Key Laboratory of Plant Diversity and Specialty Crops, Institute of Botany, Chinese Academy of SciencesAbstract Background Drought is one of the main consequences of global climate change and this problem is expected to intensify in the future. Resurrection plants evolved the ability to withstand the negative impact of long periods of almost complete desiccation and to recover at rewatering. In this respect, many physiological, transcriptomic, proteomic and genomic investigations have been performed in recent years, however, few epigenetic control studies have been performed on these valuable desiccation-tolerant plants so far. Results In the present study, for the first time for resurrection plants we provide evidences about the differential chromatin accessibility of Haberlea rhodopensis during desiccation stress by ATAC-seq (Assay for Transposase Accessible Chromatin with high-throughput sequencing). Based on gene similarity between species, we used the available genome of the closely related resurrection plant Dorcoceras hygrometricum to identify approximately nine hundred transposase hypersensitive sites (THSs) in H. rhodopensis. The majority of them corresponds to proximal and distal regulatory elements of different genes involved in photosynthesis, carbon metabolism, synthesis of secondary metabolites, cell signalling and transcriptional regulation, cell growth, cell wall, stomata conditioning, chaperons, oxidative stress, autophagy and others. Various types of binding motifs recognized by several families of transcription factors have been enriched from the THSs found in different stages of drought. Further, we used the previously published RNA-seq data from H. rhodopensis to evaluate the expression of transcription factors putatively interacting with the enriched motifs, and the potential correlation between the identified THS and the expression of their corresponding genes. Conclusions These results provide a blueprint for investigating the epigenetic regulation of desiccation tolerance in resurrection plant H. rhodopensis and comparative genomics between resurrection and non-resurrection species with available genome information.https://doi.org/10.1186/s12870-023-04673-2Resurrection plantsDesiccation toleranceATAC-seqEpigenetic regulationTranscription factorsGene expression |
| spellingShingle | Petko Mladenov Xiaohua Wang Zhaolin Yang Dimitar Djilianov Xin Deng Dynamics of chromatin accessibility and genome wide control of desiccation tolerance in the resurrection plant Haberlea rhodopensis BMC Plant Biology Resurrection plants Desiccation tolerance ATAC-seq Epigenetic regulation Transcription factors Gene expression |
| title | Dynamics of chromatin accessibility and genome wide control of desiccation tolerance in the resurrection plant Haberlea rhodopensis |
| title_full | Dynamics of chromatin accessibility and genome wide control of desiccation tolerance in the resurrection plant Haberlea rhodopensis |
| title_fullStr | Dynamics of chromatin accessibility and genome wide control of desiccation tolerance in the resurrection plant Haberlea rhodopensis |
| title_full_unstemmed | Dynamics of chromatin accessibility and genome wide control of desiccation tolerance in the resurrection plant Haberlea rhodopensis |
| title_short | Dynamics of chromatin accessibility and genome wide control of desiccation tolerance in the resurrection plant Haberlea rhodopensis |
| title_sort | dynamics of chromatin accessibility and genome wide control of desiccation tolerance in the resurrection plant haberlea rhodopensis |
| topic | Resurrection plants Desiccation tolerance ATAC-seq Epigenetic regulation Transcription factors Gene expression |
| url | https://doi.org/10.1186/s12870-023-04673-2 |
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