Characterization of the Gene Expression Profile Response to Drought Stress in <i>Populus ussuriensis</i> Using PacBio SMRT and Illumina Sequencing
In this study, we characterized the gene expression profile in the roots of <i>Populus ussuriensis</i> at 0, 6, 12, 24, 48 and 120 h after the start of polyethylene glycol (PEG)-induced drought stress using PacBio single-molecule real-time sequencing (SMRT-seq) and Illumina RNA sequencin...
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| Format: | Article |
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MDPI AG
2022-03-01
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| Series: | International Journal of Molecular Sciences |
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| Online Access: | https://www.mdpi.com/1422-0067/23/7/3840 |
| _version_ | 1797438947611115520 |
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| author | Wenlong Li Zhiwei Liu He Feng Jingli Yang Chenghao Li |
| author_facet | Wenlong Li Zhiwei Liu He Feng Jingli Yang Chenghao Li |
| author_sort | Wenlong Li |
| collection | DOAJ |
| description | In this study, we characterized the gene expression profile in the roots of <i>Populus ussuriensis</i> at 0, 6, 12, 24, 48 and 120 h after the start of polyethylene glycol (PEG)-induced drought stress using PacBio single-molecule real-time sequencing (SMRT-seq) and Illumina RNA sequencing. Compared to the control, 2244 differentially expressed genes (DEGs) were identified, and many of these DEGs were associated with the signal transduction, antioxidant system, ion accumulation and drought-inducing proteins. Changes in certain physiological and biochemical indexes, such as antioxidant activity and the contents of Ca<sup>2+</sup>, proline, and total soluble sugars, were further confirmed in <i>P. ussuriensis</i> roots. Furthermore, most of the differentially expressed transcription factors were members of the AP2/ERF, C2H2, MYB, NAC, C2C2 and WRKY families. Additionally, based on PacBio SMRT-seq results, 5955 long non-coding RNAs and 700 alternative splicing events were identified. Our results provide a global view of the gene expression profile that contributes to drought resistance in <i>P. ussuriensis</i> and meaningful information for genetic engineering research in the future. |
| first_indexed | 2024-03-09T11:45:40Z |
| format | Article |
| id | doaj.art-97d0a2948c444e2bb0916e172e238f0e |
| institution | Directory Open Access Journal |
| issn | 1661-6596 1422-0067 |
| language | English |
| last_indexed | 2024-03-09T11:45:40Z |
| publishDate | 2022-03-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | International Journal of Molecular Sciences |
| spelling | doaj.art-97d0a2948c444e2bb0916e172e238f0e2023-11-30T23:22:54ZengMDPI AGInternational Journal of Molecular Sciences1661-65961422-00672022-03-01237384010.3390/ijms23073840Characterization of the Gene Expression Profile Response to Drought Stress in <i>Populus ussuriensis</i> Using PacBio SMRT and Illumina SequencingWenlong Li0Zhiwei Liu1He Feng2Jingli Yang3Chenghao Li4State Key Laboratory of Forest Genetics and Tree Breeding, Northeast Forestry University, 26 Hexing Road, Harbin 150040, ChinaState Key Laboratory of Forest Genetics and Tree Breeding, Northeast Forestry University, 26 Hexing Road, Harbin 150040, ChinaState Key Laboratory of Forest Genetics and Tree Breeding, Northeast Forestry University, 26 Hexing Road, Harbin 150040, ChinaState Key Laboratory of Forest Genetics and Tree Breeding, Northeast Forestry University, 26 Hexing Road, Harbin 150040, ChinaState Key Laboratory of Forest Genetics and Tree Breeding, Northeast Forestry University, 26 Hexing Road, Harbin 150040, ChinaIn this study, we characterized the gene expression profile in the roots of <i>Populus ussuriensis</i> at 0, 6, 12, 24, 48 and 120 h after the start of polyethylene glycol (PEG)-induced drought stress using PacBio single-molecule real-time sequencing (SMRT-seq) and Illumina RNA sequencing. Compared to the control, 2244 differentially expressed genes (DEGs) were identified, and many of these DEGs were associated with the signal transduction, antioxidant system, ion accumulation and drought-inducing proteins. Changes in certain physiological and biochemical indexes, such as antioxidant activity and the contents of Ca<sup>2+</sup>, proline, and total soluble sugars, were further confirmed in <i>P. ussuriensis</i> roots. Furthermore, most of the differentially expressed transcription factors were members of the AP2/ERF, C2H2, MYB, NAC, C2C2 and WRKY families. Additionally, based on PacBio SMRT-seq results, 5955 long non-coding RNAs and 700 alternative splicing events were identified. Our results provide a global view of the gene expression profile that contributes to drought resistance in <i>P. ussuriensis</i> and meaningful information for genetic engineering research in the future.https://www.mdpi.com/1422-0067/23/7/3840drought stress<i>Populus ussuriensis</i>rootsingle-molecule real-time sequencingalternative splicing |
| spellingShingle | Wenlong Li Zhiwei Liu He Feng Jingli Yang Chenghao Li Characterization of the Gene Expression Profile Response to Drought Stress in <i>Populus ussuriensis</i> Using PacBio SMRT and Illumina Sequencing International Journal of Molecular Sciences drought stress <i>Populus ussuriensis</i> root single-molecule real-time sequencing alternative splicing |
| title | Characterization of the Gene Expression Profile Response to Drought Stress in <i>Populus ussuriensis</i> Using PacBio SMRT and Illumina Sequencing |
| title_full | Characterization of the Gene Expression Profile Response to Drought Stress in <i>Populus ussuriensis</i> Using PacBio SMRT and Illumina Sequencing |
| title_fullStr | Characterization of the Gene Expression Profile Response to Drought Stress in <i>Populus ussuriensis</i> Using PacBio SMRT and Illumina Sequencing |
| title_full_unstemmed | Characterization of the Gene Expression Profile Response to Drought Stress in <i>Populus ussuriensis</i> Using PacBio SMRT and Illumina Sequencing |
| title_short | Characterization of the Gene Expression Profile Response to Drought Stress in <i>Populus ussuriensis</i> Using PacBio SMRT and Illumina Sequencing |
| title_sort | characterization of the gene expression profile response to drought stress in i populus ussuriensis i using pacbio smrt and illumina sequencing |
| topic | drought stress <i>Populus ussuriensis</i> root single-molecule real-time sequencing alternative splicing |
| url | https://www.mdpi.com/1422-0067/23/7/3840 |
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