PacBio and Illumina RNA Sequencing Identify Alternative Splicing Events in Response to Cold Stress in Two Poplar Species
In eukaryotes, alternative splicing (AS) is a crucial regulatory mechanism that modulates mRNA diversity and stability. The contribution of AS to stress is known in many species related to stress, but the posttranscriptional mechanism in poplar under cold stress is still unclear. Recent studies have...
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Frontiers Media S.A.
2021-10-01
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| Series: | Frontiers in Plant Science |
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fpls.2021.737004/full |
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| author | Jingli Yang Wanqiu Lv Liying Shao Yanrui Fu Haimei Liu Chengjun Yang Aihua Chen Xieyu Xie Zhiwei Wang Chenghao Li |
| author_facet | Jingli Yang Wanqiu Lv Liying Shao Yanrui Fu Haimei Liu Chengjun Yang Aihua Chen Xieyu Xie Zhiwei Wang Chenghao Li |
| author_sort | Jingli Yang |
| collection | DOAJ |
| description | In eukaryotes, alternative splicing (AS) is a crucial regulatory mechanism that modulates mRNA diversity and stability. The contribution of AS to stress is known in many species related to stress, but the posttranscriptional mechanism in poplar under cold stress is still unclear. Recent studies have utilized the advantages of single molecular real-time (SMRT) sequencing technology from Pacific Bioscience (PacBio) to identify full-length transcripts. We, therefore, used a combination of single-molecule long-read sequencing and Illumina RNA sequencing (RNA-Seq) for a global analysis of AS in two poplar species (Populus trichocarpa and P. ussuriensis) under cold stress. We further identified 1,261 AS events in P. trichocarpa and 2,101 in P. ussuriensis among which intron retention, with a frequency of more than 30%, was the most prominent type under cold stress. RNA-Seq data analysis and annotation revealed the importance of calcium, abscisic acid, and reactive oxygen species signaling in cold stress response. Besides, the low temperature rapidly induced multiple splicing factors, transcription factors, and differentially expressed genes through AS. In P. ussuriensis, there was a rapid occurrence of AS events, which provided a new insight into the complexity and regulation of AS during cold stress response in different poplar species for the first time. |
| first_indexed | 2024-12-17T12:11:48Z |
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| id | doaj.art-8bdc4fe763aa456a9d8e1f8f7ced7795 |
| institution | Directory Open Access Journal |
| issn | 1664-462X |
| language | English |
| last_indexed | 2024-12-17T12:11:48Z |
| publishDate | 2021-10-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Plant Science |
| spelling | doaj.art-8bdc4fe763aa456a9d8e1f8f7ced77952022-12-21T21:49:22ZengFrontiers Media S.A.Frontiers in Plant Science1664-462X2021-10-011210.3389/fpls.2021.737004737004PacBio and Illumina RNA Sequencing Identify Alternative Splicing Events in Response to Cold Stress in Two Poplar SpeciesJingli Yang0Wanqiu Lv1Liying Shao2Yanrui Fu3Haimei Liu4Chengjun Yang5Aihua Chen6Xieyu Xie7Zhiwei Wang8Chenghao Li9State Key Laboratory of Forest Genetics and Tree Breeding, Northeast Forestry University, Harbin, ChinaState Key Laboratory of Forest Genetics and Tree Breeding, Northeast Forestry University, Harbin, ChinaState Key Laboratory of Forest Genetics and Tree Breeding, Northeast Forestry University, Harbin, ChinaState Key Laboratory of Forest Genetics and Tree Breeding, Northeast Forestry University, Harbin, ChinaBiology Group, Jiamusi No.1 High School, Jiamusi, ChinaState Key Laboratory of Forest Genetics and Tree Breeding, Northeast Forestry University, Harbin, ChinaEconomic Forest Laboratory, Mudanjiang Branch of Heilongjiang Academy of Forestry, Mudanjiang, ChinaState Key Laboratory of Forest Genetics and Tree Breeding, Northeast Forestry University, Harbin, ChinaState Key Laboratory of Forest Genetics and Tree Breeding, Northeast Forestry University, Harbin, ChinaState Key Laboratory of Forest Genetics and Tree Breeding, Northeast Forestry University, Harbin, ChinaIn eukaryotes, alternative splicing (AS) is a crucial regulatory mechanism that modulates mRNA diversity and stability. The contribution of AS to stress is known in many species related to stress, but the posttranscriptional mechanism in poplar under cold stress is still unclear. Recent studies have utilized the advantages of single molecular real-time (SMRT) sequencing technology from Pacific Bioscience (PacBio) to identify full-length transcripts. We, therefore, used a combination of single-molecule long-read sequencing and Illumina RNA sequencing (RNA-Seq) for a global analysis of AS in two poplar species (Populus trichocarpa and P. ussuriensis) under cold stress. We further identified 1,261 AS events in P. trichocarpa and 2,101 in P. ussuriensis among which intron retention, with a frequency of more than 30%, was the most prominent type under cold stress. RNA-Seq data analysis and annotation revealed the importance of calcium, abscisic acid, and reactive oxygen species signaling in cold stress response. Besides, the low temperature rapidly induced multiple splicing factors, transcription factors, and differentially expressed genes through AS. In P. ussuriensis, there was a rapid occurrence of AS events, which provided a new insight into the complexity and regulation of AS during cold stress response in different poplar species for the first time.https://www.frontiersin.org/articles/10.3389/fpls.2021.737004/fullPopulus trichocarpaPopulus ussuriensisalternative splicingcold stressPacBioRNA-Seq |
| spellingShingle | Jingli Yang Wanqiu Lv Liying Shao Yanrui Fu Haimei Liu Chengjun Yang Aihua Chen Xieyu Xie Zhiwei Wang Chenghao Li PacBio and Illumina RNA Sequencing Identify Alternative Splicing Events in Response to Cold Stress in Two Poplar Species Frontiers in Plant Science Populus trichocarpa Populus ussuriensis alternative splicing cold stress PacBio RNA-Seq |
| title | PacBio and Illumina RNA Sequencing Identify Alternative Splicing Events in Response to Cold Stress in Two Poplar Species |
| title_full | PacBio and Illumina RNA Sequencing Identify Alternative Splicing Events in Response to Cold Stress in Two Poplar Species |
| title_fullStr | PacBio and Illumina RNA Sequencing Identify Alternative Splicing Events in Response to Cold Stress in Two Poplar Species |
| title_full_unstemmed | PacBio and Illumina RNA Sequencing Identify Alternative Splicing Events in Response to Cold Stress in Two Poplar Species |
| title_short | PacBio and Illumina RNA Sequencing Identify Alternative Splicing Events in Response to Cold Stress in Two Poplar Species |
| title_sort | pacbio and illumina rna sequencing identify alternative splicing events in response to cold stress in two poplar species |
| topic | Populus trichocarpa Populus ussuriensis alternative splicing cold stress PacBio RNA-Seq |
| url | https://www.frontiersin.org/articles/10.3389/fpls.2021.737004/full |
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