PacBio Full-Length Transcriptome Sequencing Reveals the Mechanism of Salt Stress Response in <i>Sonneratia apetala</i>
<i>Sonneratia apetala</i> is an essential mangrove wetland restoration tree species. Studying its molecular mechanism for salt tolerance could lay a foundation for further cultivating excellent resistant germplasm. This study used a combination of PacBio isoform sequencing (Iso-seq) and...
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MDPI AG
2023-11-01
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| Series: | Plants |
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| Online Access: | https://www.mdpi.com/2223-7747/12/22/3849 |
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| author | Beibei Chen Tingting Liu Zhuanying Yang Shaoxia Yang Jinhui Chen |
| author_facet | Beibei Chen Tingting Liu Zhuanying Yang Shaoxia Yang Jinhui Chen |
| author_sort | Beibei Chen |
| collection | DOAJ |
| description | <i>Sonneratia apetala</i> is an essential mangrove wetland restoration tree species. Studying its molecular mechanism for salt tolerance could lay a foundation for further cultivating excellent resistant germplasm. This study used a combination of PacBio isoform sequencing (Iso-seq) and BGISEQ RNA sequencing (RNA-seq) to analyze the molecular mechanism to salt stress response of one-year-old <i>S. apetala</i> leaves. The growth and physiological analysis showed that physiological indexes such as growth rate, net photosynthetic rate and antioxidant enzyme activity all exhibit significant changes under salt stress. From Iso-seq, a total of 295,501 full-length transcripts, with an average length of 1418 bp, were obtained. RNA-seq produced 4712 differentially expressed genes (DEGs) as compared to a control group. Of these, 930 were identified to be co-expressed during the STEM time sequence analysis. Further, 715 and 444 co-expressed DEGs were annotated by GO and KEGG analyses, respectively. Moreover, 318 of the co-expressed DEGs were annotated as essential genes that were implicated in salt stress response of <i>S. apetala</i>, which were involved in transcription factors, signal transduction, hormone response, ROS homeostasis, osmotic balance, cell wall synthesis or modification. These results provide candidate targets for further characterization and offer insights into the salt-tolerant mechanism of <i>S. apetala</i>. |
| first_indexed | 2024-03-09T16:30:18Z |
| format | Article |
| id | doaj.art-4ec06a58f13c405c94b2c60c97e345a1 |
| institution | Directory Open Access Journal |
| issn | 2223-7747 |
| language | English |
| last_indexed | 2024-03-09T16:30:18Z |
| publishDate | 2023-11-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Plants |
| spelling | doaj.art-4ec06a58f13c405c94b2c60c97e345a12023-11-24T15:01:59ZengMDPI AGPlants2223-77472023-11-011222384910.3390/plants12223849PacBio Full-Length Transcriptome Sequencing Reveals the Mechanism of Salt Stress Response in <i>Sonneratia apetala</i>Beibei Chen0Tingting Liu1Zhuanying Yang2Shaoxia Yang3Jinhui Chen4Mangrove Research Center of Guangdong Ocean University, College of Coastal Agricultural Science, Guangdong Ocean University, Zhanjiang 524088, ChinaMangrove Research Center of Guangdong Ocean University, College of Coastal Agricultural Science, Guangdong Ocean University, Zhanjiang 524088, ChinaMangrove Research Center of Guangdong Ocean University, College of Coastal Agricultural Science, Guangdong Ocean University, Zhanjiang 524088, ChinaMangrove Research Center of Guangdong Ocean University, College of Coastal Agricultural Science, Guangdong Ocean University, Zhanjiang 524088, ChinaSchool of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), Hainan University, Sanya 572019, China<i>Sonneratia apetala</i> is an essential mangrove wetland restoration tree species. Studying its molecular mechanism for salt tolerance could lay a foundation for further cultivating excellent resistant germplasm. This study used a combination of PacBio isoform sequencing (Iso-seq) and BGISEQ RNA sequencing (RNA-seq) to analyze the molecular mechanism to salt stress response of one-year-old <i>S. apetala</i> leaves. The growth and physiological analysis showed that physiological indexes such as growth rate, net photosynthetic rate and antioxidant enzyme activity all exhibit significant changes under salt stress. From Iso-seq, a total of 295,501 full-length transcripts, with an average length of 1418 bp, were obtained. RNA-seq produced 4712 differentially expressed genes (DEGs) as compared to a control group. Of these, 930 were identified to be co-expressed during the STEM time sequence analysis. Further, 715 and 444 co-expressed DEGs were annotated by GO and KEGG analyses, respectively. Moreover, 318 of the co-expressed DEGs were annotated as essential genes that were implicated in salt stress response of <i>S. apetala</i>, which were involved in transcription factors, signal transduction, hormone response, ROS homeostasis, osmotic balance, cell wall synthesis or modification. These results provide candidate targets for further characterization and offer insights into the salt-tolerant mechanism of <i>S. apetala</i>.https://www.mdpi.com/2223-7747/12/22/3849<i>Sonneratia apetala</i>salt stressfull-length transcriptometranscriptional regulation |
| spellingShingle | Beibei Chen Tingting Liu Zhuanying Yang Shaoxia Yang Jinhui Chen PacBio Full-Length Transcriptome Sequencing Reveals the Mechanism of Salt Stress Response in <i>Sonneratia apetala</i> Plants <i>Sonneratia apetala</i> salt stress full-length transcriptome transcriptional regulation |
| title | PacBio Full-Length Transcriptome Sequencing Reveals the Mechanism of Salt Stress Response in <i>Sonneratia apetala</i> |
| title_full | PacBio Full-Length Transcriptome Sequencing Reveals the Mechanism of Salt Stress Response in <i>Sonneratia apetala</i> |
| title_fullStr | PacBio Full-Length Transcriptome Sequencing Reveals the Mechanism of Salt Stress Response in <i>Sonneratia apetala</i> |
| title_full_unstemmed | PacBio Full-Length Transcriptome Sequencing Reveals the Mechanism of Salt Stress Response in <i>Sonneratia apetala</i> |
| title_short | PacBio Full-Length Transcriptome Sequencing Reveals the Mechanism of Salt Stress Response in <i>Sonneratia apetala</i> |
| title_sort | pacbio full length transcriptome sequencing reveals the mechanism of salt stress response in i sonneratia apetala i |
| topic | <i>Sonneratia apetala</i> salt stress full-length transcriptome transcriptional regulation |
| url | https://www.mdpi.com/2223-7747/12/22/3849 |
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