1
|
Wang S, Shi Y, Zhou Y, Hu W, Liu F. Full-length transcriptome sequencing of Arabidopsis plants provided new insights into the autophagic regulation of photosynthesis. Sci Rep 2024; 14:14588. [PMID: 38918488 PMCID: PMC11199623 DOI: 10.1038/s41598-024-65555-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2024] [Accepted: 06/20/2024] [Indexed: 06/27/2024] Open
Abstract
Autophagy is a highly conserved eukaryotic pathway and plays a crucial role in cell survival under stress conditions. Here, we applied a full-length transcriptome approach to study an Arabidopsis autophagy mutant (atg5-1) subjected to nitrogen-starvation, using Oxford Nanopore Technologies. A total of 39,033 transcripts were identified, including 11,356 new transcripts. In addition, alternative splicing (AS) events and lncRNAs were also detected between Col-0 (WT) and atg5-1. Differentially expressed transcript enrichment showed that autophagy upregulates the expression of many stress-responsive genes and inhibits the transcription of photosynthesis-associated genes. The qRT-PCR results showed that the expression patterns of photosynthesis-related genes in the atg5-1 differed under the conditions of nitrogen starvation and carbon starvation. Under nitrogen starvation treatment, many genes related to photosynthesis also exhibited AS. Chlorophyll fluorescence images revealed that the Fv/Fm and ΦPSII of old atg5-1 leaves were significantly reduced after nitrogen starvation treatment, but the Y(NPQ) indices were significantly increased compared to those of the WT plants. The results of qRT-PCR suggest that autophagy appears to be involved in the degradation of genes related to photodamage repair in PSII. Taken together, the full-length transcriptiome sequencing provide new insights into how new transcripts, lncRNAs and alternative splicing (AS) are involved in plant autophagy through full-length transcriptome sequencing and suggest a new potential link between autophagy and photosynthesis.
Collapse
Affiliation(s)
- Song Wang
- Lushan Botanical Garden, Jiangxi Province and Chinese Academy of Sciences, Jiujiang, 332900, Jiangxi, China
| | - Yunfeng Shi
- Lushan Botanical Garden, Jiangxi Province and Chinese Academy of Sciences, Jiujiang, 332900, Jiangxi, China
| | - Yanhui Zhou
- Lushan Botanical Garden, Jiangxi Province and Chinese Academy of Sciences, Jiujiang, 332900, Jiangxi, China
- College of Life Science, Nanchang University, Nanchang, 330031, Jiangxi, China
| | - Weiming Hu
- Lushan Botanical Garden, Jiangxi Province and Chinese Academy of Sciences, Jiujiang, 332900, Jiangxi, China.
| | - Fen Liu
- Lushan Botanical Garden, Jiangxi Province and Chinese Academy of Sciences, Jiujiang, 332900, Jiangxi, China.
| |
Collapse
|
2
|
Hou C, Zhang Q, Xie P, Lian H, Wang Y, Liang D, Cai Y, He B. Full-length transcriptome sequencing reveals the molecular mechanism of monoterpene and sesquiterpene biosynthesis in Cinnamomum burmannii. Front Genet 2023; 13:1087495. [PMID: 36685943 PMCID: PMC9852720 DOI: 10.3389/fgene.2022.1087495] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Accepted: 11/21/2022] [Indexed: 01/09/2023] Open
Abstract
Essential oil of Cinnamomum burmannii is rich in monoterpenes and sesquiterpenes and is widely used in cosmetics and medicines. Knowledge about the enzymes that catalyze the formation of monoterpenes and sesquiterpenes in C. burmannii is insufficient. Therefore, anatomy observation of C. burmannii at the four developmental stages (7 days, CBS1; 14 days, CBS2; 21 days, CBS3, and 28 days, CBS4) were conducted to elucidate the origins of essential oil production. Twelve full-length transcriptomes of C. burmannii leaves at the four stages were generated using Oxford Nanopore Technologies. GC-MS analysis revealed 15 monoterpene and sesquiterpenes dramatically increased from CBS1 to CBS4. A weighted correlation network analysis (WGCNA) in association and differentially expressed genes across four developmental stages were performed. A total of 44 differentially expressed genes (DEGs) were involved in terpenoid syntheses during leaf development. Among them, the DEGs of the mevalonate acid (MVA) pathway were predominantly expressed at CBS1, while those of the 2-C-methyl-D-erythritol 4-phosphate (MEP) pathway showed increased expression from CBS2 to CBS4. Besides, fourteen genes were associated with monoterpene synthesis and nine with sesquiterpene synthesis. Functions of these DEGs were further predicted with regard to gene expression profile and phylogenetic relationship with those characterized in previous studies. In addition, 922 long noncoding RNAs (lncRNAs) were detected, of which twelve were predicted to regulate monoterpene and sesquiterpene biosynthesis. The present study provided new insights the molecular mechanisms of monoterpenoid and sesquiterpenoid syntheses of C. burmannii.
Collapse
|
3
|
Hu XL, You C, Zhu K, Li X, Gong J, Ma H, Sun X. Nanopore long-read RNAseq reveals transcriptional variations in citrus species. FRONTIERS IN PLANT SCIENCE 2023; 13:1077797. [PMID: 36684788 PMCID: PMC9845879 DOI: 10.3389/fpls.2022.1077797] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/23/2022] [Accepted: 12/02/2022] [Indexed: 06/17/2023]
Abstract
The number of studies on plant transcriptomes using ONT RNAseq technology is rapidly increasing in recent. It is a powerful method to decipher transcriptomic complexity, particularly alternative splicing (AS) event detection. Citrus plants are the most important widely grown fruit crops. Exploring different AS events in citrus contributes to transcriptome improvement and functional genome study. Here, we performed ONT RNAseq in 9 species (Atalantia buxifolia, Citrus clementina, C. grandis, C. ichangensis, C. reticulata, C. sinensis, Clausena lansium, Fortunella hindsii, and Poncirus trifoliata), accompanied with Illumina sequencing. Non-redundant full-length isoforms were identified between 41,957 and 76,974 per species. Systematic analysis including different types of isoforms, number of isoforms per gene locus, isoform distribution, ORFs and lncRNA prediction and functional annotation were performed mainly focused on novel isoforms, unraveling the capability of novel isoforms detection and characterization. For AS events prediction, A3, RI, and AF were overwhelming types across 9 species. We analyzed isoform similarity and evolutionary relationships in all species. We identified that multiple isoforms derived from orthologous single copy genes among different species were annotated as enzymes, nuclear-related proteins or receptors. Isoforms with extending sequences on 5', 3', or both compared with reference genome were filtered out to provide information for transcriptome improvement. Our results provide novel insight into comprehending complex transcriptomes in citrus and valuable information for further investigation on the function of genes with diverse isoforms.
Collapse
Affiliation(s)
- Xiao-Li Hu
- Collaborative Innovation Center for Efficient and Green Production of Agriculture in Mountainous Areas of Zhejiang Province, College of Horticulture Science, Zhejiang A&F University, Hangzhou, Zhejiang, China
- Key Laboratory of Quality and Safety Control for Subtropical Fruit and Vegetable, Ministry of Agriculture and Rural Affairs, Zhejiang A&F University, Hangzhou, Zhejiang, China
| | - Congjun You
- Collaborative Innovation Center for Efficient and Green Production of Agriculture in Mountainous Areas of Zhejiang Province, College of Horticulture Science, Zhejiang A&F University, Hangzhou, Zhejiang, China
- Key Laboratory of Quality and Safety Control for Subtropical Fruit and Vegetable, Ministry of Agriculture and Rural Affairs, Zhejiang A&F University, Hangzhou, Zhejiang, China
| | - Kaikai Zhu
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, Jiangsu, China
| | - Xiaolong Li
- Collaborative Innovation Center for Efficient and Green Production of Agriculture in Mountainous Areas of Zhejiang Province, College of Horticulture Science, Zhejiang A&F University, Hangzhou, Zhejiang, China
- Key Laboratory of Quality and Safety Control for Subtropical Fruit and Vegetable, Ministry of Agriculture and Rural Affairs, Zhejiang A&F University, Hangzhou, Zhejiang, China
| | - Jinli Gong
- Collaborative Innovation Center for Efficient and Green Production of Agriculture in Mountainous Areas of Zhejiang Province, College of Horticulture Science, Zhejiang A&F University, Hangzhou, Zhejiang, China
- Key Laboratory of Quality and Safety Control for Subtropical Fruit and Vegetable, Ministry of Agriculture and Rural Affairs, Zhejiang A&F University, Hangzhou, Zhejiang, China
| | - Haijie Ma
- Collaborative Innovation Center for Efficient and Green Production of Agriculture in Mountainous Areas of Zhejiang Province, College of Horticulture Science, Zhejiang A&F University, Hangzhou, Zhejiang, China
- Key Laboratory of Quality and Safety Control for Subtropical Fruit and Vegetable, Ministry of Agriculture and Rural Affairs, Zhejiang A&F University, Hangzhou, Zhejiang, China
| | - Xuepeng Sun
- Collaborative Innovation Center for Efficient and Green Production of Agriculture in Mountainous Areas of Zhejiang Province, College of Horticulture Science, Zhejiang A&F University, Hangzhou, Zhejiang, China
- Key Laboratory of Quality and Safety Control for Subtropical Fruit and Vegetable, Ministry of Agriculture and Rural Affairs, Zhejiang A&F University, Hangzhou, Zhejiang, China
| |
Collapse
|
4
|
Liu NN, Ren ZY, Ren QD, Chang ZG, Li JL, Li XA, Sun ZY, He JM, Niu QS, Xing XM. Full length transcriptomes analysis of cold-resistance of Apis cerana in Changbai Mountain during overwintering period. Gene 2022; 830:146503. [PMID: 35487395 DOI: 10.1016/j.gene.2022.146503] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Revised: 03/21/2022] [Accepted: 04/14/2022] [Indexed: 11/15/2022]
Abstract
Apis cerana in Changbai Mountain is an ecological type of Apis cerana, which is an excellent breeding material with cold-resistant developed by long-term natural selection under the ecological conditions. However, the physiological and molecular mechanisms of Changbai Mountain population under cold stress are still unclear. In this study, the Nanopore sequencing was carried out for the transcriptome of Apis cerana in Changbai Mountain in the coldest period of overwintering, which will provide a reference to the cold-resistant mechanism. We determined 5,941 complete ORF sequences, 1,193 lncRNAs, 619 TFs, 10,866 SSRs and functional annotations of 11,599 new transcripts. Our results showed that the myosin family and the C2H2 zinc finger protein transcription factor family possibly have significant impacts on the response mechanism of cold stress during overwintering. In addition, the cold environment alters genes expression profiles in honeybees via different AS and APA mechanisms. These altered genes in Hippo, Foxo, and MARK pathways help them counter the stress of cold in overwinter period. Our results might provide clues about the response of eastern honeybees to extreme cold, and reflect the possible genetic basis of physiological changes.
Collapse
Affiliation(s)
- Nan-Nan Liu
- Institute of Special Animal and Plant Sciences of Chinese Academy of Agricultural Sciences, Changchun, Jilin 130112, PR China; Apiculture Science Institute of Jilin Province, Jilin, Jilin 132108, PR China.
| | - Zhong-Yuan Ren
- Jilin Institute of Chemical Technology, Jilin, Jilin 132022, PR China
| | - Qing-Dan Ren
- Jilin Provincial Animal Husbandry General Station, Changchun, Jilin 130699, PR China
| | - Zhi-Guang Chang
- Apiculture Science Institute of Jilin Province, Jilin, Jilin 132108, PR China
| | - Jie-Luan Li
- Apiculture Science Institute of Jilin Province, Jilin, Jilin 132108, PR China
| | - Xing-An Li
- Apiculture Science Institute of Jilin Province, Jilin, Jilin 132108, PR China
| | - Zhi-Yu Sun
- Apiculture Science Institute of Jilin Province, Jilin, Jilin 132108, PR China
| | - Jin-Ming He
- Apiculture Science Institute of Jilin Province, Jilin, Jilin 132108, PR China
| | - Qing-Sheng Niu
- Apiculture Science Institute of Jilin Province, Jilin, Jilin 132108, PR China.
| | - Xiu-Mei Xing
- Institute of Special Animal and Plant Sciences of Chinese Academy of Agricultural Sciences, Changchun, Jilin 130112, PR China.
| |
Collapse
|
5
|
Feng K, Kan XY, Li R, Yan YJ, Zhao SP, Wu P, Li LJ. Integrative Analysis of Long- and Short-Read Transcriptomes Identify the Regulation of Terpenoids Biosynthesis Under Shading Cultivation in Oenanthe javanica. Front Genet 2022; 13:813216. [PMID: 35464839 PMCID: PMC9022222 DOI: 10.3389/fgene.2022.813216] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Accepted: 03/21/2022] [Indexed: 11/13/2022] Open
Abstract
Water dropwort (Oenanthe javanica) is a popular vegetable with high nutritional value and distinctive flavor. The flavor is mainly correlate with the biosynthesis of terpenoids. Shading cultivation was used to improve the flavor in the production of water dropwort. However, the changes of terpenoids and the genes involved in terpenoids biosynthesis under shading treatment remains unclear. In this study, the long- and short-reads transcriptomes of water dropwort were constructed. In total, 57,743 non-redundant high-quality transcripts were obtained from the transcriptome. 28,514 SSRs were identified from non-redundant transcripts and the mono-nucleotide repeats were the most abundant SSRs. The lncRNAs of water dropwort were recognized and their target genes were predicted. The volatile compound contents in petioles and leaf blades of water dropwort were decreased after the shading treatment. The DEGs analysis was performed to identify the terpenoids biosynthesis genes. The results indicated that 5,288 DEGs were differentially expressed in petiole, of which 22 DEGs were enriched in the terpenoids backbone biosynthesis pathway. A total of 12 DEGs in terpenoids biosynthesis pathway were selected and further verified by qRT-PCR assay, demonstrating that the terpenoids biosynthesis genes were down-regulated under shading treatment. Here, the full-length transcriptome was constructed and the regulatory genes related to terpenoids biosynthesis in water dropwort were also investigated. These results will provide useful information for future researches on functional genomics and terpenoids biosynthesis mechanism in water dropwort.
Collapse
Affiliation(s)
- Kai Feng
- College of Horticulture and Plant Protection, Yangzhou University, Yangzhou, China
| | - Xia-Yue Kan
- College of Horticulture and Plant Protection, Yangzhou University, Yangzhou, China
| | - Rui Li
- College of Horticulture and Plant Protection, Yangzhou University, Yangzhou, China
| | - Ya-Jie Yan
- College of Horticulture and Plant Protection, Yangzhou University, Yangzhou, China
| | - Shu-Ping Zhao
- College of Horticulture and Plant Protection, Yangzhou University, Yangzhou, China
| | - Peng Wu
- College of Horticulture and Plant Protection, Yangzhou University, Yangzhou, China
| | - Liang-Jun Li
- College of Horticulture and Plant Protection, Yangzhou University, Yangzhou, China.,Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Yangzhou University, Yangzhou, China
| |
Collapse
|
6
|
Chen Z, He X. Application of third-generation sequencing in cancer research. MEDICAL REVIEW (BERLIN, GERMANY) 2021; 1:150-171. [PMID: 37724303 PMCID: PMC10388785 DOI: 10.1515/mr-2021-0013] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Accepted: 08/09/2021] [Indexed: 09/20/2023]
Abstract
In the past several years, nanopore sequencing technology from Oxford Nanopore Technologies (ONT) and single-molecule real-time (SMRT) sequencing technology from Pacific BioSciences (PacBio) have become available to researchers and are currently being tested for cancer research. These methods offer many advantages over most widely used high-throughput short-read sequencing approaches and allow the comprehensive analysis of transcriptomes by identifying full-length splice isoforms and several other posttranscriptional events. In addition, these platforms enable structural variation characterization at a previously unparalleled resolution and direct detection of epigenetic marks in native DNA and RNA. Here, we present a comprehensive summary of important applications of these technologies in cancer research, including the identification of complex structure variants, alternatively spliced isoforms, fusion transcript events, and exogenous RNA. Furthermore, we discuss the impact of the newly developed nanopore direct RNA sequencing (RNA-Seq) approach in advancing epitranscriptome research in cancer. Although the unique challenges still present for these new single-molecule long-read methods, they will unravel many aspects of cancer genome complexity in unprecedented ways and present an encouraging outlook for continued application in an increasing number of different cancer research settings.
Collapse
Affiliation(s)
- Zhiao Chen
- Fudan University Shanghai Cancer Center and Institutes of Biomedical Sciences, Fudan University, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Xianghuo He
- Fudan University Shanghai Cancer Center and Institutes of Biomedical Sciences, Fudan University, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
- Key Laboratory of Breast Cancer in Shanghai, Fudan University Shanghai Cancer Center, Fudan University, Shanghai, China
| |
Collapse
|
7
|
Liang Y, Gong Z, Wang J, Zheng J, Ma Y, Min L, Chen Q, Li Z, Qu Y, Chen Q, Li X. Nanopore-Based Comparative Transcriptome Analysis Reveals the Potential Mechanism of High-Temperature Tolerance in Cotton (Gossypium hirsutum L.). PLANTS 2021; 10:plants10112517. [PMID: 34834881 PMCID: PMC8618236 DOI: 10.3390/plants10112517] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Revised: 11/16/2021] [Accepted: 11/17/2021] [Indexed: 11/16/2022]
Abstract
Extreme high temperatures are threatening cotton production around the world due to the intensification of global warming. To cope with high-temperature stress, heat-tolerant cotton cultivars have been bred, but the heat-tolerant mechanism remains unclear. This study selected heat-tolerant (‘Xinluzao36′) and heat-sensitive (‘Che61-72′) cultivars of cotton treated with high-temperature stress as plant materials and performed comparative nanopore sequencing transcriptome analysis to reveal the potential heat-tolerant mechanism of cotton. Results showed that 120,605 nonredundant sequences were generated from the raw reads, and 78,601 genes were annotated. Differentially expressed gene (DEG) analysis showed that a total of 19,600 DEGs were screened; the DEGs involved in the ribosome, heat shock proteins, auxin and ethylene signaling transduction, and photosynthesis pathways may be attributed to the heat tolerance of the heat-tolerant cotton cultivar. This study also predicted a total of 5118 long non-coding RNAs (lncRNAs)and 24,462 corresponding target genes. Analysis of the target genes revealed that the expression of some ribosomal, heat shock, auxin and ethylene signaling transduction-related and photosynthetic proteins may be regulated by lncRNAs and further participate in the heat tolerance of cotton. This study deepens our understandings of the heat tolerance of cotton.
Collapse
Affiliation(s)
- Yajun Liang
- Engineering Research Centre of Cotton of Ministry of Education, Xinjiang Agricultural University, 311 Nongda East Road, Urumqi 830001, China; (Y.L.); (Q.C.); (Y.Q.)
- Xinjiang Academy of Agricultural Science, Urumqi 830001, China; (Z.G.); (J.W.); (J.Z.)
| | - Zhaolong Gong
- Xinjiang Academy of Agricultural Science, Urumqi 830001, China; (Z.G.); (J.W.); (J.Z.)
| | - Junduo Wang
- Xinjiang Academy of Agricultural Science, Urumqi 830001, China; (Z.G.); (J.W.); (J.Z.)
| | - Juyun Zheng
- Xinjiang Academy of Agricultural Science, Urumqi 830001, China; (Z.G.); (J.W.); (J.Z.)
| | - Yizan Ma
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China; (Y.M.); (L.M.)
| | - Ling Min
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China; (Y.M.); (L.M.)
| | - Qin Chen
- Engineering Research Centre of Cotton of Ministry of Education, Xinjiang Agricultural University, 311 Nongda East Road, Urumqi 830001, China; (Y.L.); (Q.C.); (Y.Q.)
| | - Zhiqiang Li
- Adsen Biotechnology Co., Ltd., Urumqi 830022, China;
| | - Yanying Qu
- Engineering Research Centre of Cotton of Ministry of Education, Xinjiang Agricultural University, 311 Nongda East Road, Urumqi 830001, China; (Y.L.); (Q.C.); (Y.Q.)
| | - Quanjia Chen
- Engineering Research Centre of Cotton of Ministry of Education, Xinjiang Agricultural University, 311 Nongda East Road, Urumqi 830001, China; (Y.L.); (Q.C.); (Y.Q.)
- Correspondence: (Q.C.); (X.L.)
| | - Xueyuan Li
- Xinjiang Academy of Agricultural Science, Urumqi 830001, China; (Z.G.); (J.W.); (J.Z.)
- Correspondence: (Q.C.); (X.L.)
| |
Collapse
|