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Xu H, Li M, Ma D, Gao J, Tao J, Meng J. Identification of key genes for triacylglycerol biosynthesis and storage in herbaceous peony (Paeonia lactifolra Pall.) seeds based on full-length transcriptome. BMC Genomics 2024; 25:601. [PMID: 38877407 PMCID: PMC11179206 DOI: 10.1186/s12864-024-10513-w] [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: 01/13/2024] [Accepted: 06/10/2024] [Indexed: 06/16/2024] Open
Abstract
BACKGROUND The herbaceous peony (Paeonia lactiflora Pall.) is extensively cultivated in China due to its root being used as a traditional Chinese medicine known as 'Radix Paeoniae Alba'. In recent years, it has been discovered that its seeds incorporate abundant unsaturated fatty acids, thereby presenting a potential new oilseed plant. Surprisingly, little is known about the full-length transcriptome sequencing of Paeonia lactiflora, limiting research into its gene function and molecular mechanisms. RESULTS A total of 484,931 Reads of Inserts (ROI) sequences and 1,455,771 full-Length non-chimeric reads (FLNC) sequences were obtained for CDS prediction, TF analysis, SSR analysis and lncRNA identification. In addition, gene function annotation and gene structure analysis were performed. A total of 4905 transcripts were related to lipid metabolism biosynthesis pathway, belonging to 28 enzymes. We use these data to identify 10 oleosin (OLE) and 5 diacylglycerol acyltransferase (DGAT) gene members after de-redundancy. The analysis of physicochemical properties and secondary structure showed them similarity in gene family respectively. The phylogenetic analysis showed that the distribution of OLE and DGAT family members was roughly the same as that of Arabidopsis. Quantitative real-time polymerase chain reaction (qRT-PCR) analyses revealed expression changes in different seed development stages, and showed a trend of increasing and then decreasing. CONCLUSION In summary, these results provide new insights into the molecular mechanism of triacylglycerol (TAG) biosynthesis and storage during the seedling stage in Paeonia lactiflora. It provides theoretical references for selecting and breeding oil varieties and understanding the functions of oil storage as well as lipid synthesis related genes in Paeonia lactiflora.
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Affiliation(s)
- Huajie Xu
- College of Horticulture and Landscape Architecture, Yangzhou University, Yangzhou, 225009, China
| | - Miao Li
- College of Horticulture and Landscape Architecture, Yangzhou University, Yangzhou, 225009, China
| | - Di Ma
- College of Horticulture and Landscape Architecture, Yangzhou University, Yangzhou, 225009, China
| | - Jiajun Gao
- College of Horticulture and Landscape Architecture, Yangzhou University, Yangzhou, 225009, China
| | - Jun Tao
- College of Horticulture and Landscape Architecture, Yangzhou University, Yangzhou, 225009, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, the Ministry of Education of China, Yangzhou University, Yangzhou, 225009, China
| | - Jiasong Meng
- College of Horticulture and Landscape Architecture, Yangzhou University, Yangzhou, 225009, China.
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, the Ministry of Education of China, Yangzhou University, Yangzhou, 225009, China.
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Chowdhury NB, Simons-Senftle M, Decouard B, Quillere I, Rigault M, Sajeevan KA, Acharya B, Chowdhury R, Hirel B, Dellagi A, Maranas C, Saha R. A multi-organ maize metabolic model connects temperature stress with energy production and reducing power generation. iScience 2023; 26:108400. [PMID: 38077131 PMCID: PMC10709110 DOI: 10.1016/j.isci.2023.108400] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Revised: 10/30/2023] [Accepted: 11/03/2023] [Indexed: 02/18/2024] Open
Abstract
Climate change has adversely affected maize productivity. Thereby, a holistic understanding of metabolic crosstalk among its organs is important to address this issue. Thus, we reconstructed the first multi-organ maize metabolic model, iZMA6517, and contextualized it with heat and cold stress transcriptomics data using expression distributed reaction flux measurement (EXTREAM) algorithm. Furthermore, implementing metabolic bottleneck analysis on contextualized models revealed differences between these stresses. While both stresses had reducing power bottlenecks, heat stress had additional energy generation bottlenecks. We also performed thermodynamic driving force analysis, revealing thermodynamics-reducing power-energy generation axis dictating the nature of temperature stress responses. Thus, a temperature-tolerant maize ideotype can be engineered by leveraging the proposed thermodynamics-reducing power-energy generation axis. We experimentally inoculated maize root with a beneficial mycorrhizal fungus, Rhizophagus irregularis, and as a proof-of-concept demonstrated its efficacy in alleviating temperature stress. Overall, this study will guide the engineering effort of temperature stress-tolerant maize ideotypes.
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Affiliation(s)
- Niaz Bahar Chowdhury
- Chemical and Biomolecular Engineering, University of Nebraska-Lincoln, Lincoln, NE, USA
| | | | - Berengere Decouard
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), 78000 Versailles, France
| | - Isabelle Quillere
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), 78000 Versailles, France
| | - Martine Rigault
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), 78000 Versailles, France
| | | | - Bibek Acharya
- Chemical and Biological Engineering, Iowa State University, Ames, IA, USA
| | - Ratul Chowdhury
- Chemical and Biological Engineering, Iowa State University, Ames, IA, USA
| | - Bertrand Hirel
- Centre de Versailles-Grignon, Institut National de Recherche pour l’Agriculture, Versailles, France
| | - Alia Dellagi
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), 78000 Versailles, France
| | - Costas Maranas
- Chemical Engineering, The Pennsylvania State University, University Park, PA, USA
| | - Rajib Saha
- Chemical and Biomolecular Engineering, University of Nebraska-Lincoln, Lincoln, NE, USA
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Li Y, Mokrani A, Fu H, Shi C, Li Q, Liu S. Development of Nanopore sequencing-based full-length transcriptome database toward functional genome annotation of the Pacific oyster, Crassostrea gigas. Genomics 2023; 115:110697. [PMID: 37567397 DOI: 10.1016/j.ygeno.2023.110697] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Revised: 07/28/2023] [Accepted: 08/08/2023] [Indexed: 08/13/2023]
Abstract
The Pacific oyster (Crassostrea gigas) is a widely cultivated shellfish in the world, while its transcriptome diversity remains less unexplored due to the limitation of short reads. In this study, we used Oxford Nanopore sequencing to develop the full-length transcriptome database of C. gigas. We identified 77,920 full-length transcripts from 21,523 genes, and uncovered 9668 alternative splicing events and 87,468 alternative polyadenylation sites. Notably, a total of 16,721 novel transcripts were annotated in this work. Furthermore, integrative analysis of 25 publicly available RNA-seq datasets revealed the transcriptome diversity involved in post-transcriptional regulation in C. gigas. We further developed a Drupal based webserver, Cgtdb, which can be used for transcriptome visualization, sequence alignment, and functional genome annotation analyses. This work provides valuable resources and a useful tool for integrative analysis of various transcriptome datasets in C. gigas, which will serve as an essential reference for functional annotation of the oyster genome.
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Affiliation(s)
- Yin Li
- Key Laboratory of Mariculture (Ocean University of China), Ministry of Education, and College of Fisheries, Ocean University of China, Qingdao 266003, China
| | - Ahmed Mokrani
- Key Laboratory of Mariculture (Ocean University of China), Ministry of Education, and College of Fisheries, Ocean University of China, Qingdao 266003, China
| | - Huiru Fu
- Key Laboratory of Mariculture (Ocean University of China), Ministry of Education, and College of Fisheries, Ocean University of China, Qingdao 266003, China
| | - Chenyu Shi
- Key Laboratory of Mariculture (Ocean University of China), Ministry of Education, and College of Fisheries, Ocean University of China, Qingdao 266003, China
| | - Qi Li
- Key Laboratory of Mariculture (Ocean University of China), Ministry of Education, and College of Fisheries, Ocean University of China, Qingdao 266003, China
| | - Shikai Liu
- Key Laboratory of Mariculture (Ocean University of China), Ministry of Education, and College of Fisheries, Ocean University of China, Qingdao 266003, China.
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Long Non-Coding RNA lncWOX11a Suppresses Adventitious Root Formation of Poplar by Regulating the Expression of PeWOX11a. Int J Mol Sci 2023; 24:ijms24065766. [PMID: 36982841 PMCID: PMC10057709 DOI: 10.3390/ijms24065766] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Revised: 02/18/2023] [Accepted: 03/15/2023] [Indexed: 03/22/2023] Open
Abstract
Long non-coding RNAs (lncRNAs), a class of poorly conserved transcripts without protein-encoding ability, are widely involved in plant organogenesis and stress responses by mediating the transmission and expression of genetic information at the transcriptional, posttranscriptional, and epigenetic levels. Here, we cloned and characterized a novel lncRNA molecule through sequence alignment, Sanger sequencing, transient expression in protoplasts, and genetic transformation in poplar. lncWOX11a is a 215 bp transcript located on poplar chromosome 13, ~50 kbp upstream of PeWOX11a on the reverse strand, and the lncRNA may fold into a series of complex stem–loop structures. Despite the small open reading frame (sORF) of 51 bp within lncWOX11a, bioinformatics analysis and protoplast transfection revealed that lncWOX11a has no protein-coding ability. The overexpression of lncWOX11a led to a decrease in the quantity of adventitious roots on the cuttings of transgenic poplars. Further, cis-regulatory module prediction and CRISPR/Cas9 knockout experiments with poplar protoplasts demonstrated that lncWOX11a acts as a negative regulator of adventitious rooting by downregulating the WUSCHEL-related homeobox gene WOX11, which is supposed to activate adventitious root development in plants. Collectively, our findings imply that lncWOX11a is essential for modulating the formation and development of adventitious roots.
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Jagtap AB, Yadav IS, Vikal Y, Praba UP, Kaur N, Gill AS, Johal GS. Transcriptional dynamics of maize leaves, pollens and ovules to gain insights into heat stress-related responses. FRONTIERS IN PLANT SCIENCE 2023; 14:1117136. [PMID: 36875566 PMCID: PMC9975602 DOI: 10.3389/fpls.2023.1117136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Accepted: 02/02/2023] [Indexed: 06/18/2023]
Abstract
Heat stress (HS) is one of the alarming issues today due to global warming and is the foremost detrimental to crop production. Maize is one of the versatile crops grown over different agro-climatic conditions. However, it is significantly sensitive to heat stress, especially during the reproductive phase. The heat stress tolerance mechanism is yet to be elucidated at the reproductive stage. Thus, the present study focused on identifying transcriptional changes in two inbreds, LM 11 (sensitive to HS) and CML 25 (tolerant to HS), under intense heat stress at 42°C during the reproductive stage from three tissues viz. flag leaf, tassel, and ovule. Samples from each inbred were collected after 5 days of pollinations for RNA isolation. Six cDNA libraries were constructed from three separate tissues of LM 11 and CML 25 and sequenced using an Illumina HiSeq2500 platform. A total of 2,164 (1127 up-regulated and 1037 down-regulated) differentially expressed genes (DEGs) were identified with 1151, 451, and 562 DEGs in comparisons of LM 11 and CML 25, corresponding to a leaf, pollen, and ovule, respectively. Functional annotated DEGs associated with transcription factors (TFs) viz. AP2, MYB, WRKY, PsbP, bZIP, and NAM, heat shock proteins (HSP20, HSP70, and HSP101/ClpB), as well as genes related to photosynthesis (PsaD & PsaN), antioxidation (APX and CAT) and polyamines (Spd and Spm). KEGG pathways analyses showed that the metabolic overview pathway and secondary metabolites biosynthesis pathway, with the involvement of 264 and 146 genes, respectively, were highly enriched in response to heat stress. Notably, the expression changes of the most common HS-responsive genes were typically much more significant in CML 25, which might explain why CML 25 is more heat tolerant. Seven DEGs were common in leaf, pollen, and ovule; and involved in the polyamines biosynthesis pathway. Their exact role in maize heat stress response would warrant further studies. These results enhanced our understanding to heat stress responses in maize.
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Affiliation(s)
- Ashok Babadev Jagtap
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, India
| | - Inderjit Singh Yadav
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, India
| | - Yogesh Vikal
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, India
| | - Umesh Preethi Praba
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, India
| | - Navneet Kaur
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, India
| | - Adeshpal Singh Gill
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, India
| | - Gurmukh S. Johal
- Department of Botany and Pathology, Purdue University, West Lafayette, IN, United States
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