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Srikakulam N, Sridevi G, Pandi G. High-quality reference transcriptome construction improves RNA-seq quantification in Oryza sativa indica. Front Genet 2022; 13:995072. [PMID: 36246658 PMCID: PMC9558114 DOI: 10.3389/fgene.2022.995072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Accepted: 09/02/2022] [Indexed: 11/13/2022] Open
Abstract
The Reference Transcriptomic Dataset (RTD) is an accurate and comprehensive collection of transcripts originating from a given organism. It holds the key to precise transcript quantification and downstream analysis of differential expressions and regulations. Currently, transcriptome annotations for most crop plants are far from complete. For example, Oryza sativa indica (O. sativa indica) is reported to have 40,759 transcripts in the Ensembl database without alternative transcript isoforms and alternative splicing (AS) events. To generate a high-quality RTD, we conducted RNA sequencing of rice leaf samples collected at various time points during Rhizoctonia solani infection. The obtained reads were analyzed by adopting the recently developed computational analysis pipeline to assemble the RTD with increased transcript and AS diversity for O. sativa indica (IndicaRTD). After stringent quality filtering, the newly constructed transcriptome annotation was comprised of 122,968 non-redundant transcripts from 53,695 genes. This study identified many novel transcripts compared to Ensembl deposited data that are important for regulating molecular and physiological processes in the plant system. Currently, the assembled IndicaRTD must allow fast quantification of transcript and gene expression with high precision.
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Affiliation(s)
- Nagesh Srikakulam
- Laboratory of RNA Biology and Epigenomics, Department of Plant Biotechnology, School of Biotechnology, Madurai Kamaraj University, Madurai, India
- *Correspondence: Nagesh Srikakulam, ; Gopal Pandi,
| | - Ganapathi Sridevi
- Department of Plant Biotechnology, School of Biotechnology, Madurai Kamaraj University, Madurai, India
| | - Gopal Pandi
- Laboratory of RNA Biology and Epigenomics, Department of Plant Biotechnology, School of Biotechnology, Madurai Kamaraj University, Madurai, India
- *Correspondence: Nagesh Srikakulam, ; Gopal Pandi,
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RNA-Seq Analysis Demonstrates Different Strategies Employed by Tiger Nuts ( Cyperus esculentus L.) in Response to Drought Stress. LIFE (BASEL, SWITZERLAND) 2022; 12:life12071051. [PMID: 35888139 PMCID: PMC9322875 DOI: 10.3390/life12071051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Revised: 07/04/2022] [Accepted: 07/11/2022] [Indexed: 11/30/2022]
Abstract
Drought stress, an important abiotic stress, has affected global agricultural production by limiting the yield and the quality of crops. Tiger nuts (Cyperus esculentus L.) are C4 crops in the Cyperaceae family, which have high-quality wholesome ingredients. However, data on mechanisms underlying the response of tiger nuts to drought stress are few. Here, the variety of Jisha 1 and 15% polyethylene glycol (PEG; a drought stress simulator) were used to study the mechanisms of stress response in tiger nuts. Our evaluation of the changes in physiological indicators such as electrolyte leakage (El), malondialdehyde (MDA), hydrogen peroxide (H2O2), superoxide anion (O2−) and activities of reactive oxygen species (ROS) showed that 12 h was the most suitable time point to harvest and analyze the response to drought stress. Thereafter, we performed transcriptome (RNA-Seq) analysis in the control (CK) and stress treatment groups and showed that there was a total of 1760 differentially expressed genes (DEGs). Gene Ontology (GO) analysis showed that the DEGs were enriched in abscisic acid (ABA) terms, and pathways such as starch and sucrose metabolism (ko00500), phenylpropanoid biosynthesis (ko00940) and plant hormone signal transduction (ko04075) were significantly enriched in the Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis. In addition, quantitative real-time PCR (qRT-PCR) analysis of the DEGs demonstrated an upregulation of ABA and lignin content, as well as enzyme activities in enriched pathways, which validated the RNA-Seq data. These results revealed the pathways and mechanisms adopted by the tiger nuts in response to drought stress.
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Zhang Q, Zhang WJ, Yin ZG, Li WJ, Zhao HH, Zhang S, Zhuang L, Wang YX, Zhang WH, Du JD. Genome- and Transcriptome-Wide Identification of C3Hs in Common Bean ( Phaseolus vulgaris L.) and Structural and Expression-Based Analyses of Their Functions During the Sprout Stage Under Salt-Stress Conditions. Front Genet 2020; 11:564607. [PMID: 33101386 PMCID: PMC7522512 DOI: 10.3389/fgene.2020.564607] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Accepted: 08/19/2020] [Indexed: 12/24/2022] Open
Abstract
CCCH (C3H) zinc-finger proteins are involved in plant biotic and abiotic stress responses, growth and development, and disease resistance. However, studies on C3H genes in Phaseolus vulgaris L. (common bean) are limited. Here, 29 protein-encoding C3H genes, located on 11 different chromosomes, were identified in P. vulgaris. A phylogenetic analysis categorized the PvC3Hs into seven subfamilies on the basis of distinct features, such as exon–intron structure, cis-regulatory elements, and MEME motifs. A collinearity analysis revealed connections among the PvC3Hs in the same and different species. The PvC3H genes showed tissue-specific expression patterns during the sprout stage, as assessed by real-time quantitative PCR (RT-qPCR). Using RNA-sequencing and RT-qPCR data, PvC3Hs were identified as being enriched through Gene Ontology and Kyoto Encyclopedia of Genes and Genomes analyses in binding, channel activity, and the spliceosome pathway. These results provide useful information and a rich resource that can be exploited to functionally characterize and understand PvC3Hs. These PvC3Hs, especially those enriched in binding, channel activity, and the spliceosome pathway will further facilitate the molecular breeding of common bean and provide insights into the correlations between PvC3Hs and salt-stress responses during the sprout stage.
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Affiliation(s)
- Qi Zhang
- Laboratory Crop Genetics and Breeding, College of Agriculture, Heilongjiang Bayi Agricultural University, Daqing, China
| | - Wen-Jing Zhang
- Laboratory Crop Genetics and Breeding, College of Agriculture, Heilongjiang Bayi Agricultural University, Daqing, China
| | - Zhen-Gong Yin
- Crop Resources Institute of Heilongjiang Academy of Agricultural Sciences, Heilongjiang, China
| | - Wei-Jia Li
- Laboratory Crop Genetics and Breeding, College of Agriculture, Heilongjiang Bayi Agricultural University, Daqing, China
| | - Hao-Hao Zhao
- Laboratory Crop Genetics and Breeding, College of Agriculture, Heilongjiang Bayi Agricultural University, Daqing, China
| | - Shuo Zhang
- Laboratory Crop Genetics and Breeding, College of Agriculture, Heilongjiang Bayi Agricultural University, Daqing, China
| | - Lin Zhuang
- Laboratory Crop Genetics and Breeding, College of Agriculture, Heilongjiang Bayi Agricultural University, Daqing, China
| | - Yu-Xin Wang
- Laboratory Crop Genetics and Breeding, College of Agriculture, Heilongjiang Bayi Agricultural University, Daqing, China
| | - Wen-Hui Zhang
- Laboratory Crop Genetics and Breeding, College of Agriculture, Heilongjiang Bayi Agricultural University, Daqing, China
| | - Ji-Dao Du
- Laboratory Crop Genetics and Breeding, College of Agriculture, Heilongjiang Bayi Agricultural University, Daqing, China.,Laboratory Crop Genetics and Breeding, National Coarse Cereals Engineering Research Center, Daqing, China
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Subudhi PK, Garcia RS, Coronejo S, Tapia R. Comparative Transcriptomics of Rice Genotypes with Contrasting Responses to Nitrogen Stress Reveals Genes Influencing Nitrogen Uptake through the Regulation of Root Architecture. Int J Mol Sci 2020; 21:ijms21165759. [PMID: 32796695 PMCID: PMC7460981 DOI: 10.3390/ijms21165759] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Revised: 07/31/2020] [Accepted: 08/07/2020] [Indexed: 02/02/2023] Open
Abstract
The indiscriminate use of nitrogenous fertilizers continues unabated for commercial crop production, resulting in air and water pollution. The development of rice varieties with enhanced nitrogen use efficiency (NUE) will require a thorough understanding of the molecular basis of a plant’s response to low nitrogen (N) availability. The global expression profiles of root tissues collected from low and high N treatments at different time points in two rice genotypes, Pokkali and Bengal, with contrasting responses to N stress and contrasting root architectures were examined. Overall, the number of differentially expressed genes (DEGs) in Pokkali (indica) was higher than in Bengal (japonica) during low N and early N recovery treatments. Most low N DEGs in both genotypes were downregulated whereas early N recovery DEGs were upregulated. Of these, 148 Pokkali-specific DEGs might contribute to Pokkali’s advantage under N stress. These DEGs included transcription factors and transporters and were involved in stress responses, growth and development, regulation, and metabolism. Many DEGs are co-localized with quantitative trait loci (QTL) related to root growth and development, chlorate-resistance, and NUE. Our findings suggest that the superior growth performance of Pokkali under low N conditions could be due to the genetic differences in a diverse set of genes influencing N uptake through the regulation of root architecture.
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