Genome-wide analysis of long non-coding RNAs (lncRNAs) in two contrasting rapeseed (Brassica napus L.) genotypes subjected to drought stress and re-watering

Abstract Background: Drought stress is a major abiotic factor that affects rapeseed (Brassica napus L.) productivity. Though previous studies indicated that long non-coding RNAs (lncRNAs) play a key role in response to drought stress, a scheme for genome-wide identification and characterization of lncRNAs’ response to drought stress is still lacking, especially in the case of B. napus. In order to further understand the molecular mechanism of the response of B. napus to drought stress, we compared changes in the transcriptome between Q2 (a drought-tolerant genotype) and Qinyou8 (a drought-sensitive genotype) in response to drought stress and rehydration treatment at the seedling stage. Results: A total of 5,546 down-regulated and 6,997 up-regulated mRNAs were detected in Q2 compared with 7,824 and 10,251 in Qinyou8, respectively; 369 down-regulated and 108 up-regulated lncRNAs were detected in Q2 compared with 449 and 257 in Qinyou8, respectively. LncRNA- mRNA interaction network analysis indicated that the co-expression network of Q2 was composed of 145 network nodes and 5,175 connections, while the co-expression network of Qinyou8 was composed of 305 network nodes and 22,327 connections. We further identified 34 TFs corresponding to 126 differentially expressed lncRNAs in Q2, and 45 TFs corresponding to 359 differentially expressed lncRNAs in Qinyou8. Differential expression analysis of lncRNAs indicated that up- and down-regulated mRNAs co-expressed with lncRNAs participated in different metabolic pathways and were involved in different regulatory mechanisms in the two genotypes. Notably, some lncRNAs were co-expressed with BnaC07g44670D, which are associated with plant hormone signal transduction. Additionally, some mRNAs which were co-located with XLOC_052298, XLOC_094954 and XLOC_012868 were mainly categorized as signal transport and defense/stress response. Conclusions: The results of this study increased our understanding of expression characterization of rapeseed lncRNAs in response to drought stress and re-watering, which would be useful to provide a reference for the further study of the function and action mechanisms of lncRNAs under drought stress and re-watering.

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Genome-wide analysis of long non-coding RNAs (lncRNAs) in two contrasting rapeseed (Brassica napus L.) genotypes subjected to drought stress and re-watering

10.21203/rs.2.16111/v4 ◽

2020 ◽

Author(s):

Xiaoyu Tan ◽

Su Li ◽

Liyong Hu ◽

Chunlei Zhang

Keyword(s):

Drought Stress ◽

Brassica Napus ◽

Differential Expression Analysis ◽

Differentially Expressed ◽

Abiotic Factor ◽

Brassica Napus L ◽

Network Nodes ◽

Genome Wide ◽

Non Coding Rnas

Abstract Background: Drought stress is a major abiotic factor that affects rapeseed ( Brassica napus L.) productivity. Though previous studies indicated that long non-coding RNAs (lncRNAs) play a key role in response to drought stress, a scheme for genome-wide identification and characterization of lncRNAs’ response to drought stress is still lacking, especially in the case of B . napus . In order to further understand the molecular mechanism of the response of B . napus to drought stress, we compared changes in the transcriptome between Q2 (a drought-tolerant genotype) and Qinyou8 (a drought-sensitive genotype) in response to drought stress and rehydration treatment at the seedling stage. Results: A total of 5,546 down-regulated and 6,997 up-regulated mRNAs were detected in Q2 compared with 7,824 and 10,251 in Qinyou8, respectively; 369 down-regulated and 108 up-regulated lncRNAs were detected in Q2 compared with 449 and 257 in Qinyou8, respectively. LncRNA- mRNA interaction network analysis indicated that the co-expression network of Q2 was composed of 145 network nodes and 5,175 connections, while the co-expression network of Qinyou8 was composed of 305 network nodes and 22,327 connections. We further identified 34 TFs corresponding to 126 differentially expressed lncRNAs in Q2, and 45 TFs corresponding to 359 differentially expressed lncRNAs in Qinyou8. Differential expression analysis of lncRNAs indicated that up- and down-regulated mRNAs co-expressed with lncRNAs participated in different metabolic pathways and were involved in different regulatory mechanisms in the two genotypes . Notably, some lncRNAs were co-expressed with BnaC07g44670D, which are associated with plant hormone signal transduction. Additionally, some mRNAs which were co-located with XLOC_052298, XLOC_094954 and XLOC_012868 were mainly categorized as signal transport and defense/stress response. Conclusions: The results of this study increased our understanding of expression characterization of rapeseed lncRNAs in response to drought stress and re-watering, which would be useful to provide a reference for the further study of the function and action mechanisms of lncRNAs under drought stress and re-watering.

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Genome-wide analysis of long non-coding RNAs (lncRNAs) in two contrasting rapeseed (Brassica napus L.) genotypes subjected to drought stress and re-watering

10.21203/rs.2.16111/v3 ◽

2020 ◽

Author(s):

Xiaoyu Tan ◽

Su Li ◽

Liyong Hu ◽

Chunlei Zhang

Keyword(s):

Drought Stress ◽

Brassica Napus ◽

Differential Expression Analysis ◽

Differentially Expressed ◽

Abiotic Factor ◽

Brassica Napus L ◽

Network Nodes ◽

Genome Wide ◽

Non Coding Rnas

Abstract Background: Drought stress is a major abiotic factor that affects rapeseed ( Brassica napus L.) productivity. Though previous studies indicated that long non-coding RNAs (lncRNAs) play a key role in response to drought stress, a scheme for genome-wide identification and characterization of lncRNAs’ response to drought stress is still lacking, especially in the case of B . napus . In order to further understand the molecular mechanism of the response of B . napus to drought stress, we compared changes in the transcriptome between Q2 (a drought-tolerant genotype) and Qinyou8 (a drought-sensitive genotype) in response to drought stress and rehydration treatment at the seedling stage. Results: A total of 5,546 down-regulated and 6,997 up-regulated mRNAs were detected in Q2 compared with 7,824 and 10,251 in Qinyou8, respectively; 369 down-regulated and 108 up-regulated lncRNAs were detected in Q2 compared with 449 and 257 in Qinyou8, respectively. LncRNA- mRNA interaction network analysis indicated that the co-expression network of Q2 was composed of 145 network nodes and 5,175 connections, while the co-expression network of Qinyou8 was composed of 305 network nodes and 22,327 connections. We further identified 34 TFs corresponding to 126 differentially expressed lncRNAs in Q2, and 45 TFs corresponding to 359 differentially expressed lncRNAs in Qinyou8. Differential expression analysis of lncRNAs indicated that up- and down-regulated mRNAs co-expressed with lncRNAs participated in different metabolic pathways and were involved in different regulatory mechanisms in the two genotypes . Notably, some lncRNAs were co-expressed with BnaC07g44670D, which are associated with plant hormone signal transduction. Additionally, some mRNAs which were co-located with XLOC_052298, XLOC_094954 and XLOC_012868 were mainly categorized as signal transport and defense/stress response. Conclusions: The results of this study increased our understanding of expression characterization of rapeseed lncRNAs in response to drought stress and re-watering, which would be useful to provide a reference for the further study of the function and action mechanisms of lncRNAs under drought stress and re-watering.

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Genome-wide analysis of long non-coding RNAs (lncRNAs) in two contrasting rapeseed (Brassica napus L.) genotypes subjected to drought stress

10.21203/rs.2.16111/v1 ◽

2019 ◽

Author(s):

Xiaoyu Tan ◽

Su Li ◽

Liyong Hu ◽

Chunlei Zhang

Keyword(s):

Drought Stress ◽

Brassica Napus ◽

Differential Expression Analysis ◽

Abiotic Factor ◽

Brassica Napus L ◽

Network Nodes ◽

Drought Tolerant ◽

Genome Wide ◽

Non Coding Rnas

Abstract Background: Drought stress is a major abiotic factor that affects rapeseed ( Brassica napus L.) productivity. Though previous studies indicated that long non-coding RNAs (lncRNAs) play a key role in response to drought stress, a scheme for genome-wide identification and characterization of lncRNAs’ response to drought stress is still lacking, especially in the case of B . napus . In order to further understand the molecular mechanism of the response of B . napus to drought stress, we compared changes in the transcriptome between Q2 (a drought-tolerant genotype) and Qinyou8 (a drought-sensitive genotype) in response to drought stress and rehydration treatment at the seedling stage. Results: A total of 5,546 down-regulated and 6,997 up-regulated mRNAs were detected in Q2 compared with 7,824 and 10,251 in Qinyou8, respectively; 369 down-regulated and 108 up-regulated lncRNAs were detected in Q2 compared with 449 and 257 in Qinyou8, respectively. We further identified 34 TFs corresponding to 126 differently expressed lncRNAs in Q2, and 45 TFs corresponding to 359 differently expressed lncRNAs in Qinyou8. Differential expression analysis of lncRNAs indicated that up- and down-regulated mRNAs co-expressed with lncRNAs participated in different metabolic pathways and were involved in different regulatory mechanisms in the two genotypes . Notably, some lncRNAs were co-expressed and co-located with BnaC07g44670D, which are associated with plant hormone signal transduction. Additionally, some mRNAs which were co-located with LNC_002535 (XLOC_052298), LNC_004924 (XLOC_094954) and LNC_000539 (XLOC_012868) were mainly categorized as signal transport and defense/stress response. Finally, co-expression network analysis indicated that the co-expression network of Q2 was composed of 145 network nodes and 5,175 connections, while the co-expression network of Qinyou8 was composed of 305 network nodes and 22,327 connections. Conclusions: The differentially expressed mRNAs and lncRNAs may play important roles in response to drought stress and rehydration treatments and could provide basic information for new ways to improve the drought resistance of Rapeseed Brassica napus .

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