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

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.

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

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.

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

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.

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

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 .

scholarly journals Genome-wide characterization of coding and non-coding RNAs in the ovary of honeybee workers and queens

Apidologie ◽  
2020 ◽  
Vol 51 (5) ◽  
pp. 777-792
Author(s):  
Xiao Chen ◽  
Wei Shi
Keyword(s):  
Egg Laying ◽  
Differentially Expressed ◽  
Sequencing Data ◽  
Competing Endogenous Rna ◽  
Genome Wide ◽  
Competing Endogenous Rna Network ◽  
Non Coding Rnas ◽  
Virgin Queens ◽  
Potential Interactions

Abstract Adult honeybee queens and workers drastically differ in ovary state and ovary size. However, this reproductive bias is only partially understood from the view of a single RNA type. In this study, we predicted 10,271 mRNAs, 7235 lncRNAs, 11,794 circRNAs, and 164 miRNAs in the ovary of honeybee workers through bioinformatics. Combining RNA sequencing data of honeybee virgin queens, 4385 mRNAs, 2390 lncRNAs, 5602 circRNAs, and 75 miRNAs were differentially expressed in workers compared with virgins. Compared with egg-laying queens, 6536 mRNAs, 3130 lncRNAs, 5751 circRNAs, and 81 miRNAs were differentially expressed in workers. Further, functional annotation revealed that neural regulation was closely related to ovary state. Moreover, the potential interactions among circRNAs, miRNAs, lncRNAs, and mRNAs revealed that vitellogenin, ecdysone-induced protein 74, ame_circ_0001176, and ame_circ_0001243 might play critical roles in the competing endogenous RNA network. These findings suggest that the integrative RNA networks have potential effects in ovarian phenotype differences in honeybees.

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