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Research article
Xingchu Yan
Oil Crops Research Institute of Chinese Academy of Agricultural Science
Corresponding Author
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Background: Oil flax (linseed, Linum usitatissimum L.) is one of the most important oil crops., However, the increases in drought resulting from climate change have dramatically reduces linseed yield and quality, but very little is known about how linseed coordinates the expression of drought resistance gene in response to different level of drought stress (DS) on the genome-wide level.
Results: To explore the linseed transcriptional response of DS and repeated drought (RD) stress, we determined the drought tolerance of different linseed varieties. Then we performed full-length transcriptome sequencing of drought-resistant variety (Z141) and drought-sensitive variety (NY-17) under DS and RD stress at the seedling stage using single-molecule real-time sequencing and RNA-sequencing. Gene Ontology (GO) and reduce and visualize GO (REVIGO) enrichment analysis showed that upregulated genes of Z141 were enriched in more functional pathways related to plant drought tolerance than those of NY-17 were under DS. In addition, 4436 linseed transcription factors were identified, and 1190 were responsive to stress treatments. Moreover, protein-protein interaction (PPI) network analysis showed that the proline biosynthesis pathway interacts with stress response genes through RAD50 (DNA repair protein 50) interacting protein 1 (RIN-1). Finally, proline biosynthesis and DNA repair structural gene expression patterns were verified by RT- PCR.
Conclusions: The drought tolerance of Z141 may be related to its upregulation of drought tolerance genes under DS. Proline may play an important role in linseed drought tolerance by maintaining cell osmotic and protecting DNA from ROS damage. In summary, this study provides a new perspective to understand the drought adaptability of linseed.
Keywords
transcriptome, Linseed, Repeated drought, SMRT, transcription factors
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This is a list of supplementary files associated with this preprint. Click to download.
- SupplementaryFigureS1.rar
Figure S1. Bubble diagram showing the GO classification of differentially expressed transcripts between DS and RD in Z141 or NY-17. (a, b) GO terms of downregulated genes overlapping between DS and RD in Z141 (a) or NY-17 (b). (c-f) GO terms of genes up- (c, d) or downregulated (e, f) in only Z141 under DS or RD, respectively. (g-j) GO terms of genes up- (g, h) or downregulated (i, j) in only NY-17 under DS or RD respectively.
- SupplementaryFigureS2.rar
Figure S2. Bubble diagram showing the GO classification of differentially expressed transcripts between Z141 and NY-17 under DS or RD treatment. (a, b) GO terms of downregulated genes overlapping between Z141 and NY-17 under DS (a) or RD (b) treatment. (c-f) GO terms of genes up- (c, d) or downregulated (e, f) in Z141 or NY-17 under only DS. (g-j) GO terms of genes up- (g, h) or downregulated (i, j) in Z141 or NY-17 under only RD.
- SupplementaryFigureS3.rar
Figure S3. Tree diagram showing the REVIGO classification of up- or downregulated differentially expressed transcripts in Z141 or NY-17 under DS or RD. (a, b) REVIGO classification of up- (a) and downregulated (b) genes in Z141 under RD stress. (c, d) REVIGO classification of up- (c) and downregulated (d) genes in NY-17 under DS. (e, f) REVIGO classification of up- (e) and downregulated (f) genes in NY-17 under RD stress.
- SupplementaryFigureS4.rar
Figure S4. MapMan visualization of drought stress-responsive DEGs in Z141 (b) and NY-17 (a, c) under DS and RD stress, respectively. The up- and downregulated DEGs are represented in red and blue colour. The Colour brightness indicates the degree of difference, as shown in the scale on the right.
- SupplementaryFigureS5.rar
- SupplementaryTableS1S9S13S19.docx
- SupplementaryTableS10.xlsx
- SupplementaryTableS11.xlsx
- SupplementaryTableS12.xlsx
- SupplementaryTableS13.xlsx
- SupplementaryTableS14.xlsx
- SupplementaryTableS15.xlsx
- SupplementaryTableS16.xlsx
- SupplementaryTableS17.xls
- SupplementaryTableS18.xls
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On 13 Jul, 2020
Editor invited
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Review #3 received
Received 27 May, 2020
Editorial decision: Major revision
On 27 May, 2020
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On 22 Apr, 2020
Review #1 received
Received 28 Jan, 2020
Reviewers invited
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Reviewer #1 agreed
On 08 Jan, 2020
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Submission checks complete
On 29 Dec, 2019
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See the published version of this preprint at BMC Genomics.
This is a preprint, a preliminary version of a manuscript that has not completed peer review at a journal. Research Square does not conduct peer review prior to posting preprints. The posting of a preprint on this server should not be interpreted as an endorsement of its validity or suitability for dissemination as established information or for guiding clinical practice.
Learn more about In Review
Research article
Xingchu Yan
Oil Crops Research Institute of Chinese Academy of Agricultural Science
Corresponding Author
Badges
Prescreen
This manuscript passed our Prescreen assessment
Complete author information
Appropriate declaration statements
Potential risks to human health
Prescreen
Peer Review Timeline
CURRENT STATUS: Published
View the published article at BMC Genomics.
Version 4
Posted 31 Dec, 2020
No community comments so far
Editorial decision: Accept
On 10 Jan, 2021
Editor assigned
On 14 Dec, 2020
Submission checks complete
On 14 Dec, 2020
Editor invited
On 14 Dec, 2020
No comments provided
Editorial decision: Minor revision
On 11 Dec, 2020
Review #1 received
Received 09 Dec, 2020
Editor assigned
On 21 Nov, 2020
Reviewers invited
Invitations sent on 21 Nov, 2020
Reviewer #1 agreed
On 21 Nov, 2020
Submission checks complete
On 21 Nov, 2020
Editor invited
On 21 Nov, 2020
No comments provided
Editorial decision: Major revision
On 29 Oct, 2020
Reviewer #3 agreed
On 13 Oct, 2020
Review #3 received
Received 13 Oct, 2020
Review #2 received
Received 25 Aug, 2020
Reviewer #2 agreed
On 08 Aug, 2020
Reviewers invited
Invitations sent on 05 Aug, 2020
Reviewer #1 agreed
On 05 Aug, 2020
Review #1 received
Received 05 Aug, 2020
Editor assigned
On 14 Jul, 2020
Submission checks complete
On 13 Jul, 2020
Editor invited
On 13 Jul, 2020
No comments provided
Review #3 received
Received 27 May, 2020
Editorial decision: Major revision
On 27 May, 2020
Review #2 received
Received 26 May, 2020
Reviewer #3 agreed
On 29 Apr, 2020
Reviewer #2 agreed
On 22 Apr, 2020
Review #1 received
Received 28 Jan, 2020
Reviewers invited
Invitations sent on 08 Jan, 2020
Reviewer #1 agreed
On 08 Jan, 2020
Editor assigned
On 30 Dec, 2019
Submission checks complete
On 29 Dec, 2019
Editor invited
On 29 Dec, 2019
First submitted
On 26 Dec, 2019
Metrics
Comments: 0
PDF Downloads: ...
HTML Views: ...
Subject Areas
Epigenetics & Genomics
License:
This work is licensed under a CC BY 4.0 License. Read Full License
View the published article at BMC Genomics.
Background: Oil flax (linseed, Linum usitatissimum L.) is one of the most important oil crops., However, the increases in drought resulting from climate change have dramatically reduces linseed yield and quality, but very little is known about how linseed coordinates the expression of drought resistance gene in response to different level of drought stress (DS) on the genome-wide level.
Results: To explore the linseed transcriptional response of DS and repeated drought (RD) stress, we determined the drought tolerance of different linseed varieties. Then we performed full-length transcriptome sequencing of drought-resistant variety (Z141) and drought-sensitive variety (NY-17) under DS and RD stress at the seedling stage using single-molecule real-time sequencing and RNA-sequencing. Gene Ontology (GO) and reduce and visualize GO (REVIGO) enrichment analysis showed that upregulated genes of Z141 were enriched in more functional pathways related to plant drought tolerance than those of NY-17 were under DS. In addition, 4436 linseed transcription factors were identified, and 1190 were responsive to stress treatments. Moreover, protein-protein interaction (PPI) network analysis showed that the proline biosynthesis pathway interacts with stress response genes through RAD50 (DNA repair protein 50) interacting protein 1 (RIN-1). Finally, proline biosynthesis and DNA repair structural gene expression patterns were verified by RT- PCR.
Conclusions: The drought tolerance of Z141 may be related to its upregulation of drought tolerance genes under DS. Proline may play an important role in linseed drought tolerance by maintaining cell osmotic and protecting DNA from ROS damage. In summary, this study provides a new perspective to understand the drought adaptability of linseed.
Figure 1
Figure 2
Figure 3
Figure 4
Figure 5
Figure 6
Figure 7
Figure 8
Figure 9
Figure 10
Figure 11
Figure 12
This is a list of supplementary files associated with this preprint. Click to download.
- SupplementaryFigureS1.rar
Figure S1. Bubble diagram showing the GO classification of differentially expressed transcripts between DS and RD in Z141 or NY-17. (a, b) GO terms of downregulated genes overlapping between DS and RD in Z141 (a) or NY-17 (b). (c-f) GO terms of genes up- (c, d) or downregulated (e, f) in only Z141 under DS or RD, respectively. (g-j) GO terms of genes up- (g, h) or downregulated (i, j) in only NY-17 under DS or RD respectively.
- SupplementaryFigureS2.rar
Figure S2. Bubble diagram showing the GO classification of differentially expressed transcripts between Z141 and NY-17 under DS or RD treatment. (a, b) GO terms of downregulated genes overlapping between Z141 and NY-17 under DS (a) or RD (b) treatment. (c-f) GO terms of genes up- (c, d) or downregulated (e, f) in Z141 or NY-17 under only DS. (g-j) GO terms of genes up- (g, h) or downregulated (i, j) in Z141 or NY-17 under only RD.
- SupplementaryFigureS3.rar
Figure S3. Tree diagram showing the REVIGO classification of up- or downregulated differentially expressed transcripts in Z141 or NY-17 under DS or RD. (a, b) REVIGO classification of up- (a) and downregulated (b) genes in Z141 under RD stress. (c, d) REVIGO classification of up- (c) and downregulated (d) genes in NY-17 under DS. (e, f) REVIGO classification of up- (e) and downregulated (f) genes in NY-17 under RD stress.
- SupplementaryFigureS4.rar
Figure S4. MapMan visualization of drought stress-responsive DEGs in Z141 (b) and NY-17 (a, c) under DS and RD stress, respectively. The up- and downregulated DEGs are represented in red and blue colour. The Colour brightness indicates the degree of difference, as shown in the scale on the right.
- SupplementaryFigureS5.rar
- SupplementaryTableS1S9S13S19.docx
- SupplementaryTableS10.xlsx
- SupplementaryTableS11.xlsx
- SupplementaryTableS12.xlsx
- SupplementaryTableS13.xlsx
- SupplementaryTableS14.xlsx
- SupplementaryTableS15.xlsx
- SupplementaryTableS16.xlsx
- SupplementaryTableS17.xls
- SupplementaryTableS18.xls
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