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
A new preprint design is coming!
We have improved readability, clarity, accessibility, and opportunities for engagement.
Research article
Tetsuo Takano
The University of Tokyo
Corresponding Author
License:
This work is licensed under a CC BY 4.0 License. Read Full License
Background: Pearl millet (Pennisetum glaucum) is a cereal crop that possesses the ability to withstand drought, salinity and high temperature stresses. The NAC [NAM (No Apical Meristem), ATAF1 (Arabidopsis thaliana Activation Factor 1), and CUC2 (Cup-shaped Cotyledon)] transcription factor family is one of the largest transcription factor families in plants. NAC family members are known to regulate plant growth and abiotic stress response. Currently, no reports are available on the functions of the NAC family in pearl millet.
Results: Our genome-wide analysis found 151 NAC transcription factor genes (PgNACs) in the pearl millet genome. Thirty-eight and 76 PgNACs were found to be segmental and dispersed duplicated respectively. Phylogenetic analysis divided these NAC transcription factors into 11 groups (A-K). Three PgNACs (-073, -29, and -151) were found to be membrane-associated transcription factors. Seventeen other conserved motifs were found in PgNACs. Based on the similarity of PgNACs to NAC proteins in other species, the functions of PgNACs were predicted. In total, 88 microRNA target sites were predicted in 59 PgNACs. A previously performed transcriptome analysis suggests that the expression of 30 and 42 PgNACs are affected by salinity stress and drought stress, respectively. The expression of 36 randomly selected PgNACs were examined by quantitative reverse transcription-PCR. Many of these genes showed diverse salt- and drought-responsive expression patterns in roots and leaves. These results confirm that PgNACs are potentially involved in regulating abiotic stress tolerance in pearl millet.
Conclusion: The pearl millet genome contains 151 NAC transcription factor genes that can be classified into 11 groups. Many of these genes are either upregulated or downregulated by either salinity or drought stress and may therefore contribute to establishing stress tolerance in pearl millet.
Keywords
Pearl millet, NAC, Transcription factor, microRNAs, Drought, Salinity
Figure 1
Figure 1
Figure 2
Figure 2
Figure 3
Figure 3
Figure 4
Figure 4
Figure 5
Figure 5
Figure 6
Figure 6
Figure 7
Figure 7
Figure 8
Figure 8
Figure 9
Figure 9
This is a list of supplementary files associated with this preprint. Click to download.
- AdditionalFile1.doc
Additional File 1 (.doc): List of primers used in quantitative real time-PCR expression analysis of PgNAC genes.
- AdditionalFile1.doc
Additional File 1 (.doc): List of primers used in quantitative real time-PCR expression analysis of PgNAC genes.
- AdditionalFile2.xlsx
Additional File 2 (.xlsx): Detail catalogue of NAC in pearl millet
- AdditionalFile2.xlsx
Additional File 2 (.xlsx): Detail catalogue of NAC in pearl millet
- AdditionalFile3.pdf
Additional File 3 (.PDF): Gene structure of PgNACs. Image was created by submitting the sequences to the gene structure display 2.0 online tool. Red boxes denote the exon/coding region, black lines are intron and blue boxes defines
- AdditionalFile3.pdf
Additional File 3 (.PDF): Gene structure of PgNACs. Image was created by submitting the sequences to the gene structure display 2.0 online tool. Red boxes denote the exon/coding region, black lines are intron and blue boxes defines
- Additionalfile4.pdf
Additional File 4: Location of 17 Motifs on the PgNACs (.PDF). The location of motifs was derived by the multiple alignment of the motifs by online tool MAST. Each of the following 152 sequences has an E-value less than 10. The motif matches shown here have a position p-value less than 0.0001. Colored boxes represent the respective motif.
- Additionalfile4.pdf
Additional File 4: Location of 17 Motifs on the PgNACs (.PDF). The location of motifs was derived by the multiple alignment of the motifs by online tool MAST. Each of the following 152 sequences has an E-value less than 10. The motif matches shown here have a position p-value less than 0.0001. Colored boxes represent the respective motif.
- Additionalfile5.xlsx
Additional File 5: Analyzing pearl millet miRNAs targeting PgNACs
- Additionalfile5.xlsx
Additional File 5: Analyzing pearl millet miRNAs targeting PgNACs
Loading...
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.
No community comments so far
Editorial decision: Accept
On 10 Jan, 2021
Editor assigned
On 24 Dec, 2020
Submission checks complete
On 24 Dec, 2020
Editor invited
On 24 Dec, 2020
Version 2
Posted 10 Dec, 2020
No comments provided
Editorial decision: Minor revision
On 16 Dec, 2020
Review #2 received
Received 05 Dec, 2020
Review #1 received
Received 30 Nov, 2020
Reviewer #2 agreed
On 29 Nov, 2020
Editor assigned
On 24 Nov, 2020
Reviewers invited
Invitations sent on 24 Nov, 2020
Reviewer #1 agreed
On 24 Nov, 2020
Submission checks complete
On 24 Nov, 2020
Editor invited
On 24 Nov, 2020
Community comments: 1
Editorial decision: Major revision
On 11 Oct, 2020
Review #2 received
Received 05 Oct, 2020
Reviewer #2 agreed
On 22 Sep, 2020
Review #1 received
Received 10 Sep, 2020
Reviewer #1 agreed
On 24 Aug, 2020
Reviewers invited
Invitations sent on 10 Jul, 2020
Editor invited
On 29 Jun, 2020
Editor assigned
On 23 Jun, 2020
Submission checks complete
On 22 Jun, 2020
First submitted
On 21 Jun, 2020
Metrics
Comments: 0
PDF Downloads: ...
HTML Views: ...
Subject Areas
Epigenetics & Genomics
Learn more about our company.
A new preprint design is coming!
We have improved readability, clarity, accessibility, and opportunities for engagement.
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
Tetsuo Takano
The University of Tokyo
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.
No community comments so far
Editorial decision: Accept
On 10 Jan, 2021
Editor assigned
On 24 Dec, 2020
Submission checks complete
On 24 Dec, 2020
Editor invited
On 24 Dec, 2020
Version 2
Posted 10 Dec, 2020
No comments provided
Editorial decision: Minor revision
On 16 Dec, 2020
Review #2 received
Received 05 Dec, 2020
Review #1 received
Received 30 Nov, 2020
Reviewer #2 agreed
On 29 Nov, 2020
Editor assigned
On 24 Nov, 2020
Reviewers invited
Invitations sent on 24 Nov, 2020
Reviewer #1 agreed
On 24 Nov, 2020
Submission checks complete
On 24 Nov, 2020
Editor invited
On 24 Nov, 2020
Community comments: 1
Editorial decision: Major revision
On 11 Oct, 2020
Review #2 received
Received 05 Oct, 2020
Reviewer #2 agreed
On 22 Sep, 2020
Review #1 received
Received 10 Sep, 2020
Reviewer #1 agreed
On 24 Aug, 2020
Reviewers invited
Invitations sent on 10 Jul, 2020
Editor invited
On 29 Jun, 2020
Editor assigned
On 23 Jun, 2020
Submission checks complete
On 22 Jun, 2020
First submitted
On 21 Jun, 2020
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: Pearl millet (Pennisetum glaucum) is a cereal crop that possesses the ability to withstand drought, salinity and high temperature stresses. The NAC [NAM (No Apical Meristem), ATAF1 (Arabidopsis thaliana Activation Factor 1), and CUC2 (Cup-shaped Cotyledon)] transcription factor family is one of the largest transcription factor families in plants. NAC family members are known to regulate plant growth and abiotic stress response. Currently, no reports are available on the functions of the NAC family in pearl millet.
Results: Our genome-wide analysis found 151 NAC transcription factor genes (PgNACs) in the pearl millet genome. Thirty-eight and 76 PgNACs were found to be segmental and dispersed duplicated respectively. Phylogenetic analysis divided these NAC transcription factors into 11 groups (A-K). Three PgNACs (-073, -29, and -151) were found to be membrane-associated transcription factors. Seventeen other conserved motifs were found in PgNACs. Based on the similarity of PgNACs to NAC proteins in other species, the functions of PgNACs were predicted. In total, 88 microRNA target sites were predicted in 59 PgNACs. A previously performed transcriptome analysis suggests that the expression of 30 and 42 PgNACs are affected by salinity stress and drought stress, respectively. The expression of 36 randomly selected PgNACs were examined by quantitative reverse transcription-PCR. Many of these genes showed diverse salt- and drought-responsive expression patterns in roots and leaves. These results confirm that PgNACs are potentially involved in regulating abiotic stress tolerance in pearl millet.
Conclusion: The pearl millet genome contains 151 NAC transcription factor genes that can be classified into 11 groups. Many of these genes are either upregulated or downregulated by either salinity or drought stress and may therefore contribute to establishing stress tolerance in pearl millet.
Figure 1
Figure 1
Figure 2
Figure 2
Figure 3
Figure 3
Figure 4
Figure 4
Figure 5
Figure 5
Figure 6
Figure 6
Figure 7
Figure 7
Figure 8
Figure 8
Figure 9
Figure 9
This is a list of supplementary files associated with this preprint. Click to download.
- AdditionalFile1.doc
Additional File 1 (.doc): List of primers used in quantitative real time-PCR expression analysis of PgNAC genes.
- AdditionalFile1.doc
Additional File 1 (.doc): List of primers used in quantitative real time-PCR expression analysis of PgNAC genes.
- AdditionalFile2.xlsx
Additional File 2 (.xlsx): Detail catalogue of NAC in pearl millet
- AdditionalFile2.xlsx
Additional File 2 (.xlsx): Detail catalogue of NAC in pearl millet
- AdditionalFile3.pdf
Additional File 3 (.PDF): Gene structure of PgNACs. Image was created by submitting the sequences to the gene structure display 2.0 online tool. Red boxes denote the exon/coding region, black lines are intron and blue boxes defines
- AdditionalFile3.pdf
Additional File 3 (.PDF): Gene structure of PgNACs. Image was created by submitting the sequences to the gene structure display 2.0 online tool. Red boxes denote the exon/coding region, black lines are intron and blue boxes defines
- Additionalfile4.pdf
Additional File 4: Location of 17 Motifs on the PgNACs (.PDF). The location of motifs was derived by the multiple alignment of the motifs by online tool MAST. Each of the following 152 sequences has an E-value less than 10. The motif matches shown here have a position p-value less than 0.0001. Colored boxes represent the respective motif.
- Additionalfile4.pdf
Additional File 4: Location of 17 Motifs on the PgNACs (.PDF). The location of motifs was derived by the multiple alignment of the motifs by online tool MAST. Each of the following 152 sequences has an E-value less than 10. The motif matches shown here have a position p-value less than 0.0001. Colored boxes represent the respective motif.
- Additionalfile5.xlsx
Additional File 5: Analyzing pearl millet miRNAs targeting PgNACs
- Additionalfile5.xlsx
Additional File 5: Analyzing pearl millet miRNAs targeting PgNACs
Loading...