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Research article
Bowen Chen
Guangxi Forestry Research Institute
Corresponding Author
ORCiD: https://orcid.org/0000-0002-9402-6679
License:
This work is licensed under a CC BY 4.0 License. Read Full License
Background: Eucalyptus, a highly diverse genus of the Myrtaceae family, is the most widely planted hardwood in the world due to its increasing importance for fiber and energy. Somatic embryogenesis (SE) is one large-scale method to provide commercial use of the vegetative propagation of Eucalyptus and dedifferentiation is a key step for plant cells to become meristematic. However, little is known about the molecular changes during the Eucalyptus SE.
Results: We compared the transcriptome profiles of the differentiated and dedifferentiated tissues of two Eucalyptus species – E. camaldulensis (high embryogenetic potential) and E. grandis x urophylla (low embryogenetic potential). Initially, we identified 18,777 to 20,240 genes in all samples. Compared to the differentiated tissues, we identified 9,229 and 8,989 differentially expressed genes (DEGs) in the dedifferentiated tissues of E. camaldulensis and E. grandis x urophylla, respectively, and 2,687 up-regulated and 2,581 down-regulated genes shared. Next, we identified 2,003 up-regulated and 1,958 down-regulated genes only in E. camaldulensis, including 6 somatic embryogenesis receptor kinase, 17 ethylene, 12 auxin, 83 ribosomal protein, 28 zinc finger protein, 10 heat shock protein, 9 histone, 122 cell wall related and 98 transcription factor genes. Genes from other families like ABA, arabinogalactan protein and late embryogenesis abundant protein were also found to be specifically dysregulated in the dedifferentiation process of E. camaldulensis. Further, we identified 48,447 variants (SNPs and small indels) specific to E. camaldulensis, including 13,434 exonic variants from 4,723 genes (e.g., annexin, GN, ARF and AP2-like ethylene-responsive transcription factor). qRT-PCR was used to confirm the gene expression patterns in both E. camaldulensis and E. grandis x urophylla.
Conclusions: This is the first time to study the somatic embryogenesis of Eucalyptus using transcriptome sequencing. It will improve our understanding of the molecular mechanisms of somatic embryogenesis and dedifferentiation in Eucalyptus. Our results provide a valuable resource for future studies in the field of Eucalyptus and will benefit the Eucalyptus breeding program.
Keywords
Eucalyptus, vegetative propagation, somatic embryogenesis, dedifferentiation, transcriptome, callus
Figure 1
Figure 2
Figure 3
Figure 4
This is a list of supplementary files associated with this preprint. Click to download.
- AdditionalFiles.docx
- Additionalfile1.xlsx
Additional file 1. Gene expression profiles of differentiated and dedifferentiated tissues of E. camaldulensis and E. grandis x urophylla.
- Additionalfile2.xlsx
Additional file 2. Differentially expressed genes in the dedifferentiated tissues compared to the differentiated tissues of E. camaldulensis and E. grandis x urophylla.
- Additionalfile3.xlsx
Additional file 3. Cell wall related DEGs identified in the SE of E. camaldulensis and E. grandis x urophylla.
- Additionalfile4.xlsx
Additional file 4. Primers used for qRT-PCR.
- Additionalfile5.xlsx
Additional file 5. Gene variants specifically identified in E. camaldulensis.
- Additionalfile6.xlsx
Additional file 6. KEGG pathway enriched by the mutated genes specifically identified in E. camaldulensis.
- Additionalfile7.xlsx
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View the published article at BMC Genomics.
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Editorial decision: Accept
On 05 Nov, 2020
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On 02 Nov, 2020
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Editor invited
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Review #1 received
Received 24 Oct, 2020
Reviewer #2 agreed
On 14 Oct, 2020
Reviewer #1 agreed
On 13 Oct, 2020
Reviewers invited
Invitations sent on 11 Oct, 2020
Editor assigned
On 09 Oct, 2020
Submission checks complete
On 08 Oct, 2020
Editor invited
On 08 Oct, 2020
No comments provided
Editorial decision: Major revision
On 14 Sep, 2020
Review #2 received
Received 13 Sep, 2020
Review #1 received
Received 02 Sep, 2020
Reviewer #2 agreed
On 20 Aug, 2020
Reviewer #1 agreed
On 13 Aug, 2020
Reviewers invited
Invitations sent on 10 Aug, 2020
Editor assigned
On 30 Jul, 2020
Submission checks complete
On 29 Jul, 2020
Editor invited
On 29 Jul, 2020
First submitted
On 27 Jul, 2020
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Subject Areas
Epigenetics & Genomics
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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
Bowen Chen
Guangxi Forestry Research Institute
Corresponding Author
ORCiD: https://orcid.org/0000-0002-9402-6679
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 3
Posted 10 Nov, 2020
No community comments so far
Editorial decision: Accept
On 05 Nov, 2020
Editor assigned
On 02 Nov, 2020
Submission checks complete
On 02 Nov, 2020
Editor invited
On 02 Nov, 2020
No comments provided
Review #1 received
Received 24 Oct, 2020
Reviewer #2 agreed
On 14 Oct, 2020
Reviewer #1 agreed
On 13 Oct, 2020
Reviewers invited
Invitations sent on 11 Oct, 2020
Editor assigned
On 09 Oct, 2020
Submission checks complete
On 08 Oct, 2020
Editor invited
On 08 Oct, 2020
No comments provided
Editorial decision: Major revision
On 14 Sep, 2020
Review #2 received
Received 13 Sep, 2020
Review #1 received
Received 02 Sep, 2020
Reviewer #2 agreed
On 20 Aug, 2020
Reviewer #1 agreed
On 13 Aug, 2020
Reviewers invited
Invitations sent on 10 Aug, 2020
Editor assigned
On 30 Jul, 2020
Submission checks complete
On 29 Jul, 2020
Editor invited
On 29 Jul, 2020
First submitted
On 27 Jul, 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: Eucalyptus, a highly diverse genus of the Myrtaceae family, is the most widely planted hardwood in the world due to its increasing importance for fiber and energy. Somatic embryogenesis (SE) is one large-scale method to provide commercial use of the vegetative propagation of Eucalyptus and dedifferentiation is a key step for plant cells to become meristematic. However, little is known about the molecular changes during the Eucalyptus SE.
Results: We compared the transcriptome profiles of the differentiated and dedifferentiated tissues of two Eucalyptus species – E. camaldulensis (high embryogenetic potential) and E. grandis x urophylla (low embryogenetic potential). Initially, we identified 18,777 to 20,240 genes in all samples. Compared to the differentiated tissues, we identified 9,229 and 8,989 differentially expressed genes (DEGs) in the dedifferentiated tissues of E. camaldulensis and E. grandis x urophylla, respectively, and 2,687 up-regulated and 2,581 down-regulated genes shared. Next, we identified 2,003 up-regulated and 1,958 down-regulated genes only in E. camaldulensis, including 6 somatic embryogenesis receptor kinase, 17 ethylene, 12 auxin, 83 ribosomal protein, 28 zinc finger protein, 10 heat shock protein, 9 histone, 122 cell wall related and 98 transcription factor genes. Genes from other families like ABA, arabinogalactan protein and late embryogenesis abundant protein were also found to be specifically dysregulated in the dedifferentiation process of E. camaldulensis. Further, we identified 48,447 variants (SNPs and small indels) specific to E. camaldulensis, including 13,434 exonic variants from 4,723 genes (e.g., annexin, GN, ARF and AP2-like ethylene-responsive transcription factor). qRT-PCR was used to confirm the gene expression patterns in both E. camaldulensis and E. grandis x urophylla.
Conclusions: This is the first time to study the somatic embryogenesis of Eucalyptus using transcriptome sequencing. It will improve our understanding of the molecular mechanisms of somatic embryogenesis and dedifferentiation in Eucalyptus. Our results provide a valuable resource for future studies in the field of Eucalyptus and will benefit the Eucalyptus breeding program.
Figure 1
Figure 2
Figure 3
Figure 4
This is a list of supplementary files associated with this preprint. Click to download.
- AdditionalFiles.docx
- Additionalfile1.xlsx
Additional file 1. Gene expression profiles of differentiated and dedifferentiated tissues of E. camaldulensis and E. grandis x urophylla.
- Additionalfile2.xlsx
Additional file 2. Differentially expressed genes in the dedifferentiated tissues compared to the differentiated tissues of E. camaldulensis and E. grandis x urophylla.
- Additionalfile3.xlsx
Additional file 3. Cell wall related DEGs identified in the SE of E. camaldulensis and E. grandis x urophylla.
- Additionalfile4.xlsx
Additional file 4. Primers used for qRT-PCR.
- Additionalfile5.xlsx
Additional file 5. Gene variants specifically identified in E. camaldulensis.
- Additionalfile6.xlsx
Additional file 6. KEGG pathway enriched by the mutated genes specifically identified in E. camaldulensis.
- Additionalfile7.xlsx
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