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Research article
zhongxiong lai
Fujian Agriculture and Forestry University
Corresponding Author
License:
This work is licensed under a CC BY 4.0 License. Read Full License
Background
Somatic embryogenesis (SE) is a process of somatic cells that dedifferentiate to the totipotent embryonic stem cells and generate embryos in vitro. Longan SE has been established and wildly used as a model system for studying embryogenesis in woody plants, and some SE-related genes had been characterized. In spite of that, a comprehensive overview of SE at a molecular level is still absent. With the aim of understanding the molecular mechanisms underlying SE in longan, we examined the transcriptome changes by using Illumina HiSeq platform from the four distinct developmental stages, including non-embryogenic callus (NEC), embryogenic callus (EC), incomplete compact pro-embryogenic cultures (ICpEC), globular embryos (GE).
Results
RNA-seq of the four samples generated a total of 243.78 million high quality reads, approximately 81.5% of the data were mapped to the reference genome. The cDNA libraries of NEC, EC, ICpEC and GE, generated 22743, 19745, 21144, 21102 expressed transcripts and 1935, 1710, 1816, 1732 novel transcripts, and 2645, 366, 505, 588 unique genes, respectively. Comparative transcriptome analysis revealed the important role of auxin and cytokinin during longan SE. The transcripts profiling of flavonoid and fatty acid biosynthesis related genes suggested that flavonoids were mainly accumulated in NEC, while fatty acid accumulated in early SE. In addition, the extracelluar protein encoding genes LTP, CHI, GLP, AGP, EP1 were related to longan SE. Transcript profiling combined with qRT-PCR performed on selected genes confirmed that 27 SE molecular markers (LEC1, LEC1-like, PDF1.3, GH3.6, AGL80, PIN1, BBM, WOX9, WOX2, ABI3, et al.) and 28 NEC markers (LEA5, CNOT3, DC2.15, PR1-1, NsLTP2, DIR1, PIP1, PIP2.1, TIP2-1, POD-P7 and POD5 et al.) were characterized as potential molecular markers for longan early SE, respectively.
Conclusion
Our transcriptome reveals the transcription regulation of auxin, cytokinin and other hormones signaling pathway, flavonoids biosynthesis, fatty acid biosynthesis, extracelluar protein encoding genes, and other SE-related genes during early SE. Furthermore, we characterizes the potential molecular markers to distinguish NEC and early SE of longan. The present work provides new insights into future functional studies, as a means of studying the molecular mechanisms in SE.
Keywords
Dimocarpus longan, somatic embryogenesis, Illumina HiSeq, auxin and cytokinin, molecular marker gene, qRT-PCR
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CURRENT STATUS: Published
View the published article at BMC Genomics.
No community comments so far
Editorial decision: Accept
On 12 Dec, 2019
Editor assigned
On 05 Dec, 2019
Submission checks complete
On 04 Dec, 2019
Editor invited
On 04 Dec, 2019
No comments provided
Editorial decision: Major revision
On 17 Nov, 2019
Review #1 received
Received 15 Nov, 2019
Review #2 received
Received 13 Nov, 2019
Review #3 received
Received 10 Nov, 2019
Reviewer #3 agreed
On 31 Oct, 2019
Reviewer #2 agreed
On 29 Oct, 2019
Editor assigned
On 28 Oct, 2019
Reviewers invited
Invitations sent on 28 Oct, 2019
Reviewer #1 agreed
On 28 Oct, 2019
Submission checks complete
On 27 Oct, 2019
Editor invited
On 27 Oct, 2019
Version 1
Posted 29 Aug, 2019
No comments provided
Editorial decision: Major revision
On 30 Aug, 2019
Review #3 received
Received 27 Aug, 2019
Review #2 received
Received 26 Aug, 2019
Review #1 received
Received 20 Aug, 2019
Reviewer #3 agreed
On 14 Aug, 2019
Reviewer #2 agreed
On 09 Aug, 2019
Reviewer #1 agreed
On 07 Aug, 2019
Reviewers invited
Invitations sent on 06 Aug, 2019
Submission checks complete
On 23 Jul, 2019
Editor assigned
On 22 Jul, 2019
Editor invited
On 21 Jul, 2019
First submitted
On 17 Jul, 2019
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Subject Areas
Epigenetics & Genomics
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A new preprint design is coming!
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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
zhongxiong lai
Fujian Agriculture and Forestry University
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 12 Dec, 2019
Editor assigned
On 05 Dec, 2019
Submission checks complete
On 04 Dec, 2019
Editor invited
On 04 Dec, 2019
No comments provided
Editorial decision: Major revision
On 17 Nov, 2019
Review #1 received
Received 15 Nov, 2019
Review #2 received
Received 13 Nov, 2019
Review #3 received
Received 10 Nov, 2019
Reviewer #3 agreed
On 31 Oct, 2019
Reviewer #2 agreed
On 29 Oct, 2019
Editor assigned
On 28 Oct, 2019
Reviewers invited
Invitations sent on 28 Oct, 2019
Reviewer #1 agreed
On 28 Oct, 2019
Submission checks complete
On 27 Oct, 2019
Editor invited
On 27 Oct, 2019
Version 1
Posted 29 Aug, 2019
No comments provided
Editorial decision: Major revision
On 30 Aug, 2019
Review #3 received
Received 27 Aug, 2019
Review #2 received
Received 26 Aug, 2019
Review #1 received
Received 20 Aug, 2019
Reviewer #3 agreed
On 14 Aug, 2019
Reviewer #2 agreed
On 09 Aug, 2019
Reviewer #1 agreed
On 07 Aug, 2019
Reviewers invited
Invitations sent on 06 Aug, 2019
Submission checks complete
On 23 Jul, 2019
Editor assigned
On 22 Jul, 2019
Editor invited
On 21 Jul, 2019
First submitted
On 17 Jul, 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
Somatic embryogenesis (SE) is a process of somatic cells that dedifferentiate to the totipotent embryonic stem cells and generate embryos in vitro. Longan SE has been established and wildly used as a model system for studying embryogenesis in woody plants, and some SE-related genes had been characterized. In spite of that, a comprehensive overview of SE at a molecular level is still absent. With the aim of understanding the molecular mechanisms underlying SE in longan, we examined the transcriptome changes by using Illumina HiSeq platform from the four distinct developmental stages, including non-embryogenic callus (NEC), embryogenic callus (EC), incomplete compact pro-embryogenic cultures (ICpEC), globular embryos (GE).
Results
RNA-seq of the four samples generated a total of 243.78 million high quality reads, approximately 81.5% of the data were mapped to the reference genome. The cDNA libraries of NEC, EC, ICpEC and GE, generated 22743, 19745, 21144, 21102 expressed transcripts and 1935, 1710, 1816, 1732 novel transcripts, and 2645, 366, 505, 588 unique genes, respectively. Comparative transcriptome analysis revealed the important role of auxin and cytokinin during longan SE. The transcripts profiling of flavonoid and fatty acid biosynthesis related genes suggested that flavonoids were mainly accumulated in NEC, while fatty acid accumulated in early SE. In addition, the extracelluar protein encoding genes LTP, CHI, GLP, AGP, EP1 were related to longan SE. Transcript profiling combined with qRT-PCR performed on selected genes confirmed that 27 SE molecular markers (LEC1, LEC1-like, PDF1.3, GH3.6, AGL80, PIN1, BBM, WOX9, WOX2, ABI3, et al.) and 28 NEC markers (LEA5, CNOT3, DC2.15, PR1-1, NsLTP2, DIR1, PIP1, PIP2.1, TIP2-1, POD-P7 and POD5 et al.) were characterized as potential molecular markers for longan early SE, respectively.
Conclusion
Our transcriptome reveals the transcription regulation of auxin, cytokinin and other hormones signaling pathway, flavonoids biosynthesis, fatty acid biosynthesis, extracelluar protein encoding genes, and other SE-related genes during early SE. Furthermore, we characterizes the potential molecular markers to distinguish NEC and early SE of longan. The present work provides new insights into future functional studies, as a means of studying the molecular mechanisms in SE.
Figure 1
Figure 2
Figure 3
Figure 4
Figure 5
Figure 6
This is a list of supplementary files associated with this preprint. Click to download.
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