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.
Research article
Yuanyuan Zhao
Beijing Forestry University, Beijing Advanced Innovation Center for Tree Breeding by Molecular Design
Corresponding Author
License:
This work is licensed under a CC BY 4.0 License. Read Full License
Background
Ovule abortion is a common phenomenon in plants, which has an essential significance in seed production. The development of the female gametophyte (FG) is one of the crucial processes of the life cycle, and FG dysplasia is a significant cause contribute to ovule abortion in many species. However, because it is difficult to acquire the mutant about ovule development in gymnosperms, previous studies of the ovule and FG development are mainly focused on angiosperms, especially in Arabidopsis thaliana. Thus the investigation on this field of gymnosperms remains unclear.
Results
In this study, we investigated the transcriptome data of wild-type (female fertile line, FER) and natural ovule abortion mutant (female sterile line, STE) of Pinus tabuliformis Carr. to evaluate the mechanism of ovule abortion during the process of free nuclear mitosis (FNM). Using single molecule real-time (SMRT) sequencing and next-generation sequencing (NGS), we obtained 202,869 (FER), 197,977 (STE) mapped full-length non-chimeric (FLNC) reads and analyzed 18 cDNA libraries. Based on the SMRT sequencing, we found that both GO annotation and KEGG pathway terms results were similar in FER and STE. NGS analysis further showed altogether 99 differentially expressed genes (DEGs) with opposite expression patterns during the FNM process in FER and STE. According to SMRT sequencing, we found that the number of isoforms and alternative splicing (AS) patterns are variable between FER and STE. Moreover, 5,530 and 5,096 potential simple sequence repeats (SSRs) were identified in FER and STE, respectively. Functional annotation results demonstrated that genes involved in energy metabolism, signal transduction, cell division, and stress response were differentially expressed in different lines, 9 pairs of which were confirmed by quantitative real-time PCR.
Conclusion
Taken together, these results provide some new insights about the ovule abortion in gymnosperms and further reveal the regulatory mechanisms of ovule development.
Keywords
Pinus tabuliformis Carr., ovule abortion, single molecule real-time sequencing, next-generation sequencing, alternative splicing, simple sequence repeat
Figure 1
Figure 2
Figure 3
Figure 4
Figure 5
Figure 6
Figure 7
This is a list of supplementary files associated with this preprint. Click to download.
- FigS1.pdf
Fig. S1. Principal component analysis of the RNA-Seq data.
- FigS2.pdf
Fig. S2. GO classification of full-length transcriptomes of FER and STE ovule in P. tabuliformis.
- FigS3.pdf
Fig. S3. The expression patterns of DEGs analyzed by model profile.
- FigS4.pdf
Fig. S4. The model graph of TUBA generating different transcript isoforms of A3 splicing detected in FER and STE.
- SupplementaryTablesS1S9.xlsx
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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.
Research article
Yuanyuan Zhao
Beijing Forestry University, Beijing Advanced Innovation Center for Tree Breeding by Molecular Design
Corresponding Author
Badges
Prescreen
This manuscript passed our Prescreen assessment
Complete author information
Appropriate declaration statements
Potential risks to human health
Prescreen
History
CURRENT STATUS: Posted
Version 1
Posted 29 Sep, 2020
No community comments so far
Metrics
Comments: 0
PDF Downloads: ...
HTML Views: ...
Subject Areas
Plant Molecular Biology and Genetics
License:
This work is licensed under a CC BY 4.0 License. Read Full License
Background
Ovule abortion is a common phenomenon in plants, which has an essential significance in seed production. The development of the female gametophyte (FG) is one of the crucial processes of the life cycle, and FG dysplasia is a significant cause contribute to ovule abortion in many species. However, because it is difficult to acquire the mutant about ovule development in gymnosperms, previous studies of the ovule and FG development are mainly focused on angiosperms, especially in Arabidopsis thaliana. Thus the investigation on this field of gymnosperms remains unclear.
Results
In this study, we investigated the transcriptome data of wild-type (female fertile line, FER) and natural ovule abortion mutant (female sterile line, STE) of Pinus tabuliformis Carr. to evaluate the mechanism of ovule abortion during the process of free nuclear mitosis (FNM). Using single molecule real-time (SMRT) sequencing and next-generation sequencing (NGS), we obtained 202,869 (FER), 197,977 (STE) mapped full-length non-chimeric (FLNC) reads and analyzed 18 cDNA libraries. Based on the SMRT sequencing, we found that both GO annotation and KEGG pathway terms results were similar in FER and STE. NGS analysis further showed altogether 99 differentially expressed genes (DEGs) with opposite expression patterns during the FNM process in FER and STE. According to SMRT sequencing, we found that the number of isoforms and alternative splicing (AS) patterns are variable between FER and STE. Moreover, 5,530 and 5,096 potential simple sequence repeats (SSRs) were identified in FER and STE, respectively. Functional annotation results demonstrated that genes involved in energy metabolism, signal transduction, cell division, and stress response were differentially expressed in different lines, 9 pairs of which were confirmed by quantitative real-time PCR.
Conclusion
Taken together, these results provide some new insights about the ovule abortion in gymnosperms and further reveal the regulatory mechanisms of ovule development.
Figure 1
Figure 2
Figure 3
Figure 4
Figure 5
Figure 6
Figure 7
This is a list of supplementary files associated with this preprint. Click to download.
- FigS1.pdf
Fig. S1. Principal component analysis of the RNA-Seq data.
- FigS2.pdf
Fig. S2. GO classification of full-length transcriptomes of FER and STE ovule in P. tabuliformis.
- FigS3.pdf
Fig. S3. The expression patterns of DEGs analyzed by model profile.
- FigS4.pdf
Fig. S4. The model graph of TUBA generating different transcript isoforms of A3 splicing detected in FER and STE.
- SupplementaryTablesS1S9.xlsx
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