Abstract
Main conclusion
CG and CHG methylation levels in the rapid shoot growth stages (ST2–ST4) of woody bamboos were obviously decreased, which might regulate the internode elongation during rapid shoot growth, while CHH methylation was strongly associated with shoot developmental time or age.
Abstract
DNA methylation plays a critical role in the regulation of plant growth and development. Woody bamboos have a unique trait of rapid stem growth resulted from internode elongation at the shooting period. However, it is still unclear whether DNA methylation significantly controls the bamboo rapid stem growth. Here we present whole-genome DNA methylation profiles of the paleotropical woody bamboo Bonia amplexicaulis at five newly defined stages of shoot growth, named ST1–ST5. We found that CG and CHG methylation levels in the rapid shoot growth stages (ST2–ST4) were significantly lower than in the incubation (ST1) and plateau stages (ST5). The changes in methylation levels mainly occurred in flanking regions of genes and gene body regions, and 23647 differentially methylated regions (DMRs) were identified between ST1 and rapid shoot growth stages (ST2–ST4). Combined with transcriptome analysis, we found that DMR-related genes enriched in the auxin and jasmonic acid (JA) signal transduction, and other pathways closely related to plant growth. Intriguingly, CHH methylation was not involved in the rapid shoot growth, but strongly associated with shoot developmental time by gradually accumulating in transposable elements (TEs) regions. Overall, our results reveal the importance of DNA methylation in regulating the bamboo rapid shoot growth and suggest a role of DNA methylation associated with development time or age in woody bamboos.
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Data availability statement
Sequence data from this article can be found in the Genome Sequence Archive (SAR) repository of the National Genomics Data Center (NGDC), Beijing, China, under the accession number PRJCA010794.
Abbreviations
- BS:
-
Bisulfite
- DEG:
-
Differentially expressed gene
- DML:
-
Demeter-like
- DMRs:
-
Differentially methylated regions
- JA:
-
Jasmonic acid
- JAZ:
-
Jasmonate ZIM-domain
- RdDM:
-
RNA-directed DNA methylation pathway
- ST1:
-
Incubation stage
- ST2:
-
Early stage of rapid shoot growth
- ST3:
-
Middle stage of rapid shoot growth
- ST4:
-
Late stage of rapid shoot growth
- ST5:
-
Plateau stage of shoot growth
- TE:
-
Transposable element
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Acknowledgements
This work was supported by the Chinese Academy of Sciences’ Strategic Priority Research Program (grant no. 31000000 to D.-Z.L.), and the Science and Technology Leading Talent Project of Yunnan, China (2017HA014 to D.-Z.L.), and the CAS’ Youth Innovation Promotion Association (No. Y201972 to P.-F.M), and the National Natural Science Foundation of China (Project No. 31970355 to P.-F.Ma). We thank the iFlora High Performance Computing Center of Germplasm Bank of Wild Species (GBOWS) and Molecular Biology Experimental Platform of the GBOWS at Kunming Institute of Botany, Chinese Academy of Sciences for computational and experimental support.
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Niu, LZ., Xu, W., Ma, PF. et al. Single-base methylome analysis reveals dynamic changes of genome-wide DNA methylation associated with rapid stem growth of woody bamboos. Planta 256, 53 (2022). https://doi.org/10.1007/s00425-022-03962-8
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DOI: https://doi.org/10.1007/s00425-022-03962-8