DNA methylome of the 20-gigabase Norway spruce genome. Ausin, I., Feng, S., Yu, C., Liu, W., Kuo, H. Y., Jacobsen, E. L., Zhai, J., Gallego-Bartolome, J., Wang, L., Egertsdotter, U., Street, N. R., Jacobsen, S. E., & Wang, H. Proceedings of the National Academy of Sciences, 113(50):E8106–E8113, December, 2016. ![DNA methylome of the 20-gigabase Norway spruce genome [link]](https://bibbase.org/img/filetypes/link.svg "link")
Paper doi abstract bibtex DNA methylation plays important roles in many biological processes, such as silencing of transposable elements, imprinting, and regulating gene expression. Many studies of DNA methylation have shown its essential roles in angiosperms (flowering plants). However, few studies have examined the roles and patterns of DNA methylation in gymnosperms. Here, we present genome-wide high coverage single-base resolution methylation maps of Norway spruce ( Picea abies ) from both needles and somatic embryogenesis culture cells via whole genome bisulfite sequencing. On average, DNA methylation levels of CG and CHG of Norway spruce were higher than most other plants studied. CHH methylation was found at a relatively low level; however, at least one copy of most of the RNA-directed DNA methylation pathway genes was found in Norway spruce, and CHH methylation was correlated with levels of siRNAs. In comparison with needles, somatic embryogenesis culture cells that are used for clonally propagating spruce trees showed lower levels of CG and CHG methylation but higher level of CHH methylation, suggesting that like in other species, these culture cells show abnormal methylation patterns.
@article{ausin_dna_2016,
title = {{DNA} methylome of the 20-gigabase {Norway} spruce genome},
volume = {113},
issn = {0027-8424, 1091-6490},
url = {http://www.pnas.org/lookup/doi/10.1073/pnas.1618019113},
doi = {10.1073/pnas.1618019113},
abstract = {DNA methylation plays important roles in many biological processes, such as silencing of transposable elements, imprinting, and regulating gene expression. Many studies of DNA methylation have shown its essential roles in angiosperms (flowering plants). However, few studies have examined the roles and patterns of DNA methylation in gymnosperms. Here, we present genome-wide high coverage single-base resolution methylation maps of Norway spruce (
Picea abies
) from both needles and somatic embryogenesis culture cells via whole genome bisulfite sequencing. On average, DNA methylation levels of CG and CHG of Norway spruce were higher than most other plants studied. CHH methylation was found at a relatively low level; however, at least one copy of most of the RNA-directed DNA methylation pathway genes was found in Norway spruce, and CHH methylation was correlated with levels of siRNAs. In comparison with needles, somatic embryogenesis culture cells that are used for clonally propagating spruce trees showed lower levels of CG and CHG methylation but higher level of CHH methylation, suggesting that like in other species, these culture cells show abnormal methylation patterns.},
language = {en},
number = {50},
urldate = {2021-06-07},
journal = {Proceedings of the National Academy of Sciences},
author = {Ausin, Israel and Feng, Suhua and Yu, Chaowei and Liu, Wanlu and Kuo, Hsuan Yu and Jacobsen, Elise L. and Zhai, Jixian and Gallego-Bartolome, Javier and Wang, Lin and Egertsdotter, Ulrika and Street, Nathaniel R. and Jacobsen, Steven E. and Wang, Haifeng},
month = dec,
year = {2016},
pages = {E8106--E8113},
}
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Here, we present genome-wide high coverage single-base resolution methylation maps of Norway spruce ( Picea abies ) from both needles and somatic embryogenesis culture cells via whole genome bisulfite sequencing. On average, DNA methylation levels of CG and CHG of Norway spruce were higher than most other plants studied. CHH methylation was found at a relatively low level; however, at least one copy of most of the RNA-directed DNA methylation pathway genes was found in Norway spruce, and CHH methylation was correlated with levels of siRNAs. In comparison with needles, somatic embryogenesis culture cells that are used for clonally propagating spruce trees showed lower levels of CG and CHG methylation but higher level of CHH methylation, suggesting that like in other species, these culture cells show abnormal methylation patterns.","language":"en","number":"50","urldate":"2021-06-07","journal":"Proceedings of the National Academy of Sciences","author":[{"propositions":[],"lastnames":["Ausin"],"firstnames":["Israel"],"suffixes":[]},{"propositions":[],"lastnames":["Feng"],"firstnames":["Suhua"],"suffixes":[]},{"propositions":[],"lastnames":["Yu"],"firstnames":["Chaowei"],"suffixes":[]},{"propositions":[],"lastnames":["Liu"],"firstnames":["Wanlu"],"suffixes":[]},{"propositions":[],"lastnames":["Kuo"],"firstnames":["Hsuan","Yu"],"suffixes":[]},{"propositions":[],"lastnames":["Jacobsen"],"firstnames":["Elise","L."],"suffixes":[]},{"propositions":[],"lastnames":["Zhai"],"firstnames":["Jixian"],"suffixes":[]},{"propositions":[],"lastnames":["Gallego-Bartolome"],"firstnames":["Javier"],"suffixes":[]},{"propositions":[],"lastnames":["Wang"],"firstnames":["Lin"],"suffixes":[]},{"propositions":[],"lastnames":["Egertsdotter"],"firstnames":["Ulrika"],"suffixes":[]},{"propositions":[],"lastnames":["Street"],"firstnames":["Nathaniel","R."],"suffixes":[]},{"propositions":[],"lastnames":["Jacobsen"],"firstnames":["Steven","E."],"suffixes":[]},{"propositions":[],"lastnames":["Wang"],"firstnames":["Haifeng"],"suffixes":[]}],"month":"December","year":"2016","pages":"E8106–E8113","bibtex":"@article{ausin_dna_2016,\n\ttitle = {{DNA} methylome of the 20-gigabase {Norway} spruce genome},\n\tvolume = {113},\n\tissn = {0027-8424, 1091-6490},\n\turl = {http://www.pnas.org/lookup/doi/10.1073/pnas.1618019113},\n\tdoi = {10.1073/pnas.1618019113},\n\tabstract = {DNA methylation plays important roles in many biological processes, such as silencing of transposable elements, imprinting, and regulating gene expression. Many studies of DNA methylation have shown its essential roles in angiosperms (flowering plants). However, few studies have examined the roles and patterns of DNA methylation in gymnosperms. Here, we present genome-wide high coverage single-base resolution methylation maps of Norway spruce (\n Picea abies\n ) from both needles and somatic embryogenesis culture cells via whole genome bisulfite sequencing. On average, DNA methylation levels of CG and CHG of Norway spruce were higher than most other plants studied. CHH methylation was found at a relatively low level; however, at least one copy of most of the RNA-directed DNA methylation pathway genes was found in Norway spruce, and CHH methylation was correlated with levels of siRNAs. 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