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Thomas Mock - One of the best experts on this subject based on the ideXlab platform.

  • integrative analysis of Chloroplast DNA methylation in a marine alga saccharina japonica
    Plant Molecular Biology, 2021
    Co-Authors: Linhong Teng, Wentao Han, Xiao Fan, Xiaowen Zhang, Yitao Wang, Sadequr Rahman, Matteo Pellegrini, Thomas Mock
    Abstract:

    KEY MESSAGE We applied an integrative approach using multiple methods to verify cytosine methylation in the Chloroplast DNA of the multicellular brown alga Saccharina japonica. Cytosine DNA methylation is a heritable process which plays important roles in regulating development throughout the life cycle of an organism. Although methylation of nuclear DNA has been studied extensively, little is known about the state and role of DNA methylation in Chloroplast genomes, especially in marine algae. Here, we have applied an integrated approach encompassing whole-genome bisulfite sequencing, methylated DNA immunoprecipitation, gene co-expression networks and photophysiological analyses to provide evidence for the role of Chloroplast DNA methylation in a marine alga, the multicellular brown alga Saccharina japonica. Although the overall methylation level was relatively low in the Chloroplast genome of S. japonica, gametophytes exhibited higher methylation levels than sporophytes. Gene-specific bisulfite-cloning sequencing provided additional evidence for the methylation of key photosynthetic genes. Many of them were highly expressed in sporophytes whereas genes involved in transcription, translation and biosynthesis were strongly expressed in gametophytes. Nucleus-encoded photosynthesis genes were co-expressed with their Chloroplast-encoded counterparts potentially contributing to the higher photosynthetic performance in sporophytes compared to gametophytes where these co-expression networks were less pronounced. A nucleus-encoded DNA methyltransferase of the DNMT2 family is assumed to be responsible for the methylation of the Chloroplast genome because it is predicted to possess a plastid transit peptide.

  • integrative analysis of Chloroplast DNA methylation in a marine alga saccharina japonica
    Plant Molecular Biology, 2021
    Co-Authors: Linhong Teng, Wentao Han, Xiao Fan, Xiaowen Zhang, Yitao Wang, Sadequr Rahman, Matteo Pellegrini, Thomas Mock
    Abstract:

    We applied an integrative approach using multiple methods to verify cytosine methylation in the Chloroplast DNA of the multicellular brown alga Saccharina japonica. Cytosine DNA methylation is a heritable process which plays important roles in regulating development throughout the life cycle of an organism. Although methylation of nuclear DNA has been studied extensively, little is known about the state and role of DNA methylation in Chloroplast genomes, especially in marine algae. Here, we have applied an integrated approach encompassing whole-genome bisulfite sequencing, methylated DNA immunoprecipitation, gene co-expression networks and photophysiological analyses to provide evidence for the role of Chloroplast DNA methylation in a marine alga, the multicellular brown alga Saccharina japonica. Although the overall methylation level was relatively low in the Chloroplast genome of S. japonica, gametophytes exhibited higher methylation levels than sporophytes. Gene-specific bisulfite-cloning sequencing provided additional evidence for the methylation of key photosynthetic genes. Many of them were highly expressed in sporophytes whereas genes involved in transcription, translation and biosynthesis were strongly expressed in gametophytes. Nucleus-encoded photosynthesis genes were co-expressed with their Chloroplast-encoded counterparts potentially contributing to the higher photosynthetic performance in sporophytes compared to gametophytes where these co-expression networks were less pronounced. A nucleus-encoded DNA methyltransferase of the DNMT2 family is assumed to be responsible for the methylation of the Chloroplast genome because it is predicted to possess a plastid transit peptide.

Linhong Teng - One of the best experts on this subject based on the ideXlab platform.

  • integrative analysis of Chloroplast DNA methylation in a marine alga saccharina japonica
    Plant Molecular Biology, 2021
    Co-Authors: Linhong Teng, Wentao Han, Xiao Fan, Xiaowen Zhang, Yitao Wang, Sadequr Rahman, Matteo Pellegrini, Thomas Mock
    Abstract:

    KEY MESSAGE We applied an integrative approach using multiple methods to verify cytosine methylation in the Chloroplast DNA of the multicellular brown alga Saccharina japonica. Cytosine DNA methylation is a heritable process which plays important roles in regulating development throughout the life cycle of an organism. Although methylation of nuclear DNA has been studied extensively, little is known about the state and role of DNA methylation in Chloroplast genomes, especially in marine algae. Here, we have applied an integrated approach encompassing whole-genome bisulfite sequencing, methylated DNA immunoprecipitation, gene co-expression networks and photophysiological analyses to provide evidence for the role of Chloroplast DNA methylation in a marine alga, the multicellular brown alga Saccharina japonica. Although the overall methylation level was relatively low in the Chloroplast genome of S. japonica, gametophytes exhibited higher methylation levels than sporophytes. Gene-specific bisulfite-cloning sequencing provided additional evidence for the methylation of key photosynthetic genes. Many of them were highly expressed in sporophytes whereas genes involved in transcription, translation and biosynthesis were strongly expressed in gametophytes. Nucleus-encoded photosynthesis genes were co-expressed with their Chloroplast-encoded counterparts potentially contributing to the higher photosynthetic performance in sporophytes compared to gametophytes where these co-expression networks were less pronounced. A nucleus-encoded DNA methyltransferase of the DNMT2 family is assumed to be responsible for the methylation of the Chloroplast genome because it is predicted to possess a plastid transit peptide.

  • integrative analysis of Chloroplast DNA methylation in a marine alga saccharina japonica
    Plant Molecular Biology, 2021
    Co-Authors: Linhong Teng, Wentao Han, Xiao Fan, Xiaowen Zhang, Yitao Wang, Sadequr Rahman, Matteo Pellegrini, Thomas Mock
    Abstract:

    We applied an integrative approach using multiple methods to verify cytosine methylation in the Chloroplast DNA of the multicellular brown alga Saccharina japonica. Cytosine DNA methylation is a heritable process which plays important roles in regulating development throughout the life cycle of an organism. Although methylation of nuclear DNA has been studied extensively, little is known about the state and role of DNA methylation in Chloroplast genomes, especially in marine algae. Here, we have applied an integrated approach encompassing whole-genome bisulfite sequencing, methylated DNA immunoprecipitation, gene co-expression networks and photophysiological analyses to provide evidence for the role of Chloroplast DNA methylation in a marine alga, the multicellular brown alga Saccharina japonica. Although the overall methylation level was relatively low in the Chloroplast genome of S. japonica, gametophytes exhibited higher methylation levels than sporophytes. Gene-specific bisulfite-cloning sequencing provided additional evidence for the methylation of key photosynthetic genes. Many of them were highly expressed in sporophytes whereas genes involved in transcription, translation and biosynthesis were strongly expressed in gametophytes. Nucleus-encoded photosynthesis genes were co-expressed with their Chloroplast-encoded counterparts potentially contributing to the higher photosynthetic performance in sporophytes compared to gametophytes where these co-expression networks were less pronounced. A nucleus-encoded DNA methyltransferase of the DNMT2 family is assumed to be responsible for the methylation of the Chloroplast genome because it is predicted to possess a plastid transit peptide.

H T Hart - One of the best experts on this subject based on the ideXlab platform.

  • phylogenetic relationships in the crassulaceae inferred from Chloroplast DNA restriction site variation
    American Journal of Botany, 1998
    Co-Authors: R C H J Van Ham, H T Hart
    Abstract:

    A restriction-site analysis of Chloroplast DNA from 44 species, representing 19 genera and all six subfamilies of the Crassulaceae was conducted using 12 restriction endonucleases. A total of 969 variable sites was detected, 608 of which were phylogenetically informative and used in parsimony analysis. Estimated values of nucleotide sequence divergence were used to construct a distance tree by the neighbor-joining method. Maximum sequence divergence in the family was ~7%. Different tree inference methods yielded only moderately different topologies. The amount of support for the monophyletic groups obtained in the Wagner parsimony analysis was evaluated by bootstrap and decay analysis. There is very strong support for a basal division of the family, which separates the monophyletic subfamily Crassuloideae from all other taxa. Four of the six traditionally recognized subfamilies are indicated to be polyphyletic. These include the Cotyledonoideae, Sempervivoideae, Sedoideae, and Echeverioideae. The Kalanchoideae and the genera Cotyledon and Adromischus exhibit low levels of cpDNA sequence divergence relative to one another, suggesting a relatively recent radiation. The genera Sedum and Rosularia are indicated to be polyphyletic. Sedum comprises sister taxa of most of the other genera of the family.

Yitao Wang - One of the best experts on this subject based on the ideXlab platform.

  • integrative analysis of Chloroplast DNA methylation in a marine alga saccharina japonica
    Plant Molecular Biology, 2021
    Co-Authors: Linhong Teng, Wentao Han, Xiao Fan, Xiaowen Zhang, Yitao Wang, Sadequr Rahman, Matteo Pellegrini, Thomas Mock
    Abstract:

    KEY MESSAGE We applied an integrative approach using multiple methods to verify cytosine methylation in the Chloroplast DNA of the multicellular brown alga Saccharina japonica. Cytosine DNA methylation is a heritable process which plays important roles in regulating development throughout the life cycle of an organism. Although methylation of nuclear DNA has been studied extensively, little is known about the state and role of DNA methylation in Chloroplast genomes, especially in marine algae. Here, we have applied an integrated approach encompassing whole-genome bisulfite sequencing, methylated DNA immunoprecipitation, gene co-expression networks and photophysiological analyses to provide evidence for the role of Chloroplast DNA methylation in a marine alga, the multicellular brown alga Saccharina japonica. Although the overall methylation level was relatively low in the Chloroplast genome of S. japonica, gametophytes exhibited higher methylation levels than sporophytes. Gene-specific bisulfite-cloning sequencing provided additional evidence for the methylation of key photosynthetic genes. Many of them were highly expressed in sporophytes whereas genes involved in transcription, translation and biosynthesis were strongly expressed in gametophytes. Nucleus-encoded photosynthesis genes were co-expressed with their Chloroplast-encoded counterparts potentially contributing to the higher photosynthetic performance in sporophytes compared to gametophytes where these co-expression networks were less pronounced. A nucleus-encoded DNA methyltransferase of the DNMT2 family is assumed to be responsible for the methylation of the Chloroplast genome because it is predicted to possess a plastid transit peptide.

  • integrative analysis of Chloroplast DNA methylation in a marine alga saccharina japonica
    Plant Molecular Biology, 2021
    Co-Authors: Linhong Teng, Wentao Han, Xiao Fan, Xiaowen Zhang, Yitao Wang, Sadequr Rahman, Matteo Pellegrini, Thomas Mock
    Abstract:

    We applied an integrative approach using multiple methods to verify cytosine methylation in the Chloroplast DNA of the multicellular brown alga Saccharina japonica. Cytosine DNA methylation is a heritable process which plays important roles in regulating development throughout the life cycle of an organism. Although methylation of nuclear DNA has been studied extensively, little is known about the state and role of DNA methylation in Chloroplast genomes, especially in marine algae. Here, we have applied an integrated approach encompassing whole-genome bisulfite sequencing, methylated DNA immunoprecipitation, gene co-expression networks and photophysiological analyses to provide evidence for the role of Chloroplast DNA methylation in a marine alga, the multicellular brown alga Saccharina japonica. Although the overall methylation level was relatively low in the Chloroplast genome of S. japonica, gametophytes exhibited higher methylation levels than sporophytes. Gene-specific bisulfite-cloning sequencing provided additional evidence for the methylation of key photosynthetic genes. Many of them were highly expressed in sporophytes whereas genes involved in transcription, translation and biosynthesis were strongly expressed in gametophytes. Nucleus-encoded photosynthesis genes were co-expressed with their Chloroplast-encoded counterparts potentially contributing to the higher photosynthetic performance in sporophytes compared to gametophytes where these co-expression networks were less pronounced. A nucleus-encoded DNA methyltransferase of the DNMT2 family is assumed to be responsible for the methylation of the Chloroplast genome because it is predicted to possess a plastid transit peptide.

Sadequr Rahman - One of the best experts on this subject based on the ideXlab platform.

  • integrative analysis of Chloroplast DNA methylation in a marine alga saccharina japonica
    Plant Molecular Biology, 2021
    Co-Authors: Linhong Teng, Wentao Han, Xiao Fan, Xiaowen Zhang, Yitao Wang, Sadequr Rahman, Matteo Pellegrini, Thomas Mock
    Abstract:

    KEY MESSAGE We applied an integrative approach using multiple methods to verify cytosine methylation in the Chloroplast DNA of the multicellular brown alga Saccharina japonica. Cytosine DNA methylation is a heritable process which plays important roles in regulating development throughout the life cycle of an organism. Although methylation of nuclear DNA has been studied extensively, little is known about the state and role of DNA methylation in Chloroplast genomes, especially in marine algae. Here, we have applied an integrated approach encompassing whole-genome bisulfite sequencing, methylated DNA immunoprecipitation, gene co-expression networks and photophysiological analyses to provide evidence for the role of Chloroplast DNA methylation in a marine alga, the multicellular brown alga Saccharina japonica. Although the overall methylation level was relatively low in the Chloroplast genome of S. japonica, gametophytes exhibited higher methylation levels than sporophytes. Gene-specific bisulfite-cloning sequencing provided additional evidence for the methylation of key photosynthetic genes. Many of them were highly expressed in sporophytes whereas genes involved in transcription, translation and biosynthesis were strongly expressed in gametophytes. Nucleus-encoded photosynthesis genes were co-expressed with their Chloroplast-encoded counterparts potentially contributing to the higher photosynthetic performance in sporophytes compared to gametophytes where these co-expression networks were less pronounced. A nucleus-encoded DNA methyltransferase of the DNMT2 family is assumed to be responsible for the methylation of the Chloroplast genome because it is predicted to possess a plastid transit peptide.

  • integrative analysis of Chloroplast DNA methylation in a marine alga saccharina japonica
    Plant Molecular Biology, 2021
    Co-Authors: Linhong Teng, Wentao Han, Xiao Fan, Xiaowen Zhang, Yitao Wang, Sadequr Rahman, Matteo Pellegrini, Thomas Mock
    Abstract:

    We applied an integrative approach using multiple methods to verify cytosine methylation in the Chloroplast DNA of the multicellular brown alga Saccharina japonica. Cytosine DNA methylation is a heritable process which plays important roles in regulating development throughout the life cycle of an organism. Although methylation of nuclear DNA has been studied extensively, little is known about the state and role of DNA methylation in Chloroplast genomes, especially in marine algae. Here, we have applied an integrated approach encompassing whole-genome bisulfite sequencing, methylated DNA immunoprecipitation, gene co-expression networks and photophysiological analyses to provide evidence for the role of Chloroplast DNA methylation in a marine alga, the multicellular brown alga Saccharina japonica. Although the overall methylation level was relatively low in the Chloroplast genome of S. japonica, gametophytes exhibited higher methylation levels than sporophytes. Gene-specific bisulfite-cloning sequencing provided additional evidence for the methylation of key photosynthetic genes. Many of them were highly expressed in sporophytes whereas genes involved in transcription, translation and biosynthesis were strongly expressed in gametophytes. Nucleus-encoded photosynthesis genes were co-expressed with their Chloroplast-encoded counterparts potentially contributing to the higher photosynthetic performance in sporophytes compared to gametophytes where these co-expression networks were less pronounced. A nucleus-encoded DNA methyltransferase of the DNMT2 family is assumed to be responsible for the methylation of the Chloroplast genome because it is predicted to possess a plastid transit peptide.