Genome-wide and single-base resolution DNA methylomes of the Pacific oyster Crassostrea gigas provide insight into the evolution of invertebrate CpG methylation
Comparative analysis of the oyster DNA methylomes and that of other animal species revealed that the characteristics of DNA methylation were generally conserved during invertebrate evolution, while some unique features were derived in the insect lineage. The preference of methylation modification on...
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ftdatacite:10.26036/cnphis0002886 2023-05-15T15:59:03+02:00 Genome-wide and single-base resolution DNA methylomes of the Pacific oyster Crassostrea gigas provide insight into the evolution of invertebrate CpG methylation BGI 2012 https://dx.doi.org/10.26036/cnphis0002886 https://db.cngb.org/search/project/CNPhis0002886/ en eng CNGB Epigenomics Multiisolate Comparative analysis of the oyster DNA methylomes and that of other animal species revealed that the characteristics of DNA methylation were generally conserved during invertebrate evolution, while some unique features were derived in the insect lineage. The preference of methylation modification on genes originating in the eukaryotic ancestor rather than the oldest genes is unexpected, probably implying that the emergence of methylation regulation in these 'relatively young' genes was critical for the origin and radiation of eukaryotes.Overall design: Two Pacific oysters were used for methylome profiling in this study. One is an inbred oyster (05x7-T-G4-1.051#20) that was produced by four generations of sister-brother mating (coefficient of inbreeding, F = 0.59) and has been used for whole genome-sequencing. The other was a wild oyster collected from Weihai, Shandong Province, China. Both oysters were about two years of age. The inbred oyster was produced as single oysters and culture 2012 ftdatacite https://doi.org/10.26036/cnphis0002886 2021-11-05T12:55:41Z Comparative analysis of the oyster DNA methylomes and that of other animal species revealed that the characteristics of DNA methylation were generally conserved during invertebrate evolution, while some unique features were derived in the insect lineage. The preference of methylation modification on genes originating in the eukaryotic ancestor rather than the oldest genes is unexpected, probably implying that the emergence of methylation regulation in these 'relatively young' genes was critical for the origin and radiation of eukaryotes.Overall design: Two Pacific oysters were used for methylome profiling in this study. One is an inbred oyster (05x7-T-G4-1.051#20) that was produced by four generations of sister-brother mating (coefficient of inbreeding, F = 0.59) and has been used for whole genome-sequencing. The other was a wild oyster collected from Weihai, Shandong Province, China. Both oysters were about two years of age. The inbred oyster was produced as single oysters and cultured intertidally at southern Puget Sound, Washington, USA, where the water temperature ranges from 7 to 16 °C. The wild oyster was an attached oyster from an oyster farm in its native range at Weihai, China, where the water temperature ranges from 4 to 27 °C.For DNA from each of the two individuals, we constructed two independent libraries. For each library, 5 µg genomic DNA mixed with 25 ng cl857 Sam7 Lambda DNA was fragmented by sonication with a Covaris S2 system (Covaris, MA) to a mean size of approximately 250 bp. End-repair, 3’-end dA addition and adapter ligation were subsequently performed. Methylated adapters were used according to the manufacturer’s instructions (Illumina). The bisulfite conversion of DNA was performed according to a modified NH4HSO3-based protocol and amplified with nine cycles of PCR. All libraries were subjected to 90-bp paired-end sequencing on an Illumina HiSeq 2000 platform. Text Crassostrea gigas Pacific oyster DataCite Metadata Store (German National Library of Science and Technology) Pacific Lambda ENVELOPE(-62.983,-62.983,-64.300,-64.300) |
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Open Polar |
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DataCite Metadata Store (German National Library of Science and Technology) |
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ftdatacite |
language |
English |
topic |
Epigenomics Multiisolate |
spellingShingle |
Epigenomics Multiisolate BGI Genome-wide and single-base resolution DNA methylomes of the Pacific oyster Crassostrea gigas provide insight into the evolution of invertebrate CpG methylation |
topic_facet |
Epigenomics Multiisolate |
description |
Comparative analysis of the oyster DNA methylomes and that of other animal species revealed that the characteristics of DNA methylation were generally conserved during invertebrate evolution, while some unique features were derived in the insect lineage. The preference of methylation modification on genes originating in the eukaryotic ancestor rather than the oldest genes is unexpected, probably implying that the emergence of methylation regulation in these 'relatively young' genes was critical for the origin and radiation of eukaryotes.Overall design: Two Pacific oysters were used for methylome profiling in this study. One is an inbred oyster (05x7-T-G4-1.051#20) that was produced by four generations of sister-brother mating (coefficient of inbreeding, F = 0.59) and has been used for whole genome-sequencing. The other was a wild oyster collected from Weihai, Shandong Province, China. Both oysters were about two years of age. The inbred oyster was produced as single oysters and cultured intertidally at southern Puget Sound, Washington, USA, where the water temperature ranges from 7 to 16 °C. The wild oyster was an attached oyster from an oyster farm in its native range at Weihai, China, where the water temperature ranges from 4 to 27 °C.For DNA from each of the two individuals, we constructed two independent libraries. For each library, 5 µg genomic DNA mixed with 25 ng cl857 Sam7 Lambda DNA was fragmented by sonication with a Covaris S2 system (Covaris, MA) to a mean size of approximately 250 bp. End-repair, 3’-end dA addition and adapter ligation were subsequently performed. Methylated adapters were used according to the manufacturer’s instructions (Illumina). The bisulfite conversion of DNA was performed according to a modified NH4HSO3-based protocol and amplified with nine cycles of PCR. All libraries were subjected to 90-bp paired-end sequencing on an Illumina HiSeq 2000 platform. |
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Text |
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author_facet |
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author_sort |
BGI |
title |
Genome-wide and single-base resolution DNA methylomes of the Pacific oyster Crassostrea gigas provide insight into the evolution of invertebrate CpG methylation |
title_short |
Genome-wide and single-base resolution DNA methylomes of the Pacific oyster Crassostrea gigas provide insight into the evolution of invertebrate CpG methylation |
title_full |
Genome-wide and single-base resolution DNA methylomes of the Pacific oyster Crassostrea gigas provide insight into the evolution of invertebrate CpG methylation |
title_fullStr |
Genome-wide and single-base resolution DNA methylomes of the Pacific oyster Crassostrea gigas provide insight into the evolution of invertebrate CpG methylation |
title_full_unstemmed |
Genome-wide and single-base resolution DNA methylomes of the Pacific oyster Crassostrea gigas provide insight into the evolution of invertebrate CpG methylation |
title_sort |
genome-wide and single-base resolution dna methylomes of the pacific oyster crassostrea gigas provide insight into the evolution of invertebrate cpg methylation |
publisher |
CNGB |
publishDate |
2012 |
url |
https://dx.doi.org/10.26036/cnphis0002886 https://db.cngb.org/search/project/CNPhis0002886/ |
long_lat |
ENVELOPE(-62.983,-62.983,-64.300,-64.300) |
geographic |
Pacific Lambda |
geographic_facet |
Pacific Lambda |
genre |
Crassostrea gigas Pacific oyster |
genre_facet |
Crassostrea gigas Pacific oyster |
op_doi |
https://doi.org/10.26036/cnphis0002886 |
_version_ |
1766394837829943296 |