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| Status |
Public on Dec 18, 2014 |
| Title |
Genome-wide and single-base resolution DNA methylomes of the Pacific oyster Crassostrea gigas provide insight into the evolution of invertebrate CpG methylation |
| Organism |
Magallana gigas |
| Experiment type |
Methylation profiling by high throughput sequencing
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| Summary |
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.
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| 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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| Contributor(s) |
Wang X, Li Q, Lian J, Li L, Jin L, Cai H, Xu F, Qi H, Zhang L, Wu F, Meng J, Que H, Fang X, Guo X, Zhang G |
| Citation(s) |
25514978 |
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| Submission date |
Aug 22, 2012 |
| Last update date |
Jun 12, 2019 |
| Contact name |
Hong zhi Cao |
| E-mail(s) |
caohongzhi@genomics.cn
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| Phone |
8675525274032
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| Organization name |
BGI-SHENZHEN
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| Department |
Bioinformatics
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| Street address |
F5, Main Building, Beishan Industrial Zone, Beishan Road, Yantian District
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| City |
Shenzhen |
| State/province |
Guangdong |
| ZIP/Postal code |
518083 |
| Country |
China |
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| Platforms (1) |
| GPL13986 |
Illumina HiSeq 2000 (Crassostrea gigas) |
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| Samples (2) |
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| Relations |
| BioProject |
PRJNA173440 |
| SRA |
SRP015008 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE40302_Cdepth_file_readme.txt |
3.6 Kb |
(ftp)(http) |
TXT |
| GSE40302_RAW.tar |
2.4 Gb |
(http)(custom) |
TAR (of TXT) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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