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Pipeline publication

[…] lated gene (BCHGM gene) and Body-CHH-methylated gene (BCHHM gene) were defined as above, respectively. Based on this framework, then, duplicated gene pairs containing at least one BCGM copy was called Body CG-methylated (BCGM) duplicated genes. Finally, duplicates with CG-only methylation were defined if both copies of a body CG-methylated (BCGM) duplicated gene pair was neither body-CHG-methylated (BCHGM) nor body-CHH-methylated (BCHHM). The rest of the duplicated genes were defined as duplicates with all-context methylation., This was done based on criteria defined previously in rice. In brief, non-TE-related genes were extracted from the rice reference genome (MSU7). Then, the all-vs-all Blastp was used to identify candidate duplicates and a gene pair that was top 5 matched and with an E-value < 10−10 was considered as a candidate duplicates. Then, MCscanX was performed to categorize different types of duplicates, included WGD, tandem, proximal and transposed duplicates, with default parameters. Finally, we only selected those duplicates that have methylation information in both the OsMet1-2 mutant and WT for further analysis., Synonymous (d S) and non-synonymous (d N) mutations were calculated as follows: all coding region sequences and protein sequences of duplicates were pairwise aligned using the default options in MUSCLE, and the alignment results were used to calculate d S and d N values using the ‘seqinr’ package in R. As per the previous study in rice, when d S > 3, duplicates were excluded., Total RNAs were independently isolated from the two genotypes under the same conditions as those for RNA-seq. A set of 10 duplicated genes pairs were randomly chosen and copy-specific qRT-PCR primers were successfully designed for 10 genes (Supplementary Table ). For each of these 10 duplicate genes, the relative expression level of the higher and lower expression copies in WT and mutant were calculated. The Student’s t-test was used to test for statistical difference in relative expression level between WT and mutant for each copy of a given duplicated gene pair., All Statistical tests in th […]

Pipeline specifications

Software tools BLASTP, MCScanX, MUSCLE, seqinr
Organisms Oryza sativa