Figure 6
From: Functional divergence and origin of the DAG-like gene family in plants
GC content and DNA methylation analysis of DAL genes in higher plants. (a,b) GC content and CpG islands of plant DAL genes were identified and displayed using CpGplot of EMBOSS (http://www.ebi.ac.uk/Tools/emboss/) with a window size of 100 bp and the following set options: Observed/Expected ratio >0.60, Percent C+ Percent G >50.00 and Length >200. The DNA sequences of the DAL genes used here contain 1000 bp before the start codon and 1000 bp after the stop codon. Two CpG islands within the 607-bp (nucleotides 817–1423) and 359-bp (nucleotides 817–1423) regions (817–1423) were observed and delimited by two close red lines, respectively. (c) The DNA methylation of the 607-bp CpG island was analyzed using bisulfite sequencing with the primers listed in Supplementary Table S2, and the data were displayed using Kismeth software (http://katahdin.mssm.edu/kismeth/revpage.pl). (d) Codon base composition of DAL genes in flowering plants. The significant differences of codon base composition between dicot and monocot DAL genes were statistically analyzed according to Student’s t-test. *P < 0.05; **P < 0.01. GC1, the GC contents at the first base of one codon; GC2, the GC contents at the second base; GC3, the GC contents at the third base.
