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Pipeline publication

[…] d within DIVERGR v3.0 was used to calculate the coefficients of type I and type II functional divergence (θ I and θ II, respectively) between two groups after gene duplication and to predict functionally divergent amino acids based on their different evolutionary rates. Within two duplicated groups of a gene family, type I functional divergence helps identify the relaxation of functional constraint in one group relative to that of another, while type II identifies shifting patterns of functional constraint., The entire DNA sequences of plant DAL genes together with 1 kb of upstream and downstream flanking sequences were used for calculation of GC content and prediction of CpG islands in the EMBOSS CpGplot online server (http://www.ebi.ac.uk/Tools/seqstats/emboss_cpgplot/). To confirm the DNA methylation of ZmDAL DNA sequences, leaf DNA of B73 seedlings was isolated and treated with bisulfate using the EpiTect® bisulfite kit (QIAGEN, USA) according to the manufacturer’s instructions. The primers for detection of DNA methylation were designed using MethPrimer (http://www.urogene.org/methprimer/) and modified using Primer3web (http://primer3.ut.ee/). PCR products were cloned into a pGEM-T vector (Promega, USA) and subsequently sequenced using an ABI3730 DNA sequencer (Shanghai Sunny Bio., China). DNA methylation states via bisulfite sequencing were analyzed and displayed using Kismeth software (http://katahdin.mssm.edu/kismeth/revpage.pl)., To investigate the spatiotemporal expression patterns of ZmDAL genes, the log2-transformed and RMA-normalized data for ZmDAL genes were downloaded from PLEXdb (http://www.plexdb.org/), and cluster analysis of these expression data were performed using Cluster v3.0 with the hierarchic method. A heat map was produced using Java TreeView v1.1.5. The coefficient of vari […]

Pipeline specifications

Software tools EMBOSS, methPrimer, Primer3
Databases PLEXdb