Computational protocol: Genome-Wide Analysis of the AP2/ERF Gene Family in Physic Nut and Overexpression of the JcERF011 Gene in Rice Increased Its Sensitivity to Salinity Stress

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Protocol publication

[…] Sequences of AP2/ERF domain-containing proteins from Arabidopsis were downloaded from the Arabidopsis genome sequence, TAIR 9.0 release (http://www.Arabidopsis.org/), while sequences for rice, castor bean, Chlamydomonas reinhardtii, and Physcomitrella patens were downloaded from Phytozome (http://phytozome.jgi.doe.gov/pz/portal.html) and sequences for grapevine were downloaded from Licausi et al [].We searched for AP2/ERF domain-containing genes in the physic nut (J. curcas L.) genome database of the Kazusa DNA Research Institute (http://www.kazusa.or.jp/jatropha/) [] and in our own genome database (available from DDBJ/EMBL/GenBank under the accession number AFEW00000000) []. To search for AP2/ERF domain-containing genes in the physic nut, we used Arabidopsis AP2/ERF proteins from each subgroup as query sequences for tBlastn and Blastp searches against the physic nut genome sequences and against predicted protein sequences. Next, we corrected errors in the annotation of AP2/ERF coding domain sequences on the basis of the physic nut EST database available from GenBank (http://www.ncbi.nlm.nih.gov/), and our own physic nut and J. integerrima EST datasets (accessions SRA197144 and SRA197148 in GenBank). The exon—intron structures of AP2/ERF genes were determined by comparing the coding sequences and the corresponding genomic sequences using the Gene Structure Display Server (http://gsds.cbi.pku.edu.cn/). Chromosomal positions of the AP2/ERF genes were mapped onto the physic nut linkage map []. [...] Multiple sequence alignments of the conserved AP2/ERF domain sequences were performed using Clustal W2 (http://www.ebi.ac.uk/Tools/msa/clustalw2/). Unrooted maximum-likelihood (ML) trees were constructed using the LG model with approximate likelihood ratio test (aLRT) SH-like branch support steps in PhyML version 3.0 (http://atgc.lirmm.fr/phyml/) [], and the results were displayed with the Mega software package version 5 []. […]

Pipeline specifications

Software tools TBLASTN, BLASTP, GSDS, Clustal W, PhyML, MEGA
Databases ATGC
Applications Phylogenetics, Amino acid sequence alignment
Organisms Oryza sativa
Chemicals Nitrogen, Phosphates