Computational protocol: Genome-wide identification and expression analysis of ClLAX, ClPIN and ClABCB genes families in Citrullus lanatus under various abiotic stresses and grafting

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Protocol publication

[…] The chromosomal location data of ClLAX, ClPIN and ClABCB family genes were obtained from Cucurbit Genomics Database. A map of the distribution of ClLAX, ClPIN and ClABCB family genes was drawn based on their chromosomal position. The alignment file of LAX, PIN and ABCB family proteins in watermelon and Arabidopsis was generated by ClustalW program with the default parameters. The amino acid sequences of AtLAX, AtPIN and AtABCB proteins were obtained from Yue et al. []. Phylogenetic tree was performed by MEGA6.0 (http://www.megasoftware.net/) using the neighbor-joining (NJ) method with the p-distance and complete deletion parameters. Exon-intron structure of ClLAX, ClPIN and ClABCB family genes were employed by Gene Structure Display Server (GSDS) tool (http://gsds.cbi.pku.edu.cn/). […]

Pipeline specifications

Software tools Clustal W, MEGA, GSDS
Databases AtPIN
Application Phylogenetics
Organisms Citrullus lanatus, Arabidopsis thaliana
Chemicals Adenosine Triphosphate