Computational protocol: Bioinformatic Identification and Analysis of Extensins in the Plant Kingdom

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Protocol publication

[…] The functional module of BLAST was integrated into the BIO OHIO 2.0. All candidate EXTs identified were subjected to NCBI BLASTP analysis using the current Arabidopsis protein BLAST dataset (November 2010 TAIR10 Genome Release) downloaded from The Arabidopsis Information Resource (TAIR; www.arabidopsis.org). [...] Amino acid sequences were aligned by use of the Geneious software program (http://www.geneious.com/) to obtain conserved domains. Aligned sequences of LRXs, PERKs, and FH EXTs were input into Mega 6 for phylogenetic analysis using the maximum likelihood and the maximum parsimony methods []. For LRXs, the analysis involved 78 protein sequences. There were a total of 294 amino acid positions in the final dataset. The evolutionary history inferred by the Maximum Likelihood method was based on the JTT matrix-based model []. The evolutionary history inferred by the Maximum Parsimony method used the Tree-Bisection-Regrafting (TBR) algorithm with search level 1 in which the initial trees were obtained by the random addition of sequences (10 replicates) []. The bootstrap consensus tree inferred from 1000 replicates was shown and branches corresponding to partitions reproduced in less than 50% bootstrap replicates are collapsed. For the phylogenetic analysis of PERKs and FH EXTs, the same methods were used as for analysis of the LRXs. The analysis of PERKs involved 93 protein sequences, and a total of 283 amino acid positions were present in the final dataset. The analysis of FH EXTs involved 76 protein sequences, and a total of 377 amino acid positions were present in the final dataset. […]

Pipeline specifications

Software tools Geneious, MEGA
Application Phylogenetics
Organisms Arabidopsis thaliana, Ostreococcus 'lucimarinus', Chlamydomonas reinhardtii, Volvox carteri, Klebsormidium flaccidum, Physcomitrella patens, Selaginella moellendorffii, Pinus taeda, Picea abies, Brachypodium distachyon, Zea mays, Oryza sativa, Glycine max, Medicago truncatula, Brassica rapa, Solanum lycopersicum, Solanum tuberosum, Populus trichocarpa
Chemicals Tyrosine