Arabidopsis thaliana, L.

Costa, Laura S. M., Allan, Pires, S., Damaceno, Neila B., Rigueiras, Pietra O., Maximiano, Mariana R., Franco, Octavio L. & Porto, William F., 2020, In silico characterization of class II plant defensins from Arabidopsis thaliana, Phytochemistry (112511) 179, pp. 1-8 : 2

2.1. The majority of A. thaliana defensins belongs to class I defensins

In order to identify class II defensin sequences, we designed a semiautomatic pipeline ( Fig. 1 ). For that, initially all proteins from the A. thaliana Uniprot database were downloaded. The dataset consisted of 86,486 sequences ( March 2017). From this dataset, 387 sequences were retrieved by using regular expression (RegEx) search (step 2, Fig. 1 ). From these, 285 had up to 130 amino acid residues (step 3, Fig. 1 ). This criterion allows eventual larger C-terminal prodomains to be identified. Then, we used a PERL script to select the sequences with the following flags: hypothetical, unknown, unnamed and/or uncharacterized (step 4, Fig. 1 ), resulting in 15 sequences. From 15 sequences, seven were incomplete and therefore were discarded, (step 5, Fig. 1 ). From the remaining sequences, two sequences without signal peptide or with transmembrane domains were discarded (step 6, Fig. 1 ). Finally, from six remaining sequences, two sequences with a potential C-Terminal prodomain were selected, with accession codes A7 REG2 and A7 REG4 .

Figures

Fig. 1. Flowchart of identification of class II defensins. The indigo boxes indicated steps performed by Perl scripts and the red boxes, steps curated by hand. The white boxes indicated the number of sequences for each respective step. The sequences from A. thaliana were retrieved from UniProt database; the defensin RegEx “CX2-18CX3CX2-10[GAPSIDERYW]XCX4-17CXC” was determined by Zhu (Zhu, 2008). The complete sequences were retrieved according the UniProt annotations; and the sequences predicted to be secreted were selected according to the Phobius prediction, presenting signal peptide and no transmembrane domains. The selected sequences at the end of the process represented less than 1% of all defensin sequences from A. thaliana. (For interpretation of the references to colour in this figure legend, the reader is referred to the Web version of this article.)