Search for PIN family members from different plant species

• Search for PIN family members from Marchantia polymorpha, Physcomitrella patens, Selaginella moellendorffii, Capsella rubella, Arabidopsis thaliana, Oryza sativa, Zea mays, and Brachypodium arboreum.

1. Download the sequence of Arabidopsis thaliana PIN1 protein from the TAIR database (https://www.arabidopsis.org/).

2. Open the link of Phytozome database (https://phytozome.jgi.doe.gov/pz/portal.html),

3. Find the top menu ”Tools”, click it and go to the “BLAST” page (https://phytozome.jgi.doe.gov/pz/portal.html#!search?show=BLAST).

4. At the left of the page, select and tick the target plant species, including Marchantia polymorpha, Physcomitrella patens, Selaginella moellendorffii, Capsella rubella, Arabidopsis thaliana, Oryza sativa, Zea mays, and Brachypodium arboretum, which are used for the subsequent sequence blast.

5. At the right of the “BLAST” page, paste the A. thaliana PIN1 protein sequence as the query sequence. Concerning the Algorithm parameters, choose the “Proteome” as the “Target type” and use “BLASTP” as the designated “Program”.

6. Click the “GO” button to start the query. In the BLAST results, a series of PIN members are extracted and listed according to the scores, which represent the sequence similarity between the query and hit PIN sequences among the selected Species.

7. Click the green button “G” to gain an overview of the selected gene.

8. Find and click the menu “Sequence” in the page of gene view, where the PIN sequences from certain plant species can be visualized.

 

• Search for PIN family members from the gymnosperm Picea abies and Pinus taeda

1. Open the homepage of Spruce Genome Project database (http://congenie.org/start).

2. Find the top menu ”Genome Tools” and go to the main “BLAST” page (https://congenie.org/blast).

3. Enter the Arabidopsis PIN1 protein sequence as the query sequence.

4. Set up the BLAST program (choosing the “BLASTP”) and select the blast database, which is denoted by “Select Blast DB” and can be found at the end of the webpage.

5. Click the orange button “BLAST”. The extracted the PIN family members from Picea abies and Pinus taeda will be listed according to the scores based on the sequence similarity between PIN proteins from Arabidopsis and other species.

6. Tick the Query ID and click the button “FASTA” at the bottom of the page to visualize the sequences of blasted PIN proteins from Picea abies and Pinus taeda.

• Search for PIN family members from Amborella trichopoda.

1. Go to the Amborella database, which is included in the EnsemblPlants database (https://plants.ensembl.org/Amborella_trichopoda/Info/Annotation/).

2. Find the top menu ”BLAST” and click it to link to the main EnsemblPlants “BLAST” page (https://plants.ensembl.org/Amborella_trichopoda/Tools/Blast).

3. Paste the Arabidopsis PIN1 protein sequence into the blank box at the right of “Sequence data”.

4. Choose the “BLASTP” as the search tool.

5. Click the green button “Run” to start the sequence alignment.

6. Choose the “View results” to jump to the page of BLAST result, where the sequences of PIN family members from Amborella trichopoda can be found.

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