Creation of a new database with RESCRIPt
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1. Download of NCBI resources for plants species:

qiime rescript get-ncbi-data \
  --p-query 'txid33090[ORGN] AND (ITS OR Internal Transcribed Spacer) NOT environmental sample[Title] NOT environmental samples[Title] NOT environmental[Title] NOT uncultured[Title] NOT unclassified[Title] NOT unidentified[Title] NOT unverified[Title]'\
  --p-n-jobs 5 \
  --o-sequences ncbi-refseqs-unfiltered_viridiplant.qza \
  --o-taxonomy ncbi-refseqs-taxonomy-unfiltered_viridiplant.qza

	(the qiime rescript get-ncbi-data command have to be done between 9pm and 5am (US time))

qiime metadata tabulate \
  --m-input-file ncbi-refseqs-taxonomy-unfiltered_viridiplant.qza \
  --o-visualization ncbi-refseqs-taxonomy-unfiltered_viridiplant.qzv

qiime metadata tabulate \
  --m-input-file ncbi-refseqs-unfiltered_viridiplant.qza \
  --o-visualization ncbi-refseqs-unfiltered_viridiplant.qzv


In my case study, I had to retrieve only the NCBI resources for my plant list 
(I used Excel to create my file called taxonomy_toronto_plants.txt from the taxonomy of viridiplants, keeping only the species of my list, I left the file containing the reference sequences as is)


2. Download of NCBI resources for fungi species: (I used a bioproject that gathers the ITS reference sequences for fungi). 

qiime rescript get-ncbi-data \
  --p-query '177353[BioProject]'\
  --p-n-jobs 5 \
  --o-sequences ncbi-refseqs-unfiltered_fungi.qza \
  --o-taxonomy ncbi-refseqs-taxonomy-unfiltered_fungi.qza

	(the qiime rescript get-ncbi-data command have to be done between 9pm and 5am (US time) to make sure you don't have problems running the command until you get results)

qiime metadata tabulate \
  --m-input-file ncbi-refseqs-taxonomy-unfiltered_fungi.qza \
  --o-visualization ncbi-refseqs-taxonomy-unfiltered_fungi.qzv

qiime metadata tabulate \
  --m-input-file ncbi-refseqs-unfiltered_fungi.qza \
  --o-visualization ncbi-refseqs-unfiltered_fungi.qzv


3.Creation of the custom database for taxonomic classification: 

Importation of the data and Taxonomy assignment: (here I used my own plant taxonomy but if you want to use the whole Viridiplant database, use : ncbi-refseqs-taxonomy-unfiltered_viridiplant.qza)
qiime tools import \
  --type 'FeatureData[Taxonomy]' \
  --input-format HeaderlessTSVTaxonomyFormat \
  --input-path taxonomy_toronto_plants.txt \
  --output-path taxonomy_toronto_plants.qza

Merging of taxo and ref-seqs of Toronto plants and fungi:
qiime feature-table merge-taxa \
  --i-data taxonomy_toronto_plants.qza \
  --i-data ncbi-refseqs-taxonomy-unfiltered_fungi.qza \
  --o-merged-data taxonomy_toronto_plants_fungi.qza

qiime feature-table merge-seqs \
  --i-data ncbi-refseqs-unfiltered_viridiplant.qza \
  --i-data ncbi-refseqs-unfiltered_fungi.qza \
  --o-merged-data ref-seqs_toronto_plants_fungi.qza

4. Taxonomy classification (here I used Naive bayes classifier):

qiime feature-classifier fit-classifier-naive-bayes \
  --i-reference-reads ref-seqs_toronto_plants_fungi.qza \
  --i-reference-taxonomy taxonomy_toronto_plants_fungi.qza \
  --o-classifier classifier_plant_and_fungi.qza

qiime feature-classifier classify-sklearn \
  --i-classifier classifier_plant_and_fungi.qza \
  --i-reads rep-seqs-dada2.qza \
  --o-classification R_taxonomy_plants_toronto_fungi_NCBI.qza

qiime metadata tabulate \
  --m-input-file R_taxonomy_plants_toronto_fungi_NCBI.qza \
  --o-visualization R_taxonomy_plants_toronto_fungi_NCBI.qzv