This question has been already asked here,

Fetching Genbank Entries For List Of Accession Numbers.

You will find several biopython scripts inside.

When you have your genomes, make a database out of them with makeblastdb.

makeblastdb -in input_file (nucleotide file-name) -dbtype nucl (if nucleotide) -out dbname (the database

name)

Use input file in *.fa-format.

2) Run the blast-program:

blastn -query input (with the gene file) -db (database name, which was created in step 1) -out outname (file name with the results)

So use blastn for this search in the nucleotide database.