In Python, the solution may look like this:

import re
import sys

d = {}

fh = open(sys.argv[1])
for line in fh:
    species = line.split('=')[0]
    genes = re.findall('=\(([^\)]+)', line)[0].split(',')
    d[species] = genes
fh.close()

fh = open(sys.argv[2])
tree = fh.read()
for species in d:
    for gene in d[species]:
        tree = tree.replace(gene, species)

oh = open(sys.argv[2]+'.out', 'w')
oh.write(tree)
oh.close()

Assuming you have saved this code as gene2species.py and the newick tree is in the tree.newick file and the list of genes and species is in the genes.txt file, run the script as follows:

python gene2species.py genes.txt tree.newick

The translated newick tree will be saved in tree.newick.out:

((speciesA:1,speciesB:1)100:1,speciesC:1)100;
((speciesA:1,speciesB:1)100:1,speciesC:1)100;