Company Y succeeded/superseded/supplanted Company X.
From oxforddictionaries.com:
succeed
VERB
2.2 Come after and take the place of: her embarrassment was succeeded by fear
Synonyms: follow, come after, follow after;
take the place of, replace; subsequent, successive,
following, ensuing, later, future, next, coming
supersede
VERB [WITH OBJECT]
Take the place of (a person or thing previously in authority or use); supplant: the older models of car have now been
superseded
Synonyms: replace, supplant, take the place of, take over from,
substitute for, displace, oust, overthrow, remove, unseat, override;
succeed, come after, step into the shoes of
informal crowd out, fill someone's boots
supplant
VERB [WITH OBJECT]
Supersede and replace: domestic production has been supplanted by
imports and jobs have been lost
Synonyms: replace, displace, supersede, take the place of, take over
from, substitute for, undermine, override; oust, usurp, overthrow,
remove, topple, unseat, depose, dethrone, eject, dispel; succeed, come
after, step into the shoes of
Company Y is called the successor (company).
From smallbusiness.chron.com:
Entrepreneurs create business ideas that can be transformed into a
small business. Sometimes the business will not succeed because of
factors that may include financing or marketing. In these situations,
successor companies can arise from the previous company after liquidation. They are also referred to as "Phoenix" companies because
they rise out of the ashes of the previous company.