a ship carrying the flag officer or the commander of a fleet, squadron, or the like, and displaying the officer's flag.
the main vessel of a shipping line.
any of the best or largest ships or airplanes operated by a passenger line.
the best or most important one of a group or system: This store is the flagship of our retail chain.
being or constituting a flagship.

1665–75; flag1 + ship

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World English Dictionary
flagship (ˈflæɡˌʃɪp)
1.  a ship, esp in a fleet, aboard which the commander of the fleet is quartered
2.  the most important ship belonging to a shipping company
3.  a single item from a related group considered as the most important, often in establishing a public image: the nine o'clock news is the flagship of the BBC

Collins English Dictionary - Complete & Unabridged 10th Edition
2009 © William Collins Sons & Co. Ltd. 1979, 1986 © HarperCollins
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Word Origin & History

1670s, ship bearing an admiral's flag, from flag (n.) + ship (n.).
Online Etymology Dictionary, © 2010 Douglas Harper
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Example sentences
Gotham's flagship orchestra is keeping busy in the city's increasingly active
  preseason schedule.
Flagship missions at risk as astrophysics funding shrinks.
The polar bear has become the flagship species in the climate-change discussion.
It will always be synonymous with the flagship operation of its heyday, the
  dreaded prefrontal lobotomy.
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