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The Serpent Sea (The Books of the Raksura) (original 2012; edition 2012)
by Martha Wells
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Moon, once a solitary wanderer, has become consort to Jade, sister queen of the Indigo Cloud court. Together, they travel with their people on a pair of flying ships in hopes of finding a new home for their colony. Moon finally feels like he's found a tribe where he belongs. But when the travelers reach the ancestral home of Indigo Cloud, shrouded within the trunk of a mountain-sized tree, they discover a blight infecting its core.
(summary from another edition)