British Yoruba author Tade Thompson has won the Arthur C Clarke award, the UK’s most prestigious prize for science fiction novels, for Rosewater, his alien invasion novel set in a future Africa.

Opening in 2066, in the aftermath of an alien invasion that has left much of humanity powerless through airborne microscopic fungal spores, Rosewater is the name of a new town that forms on the outskirts of an alien biodome dropped in rural Nigeria. The dome opens just once a year, heals all nearby sick people, gives new life to the dead and begins to influence people in unusual ways. The alien presence has also awakened telepathic skills among select humans, dubbed “sensitives”, and the novel follows one, Kaaro, who investigates when other sensitives begin to die.

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In his review for the Guardian, sci-fi author Adam Roberts described Rosewater as “brilliant science fiction, at the cutting edge of contemporary genre … Thompson expertly juggles all his disparate elements – alien encounter, cyberpunk-biopunk-Afropunk thriller, zombie-shocker, an off-kilter love story and an atmospheric portrait of a futuristic Nigeria.”

Chair of the prize judges Andrew M Butler said: “Alien invasion is always a political subject, and Tade Thompson … expertly explores the nature of the alien, global power structures and pervasive technologies with a winning combination of science fictional invention, gritty plotting and sly wit.”

Butler said the judging process was “an incredibly close but good-natured argument”.

Thompson, who works as a psychiatrist in the south of England, saw off competition from 124 other novels, the highest number ever submitted for the prize. However, in May, prize organiser Tom Hunter pleaded for publishers to submit and publish more sci-fi by writers from diverse cultures and backgrounds after he found only 7% of novels sent in for the prize were by writers of colour.

Book awards, Hunter wrote, are “a mirror of the publishing industry, not its decision-makers and budget-holders, but maybe sometimes we can reflect back uncomfortable truths as well as hand out prizes.”

Rosewater was shortlisted alongside Iraqi novelist Ahmed Saadawi’s Frankenstein in Baghdad, which was nominated for the Man Booker International prize; debut US author Sue Burke’s Semiosis, a first contact novel; American author Yoon Ha Lee’s Revenant Gun, the concluding novel in his space opera series; Swedish artist Simon Stålenhag’s illustrated novel The Electric State; and British author Aliya Whiteley’s The Loosening Skin, set in a world where people shed their skin every seven years.

Thompson received a trophy and the £2,019 prize – the winnings are adjusted annually to match the year – at a ceremony on Wednesday night in Foyles bookshop in central London.