I think O'Reilly was the last commercial publisher with a troff toolchain.  Nowadays they accept HTMLBook (their own static subset of HTML5), DocBook, ASCIIDoc (analogous to Markdown but plain-text DocBook as opposed to plain-text HTML), Word, and in some cases InDesign or PDF.

John Cowan          http://vrici.lojban.org/~cowan        cowan@ccil.org
And through this revolting graveyard of the universe the muffled,
maddening beating of drums, and thin, monotonous whine of blasphemous
flutes from inconceivable, unlighted chambers beyond Time; the
detestable pounding and piping whereunto dance slowly, awkwardly, and
absurdly the gigantic tenebrous ultimate gods --the blind, voiceless,
mindless gargoyles whose soul is Nyarlathotep. (Lovecraft)