During the Caesarian Civil War, Pompey raised legions in the east. Leaving aside auxiliary forces, only Roman citizens could fight in the legions. From where and whom would these legions have been raised?
I remember in the Mithridatic uprising thousands of Roman citizens / colonists were slaughtered. Would the legions have been raised from such people; Roman citizens living in the East?
As far as we know, the legions raised by Pompey (rather by other men associated with the cause) were Roman citizens, precisely in the way you describe: Romans living in Syria, in the Levant, and elsewhere. Many of these were formerly "Italians," Roman citizens since 90-89 BCE, but by the early 40s BCE this distinction no longer mattered.
Lentulus Crus, technically a consul, had raised two legions in Asia. We know these were Romans because we know that Romans of Jewish descent were exempted in this conscription effort thanks to his decree, preserved by Josephus (Josephus, Antiquitates Judaicae, 14.228ff). Metellus Scipio was to bring two additional legions from Syria, and Pompey's own son went to Egypt to round up what he could find. These legions might have, and probably were, under-strength, but they formed the citizen core of Pompey's army. By the time of Pharsalus, we hear of legions from Cilicia on the right wing, supported by auxiliary infantry from Spain. We know he also sought and obtained massive numbers of auxiliaries from the various remaining client kingdoms in the East, and he even sent overtures to Parthia asking for support (Dio 42.2.5). Cicero was certainly disgusted by the notion of Pompey's not-so-citizen legions bearing down on Italia: " I—whom some called the preserver of this city, some its parent—I to bring against it armies of the Getae, Armenians, and Colchians! I to inflict famine on my fellow citizens, devastation upon Italy!" (Cic. ad Att. 9.10)