The Thirteenth that fought at Pharsalus (like most of Caesar's foot soldiers) was largely recruited in Cisalpine/Italian Gaul, that is, the part of modern Italy just south of the Alps which was then considered part of Gaul. This was Caesar's province of which he was the lawful (at least originally) governor, and Pompey would not have had any reason or authority to recruit troops there.

So the ordinary rank and file, made up of men of largely Gallic blood who weren't even Roman citizens (Caesar granted Italian Gaul the Roman citizenship in 49 BC, a year after he crossed the Rubicon), would probably not have been actually related by blood to anybody fighting on the other side except in unusual circumstances. In fact, it's unlikely they'd even have met them; at this period of Roman history there wasn't much in the way of troop transfers between generals.An exception to this, though, is that Pompey loaned Caesar his sixth legion (previously stationed in Spain), which served under Caesar for possibly several years during his conquest of Gaul. Pompey outmaneuvered Caesar's surrogates in Rome and got the legion back during the political crisis of 50 BC, whereupon it returned to Spain. It was part of the defeated army at the Battle of Ilerda, but some of its soldiers (and those of other legions loyal to Pompey) escaped the surrender that followed the battle, and made it to Greece. So your trooper of the thirteenth, getting ready to fight at Ilerda, might well have known he was going to be fighting some of those guys from Pompey's sixth, whom he might have met or served with during the Gallic campaign. But it's less likely they'd have been aware that some fugitives from the sixth were going to be across the field at Pharsalus, specifically.

For what it's worth, A plurality of the sixth actually survived Pharsalus, and switched sides back to Caesar. The Legion as an institution saw important combat through the rest of the war and beyond.