pdfunite $(sed 's/$/_*.pdf/' filenames.txt) output.pdf
Então, se filenames.txt
contiver
CSAI_isotig00407:342-556
CSAI_isotig00408:342-556
Esse comando fará efetivamente
pdfunite CSAI_isotig00407:342-556_*.pdf CSAI_isotig00408:342-556_*.pdf output.pdf