Apple_1   1      300
Apple_2   1      500
Apple_2   500    1500
Apple_2   1500   2450
Apple_3   1      1250
Apple_3   1250   2000

Apple_1   1      300     1
Apple_2   1      500     1
Apple_2   500    1500    2
Apple_2   1500   2450    3
Apple_3   1      1250    1
Apple_3   1250   2000    2

awk '{ print $0 "t" ++count[$1] }'

Apple_1   1      300
Apple_2   1      500
Apple_1   500    1500

Apple_1   1      300     1
Apple_2   1      500     1
Apple_1   500    1500    2

awk '{ if (word == $1) { counter++ } else { counter = 1; word = $1 }; print $0 "t" counter }'

cut -f1 file.txt | sort | uniq -c

cut -f1 file.txt | uniq -c

cut -f1 file.txt | uniq -c | join -2 2 file.txt -

Apple_1 1 300 1
Apple_2 1 500 3
Apple_2 500 1500 3
Apple_2 1500 2450 3
Apple_3 1 1250 2
Apple_3 1250 2000 2

col1 col2 col3 identifier
Apple_1 1 300 000001
Apple_2 1 500 000002
Apple_2 500 1500 000002
Apple_2 1500 2450 000002
Apple_3 1 1250 000003
Apple_3 1250 2000 000003