COURSE

STAB3343 MOLECULAR SYSTEMATICS

SEMESTER 2 2022/2023
SET 1

TITLE
LABORATORY REPORT ON PRACTICAL 1 – PCR-RFLP DATA SCORING

LECTURER
PROF. MADYA DR. CHOONG CHEE YEN

NAME
ADILAH AIMAN BINTI ZAFIR KHAN (A184381)
1.0 TITLE
PCR-RFLP Data Scoring

2.0 OBJECTIVES
To determine the phylogenetic relationships of seven dipterocarp taxa by using PCR-RFLP
data.

3.0 RESULTS & DISCUSSION

3.1 Score the PCR-RFLP data for each of the restriction enzymes. Presence of a
restriction site is scored as 1 and absence of a restriction site is scored as 0.
Character
Taxon
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15
Anisoptera 1 0 1 0 0 1 0 1 0 0 1 0 1 0 1
Vatica 1 0 1 0 0 1 0 1 0 0 1 0 1 0 1
Shorea 1 0 0 1 0 1 0 1 0 1 0 0 1 1 1
Hopea 1 1 1 0 0 1 0 1 0 1 0 0 1 0 1
Dipterocarpus 0 0 0 1 1 1 1 0 0 0 0 0 0 0 1
Dryobalanops 1 0 0 1 0 1 0 1 0 0 0 0 1 0 1
Upuna 1 0 0 1 0 0 0 1 1 0 0 1 0 0 0

Restriction enzyme Character Description

Character 1 2000 = 1000 + 1000
CfoI
Character 2 1000 = 550 + 450
Character 3 1000 = 650 + 350
DdeI
Character 4 1000 = 850 + 150
MboI Character 5 400 = 300 + 100
Character 6 2000 = 1350 + 650
AluI
Character 7 650 = 550 + 100
Character 8 2000 = 1500 + 500
HaeIII Character 9 1500 = 1000 + 500
Character 10 500 = 300 + 200
Character 11 1900 = 1000 + 900
EcoRI
Character 12 1900 = 1150 + 750
 Character 13 2000 = 1600 + 400
DraI
Character 14 1600 = 1400 + 200
HindIII Character 15 2000 = 1800 + 200

3.2 Present your scoring in the format of nexus as shown in Appendix B.

#nexus
begin data;
dimensions ntax=enter-the-number-of-taxa nchar=enter-the-
number-of-characters;
format symbols=”01”;
matrix
[PCR-RFLP data]
Anisoptera 101001010010101
Vatica 101001010010101
Shorea 100101010100111
Hopea 111001010100101
Dipterocarpus 000111100000001
Dryobanalops 100101010000101
Upuna 100100011001000
;
endblock;

3.3 Categorize the restriction enzymes into 4-base and 6 base cutters.
4-base cutters 6-base cutters
CfoI
MboI EcoRI
AluI DraI
HaeIII HindIII
DdeI

3.4 Give the DNA sequence recognized by each of the restriction enzymes.
RESTRICTION ENZYME DNA SEQUENCE
CfoI 5’ GCGC 3’
DdeI 5’ CTNAG 3’
MboI 5’ GATC 3’
HaeIII 5’ GGCC 3’
EcoRI 5’ GAATTC 3’
DraI 5’ TTTAAA 3’
 HindIII 5’ AAGCTT 3’

3.5 Determine the genetic distance between the dipterocarp taxa.

Number of characters showing different states
Formula of pairwise distance =
Total number of characters being compared
Number of characters showing different states
=
15
Anisoptera Vatica Shorea Hopea Dipterocarpus Dryobalanops Upuna

Anisoptera

0
Vatica = 0.000
15
5 5
Shorea = 0.333 = 0.333
15 15
Hopea 3 3 4
= 0.200 = 0.200 = 0.267
15 15 15
Dipterocarpus 8 8 7 9
= 0.533 = 0.533 = 0.467 = 0.600
15 15 15 15
Dryobalanops 3 3 2 4 5
= 0.200 = 0.200 = 0.133 = 0.267 = 0.333
15 15 15 15 15
8 8 7 9 8 5
Upuna = 0.533 = 0.533 = 0.467 = 0.600 = 0.533 = 0.333
15 15 15 15 15 15