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Nuclear DNA in Molecular

systematics

Nuclear DNA
- Nuclear DNA is double stranded DNA located in
chromosomes / nucleus of a cell.
- 6-30 billion bp per haploid genome in gymnosperm,
250 million to 15 billion bp per haploid genome in
angiosperm, 3 billion bp per haploid genome in
human.
- The difference in genome size is mainly due to the
amount of repetitive DNA. Repetitive DNA is
distributed throughout the genome.
- For example, pine (Pinus stobus) genome contains
75% repetitive DNA and 25% low number single copy
DNA. Only 0.1% of the genome is expressed as
mRNA.

Nuclear DNA
- Recombination occurs between homologous
chromosomes.
- Biparentally inherited.
- Mutational rate is high.

Molecular Systematics
- Nuclear DNA regions commonly used for
plant/animal systematics study is nuclear
ribosomal DNA (nrDNA) including 18S,
28S, ITS and 5S.
- nrDNA occurs in high number of copy in
the genome, and it experiences concerted
evolution.

Nuclear Ribosomal DNA

A typical plant rDNA repeat unit shown to scale. EST =


external transcribed region; ITS = internal transcribed
region.

Molecular Systematics
- nrDNA sometimes is claimed to be
problematic in some plant families.
- Copies of the ITS regions may display a
high degree of polymorphism within plant
genomes, and relationships among
paralogues can be difficult to interpret at
species level.

Nuclear DNA in Plant Systematics


- Other nuclear DNA regions used in plant
systematics are genes AdhC, PgiC, malate
synthase, phosphoribulokinase etc. [lowcopy nuclear genes]
- These low-copy nuclear gene sequences
are found to be informative and provide
robust resolved phylogeny.
- e.g. in Gossypium, the base substitution of
AdhC sequences are three- to sixfold
higher than that of cpDNA.

Tree length = 277


CI = 0.9206
RI = 0.9415
100

H. subalata

100

H. nervosa
H. dyeri

86

H. pubescens
94

64
62

H. beccariana
H. pierrei
H. mengerawan

Subsection
Dryobalanoides

H. dryobalanoides

70

Dryobalanoides
clade

100

Hopea clade
52

D
r
y
o
b
a
l
a
n
o
i
d
e
s

H. sangal
H. odorata

100

100

H. myrtifolia
H. ferruginea

98

18-bp
deletion
in the
PgiC

Subsection
Sphaerocarpae

Subsection
Hopea

H. apiculata
H. bilitonensis
H. helferi
H. nutans

Subsection
Pierrea

H
o
p
e
a

H. wightiana
Neobalanocarpus heimii
Upuna borneensis

Phylogeny based on the PgiC sequences.

Outgroup