Download Nuclear DNA in Molecular systematics Nuclear DNA is double

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
Subsection
Sphaerocarpae
H. dyeri
86
H. pubescens
94
64
62
H. beccariana
H. pierrei
H. mengerawan
H. dryobalanoides
70
Dryobalanoides
clade
100
Hopea clade
H. sangal
H. odorata
100
52
100
H. myrtifolia
H. ferruginea
98
18-bp
deletion
in the
PgiC
Subsection
Dryobalanoides
D
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y
o
b
a
l
a
n
o
i
d
e
s
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