Nuclear DNA in Molecular systematics

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Nuclear DNA in Molecular systematics
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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.

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Nuclear DNA

• Recombination occurs between homologous
  chromosomes.
• Biparentally inherited.
• Mutational rate is high.

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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.

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Nuclear Ribosomal DNA
A typical plant rDNA repeat unit shown to scale.
EST external transcribed region ITS internal
transcribed region.
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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.

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Nuclear DNA in Plant Systematics

• Other nuclear DNA regions used in plant
  systematics are genes AdhC, PgiC, malate
  synthase, phosphoribulokinase etc. low-copy
  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.

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Dryobalanoides
Subsection Sphaerocarpae
H. subalata
Tree length 277 CI 0.9206 RI 0.9415
100
H. nervosa
100
H. dyeri
86
H. pubescens
94
H. beccariana
64
62
H. pierrei
Subsection Dryobalanoides
H. mengerawan
H. dryobalanoides
70
H. myrtifolia
100
Dryobalanoides clade
H. ferruginea
H. sangal
98
Subsection Hopea
Hopea clade
H. odorata
Hopea
H. apiculata
100
18-bp deletion in the PgiC
H. bilitonensis
52
Subsection Pierrea
H. helferi
100
H. nutans
H. wightiana
Neobalanocarpus heimii
Outgroup
Upuna borneensis
Phylogeny based on the PgiC sequences.