Chloroplast DNA in Molecular Systematics

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Chloroplast DNA in Molecular Systematics
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Chloroplast

• organelle found in plant cells and eukaryotic
  algae
• Photosynthesis

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Chloroplast genome

• Chloroplast DNA (cpDNA) is also known as plastid
  DNA (ptDNA).
• Circular double stranded DNA molecule
• Chloroplast genome size ranges 120-217kb with
  majority of plants fall into 120-160kb.
  (Pelargonium has a chloroplast genome size 217kb)
• contain about 100 genes to synthesize proteins
• cpDNA regions includes Large Single-Copy (LSC)
  Small Single-Copy (SSC) regions, and Inverted
  Repeats (IRA IRB).
• Conifers and a group of legumes lack Inverted
  Repeats.

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LSC
SSC
IRA
IRB
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Chloroplast genome

• Complete chloroplast DNA sequences of four land
  plants (Nicotiana tabacum, Marchantia polymorpha,
  Oryza sativa and Epifagus virginiana) were
  available for comparative study on structure and
  gene content of chloroplast genomes in 1980s.
• At present, the number of complete chloroplast
  genome sequences is 122 (from 114 different
  organisms).
• eg. Arabidopsis thaliana, Coffea arabica,
  Eucalyptus globulus, Glycine max, Gossypium
  hirsutum, Helianthus annuus, Lycopersicon
  esculentum, Nymphaea alba, Phaseolus vulgaris,
  Pinus koraiensis, Piper cenocladum, Solanum
  tuberosum, Triticum aestivum, Vitis vinifera, Zea
  mays etc.

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Characteristics of Chloroplast Genome

• cpDNA is a relatively abundant component of plant
  total DNA, thus facilitating extraction and
  analysis.
• Conservative rate of nucleotide substitution
  enables to resolve plant phylogenetic
  relationships at deep levels of evolution.
• eg. familial level mono- dicotyledonous
• Chloroplast protein-coding genes evolve at a rate
  that is on average fivefold slower than plant
  nuclear genes.

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Characteristics of Chloroplast Genome

• Strictly maternally inherited in most angiosperms
  while in conifers, inheritance is paternal.
• Chloroplast DNA is passed on from one generation
  to the next with only an occasional mutation
  altering the molecule sexual recombination does
  not occur.

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Molecular Systematics on cpDNA

• cpDNA regions can be amplified by means of PCR.
• The resulted PCR products may be subjected to
  RFLP or DNA sequencing.
• Common cpDNA regions used in systematic study
• rbcL (1400bp), trnL-trnF (250-800bp), atpB-rbcL
  (1000bp), trnL intron (300bp), matK (2600bp),
  trnT-trnL (400-800bp), 16S (1400bp), rpoC
  (3600bp) etc.

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LSC
atpB-rbcL
rbcL
rpoC
trnT-trnL
trnL intron
trnL-trnF
matK
SSC
IRA
IRB
16S
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Molecular Systematics on cpDNA

• Restriction site mapping of the entire
  chloroplast genome. (involve the isolation of
  chloroplast DNA from the total DNA)

The whole chloroplast genomes of different
Brassica species were digested with SacI
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Molecular Systematics on cpDNA

• Singular structural rearrangements (e.g.
  inversions and intron losses).
• Loss of intron of rpl2 gene was found in species
  of order Caryophyllales (cacti, amaranths,
  carnations, carnivorous plants).

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Molecular Systematics on cpDNA

• On of the most comprehensive phylogenetic study
  of cpDNA rearrangement involved a 22kb inversion
  found to be shared by 57 genera representing all
  tribes of the family Asteraceae (sunflowers), a
  large plant family with 20,000 species and 1100
  genera.
• 50kb inversion brought psbA closer to rbcL in
  legumes.
• 25kb inversion brought atpA closer to rbcL in
  wheat.

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Subsection Sphaerocarpae
Dryobalanoides
H. subalata
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H. nervosa
Dryobalanoides clade
H. dyeri
H. dryobalanoides
H. pubescens
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92
Tree length 143 CI 0.8811 RI 0.8651
H. mengerawan
H. pierrei
Subsection Dryobalanoides
H. latifolia
75
H. beccariana
72
H. myrtifolia
100
H. ferruginea
72-bp deletion in the trnL-trnF
H. sangal
89
Subsection Hopea
H. nutans
Hopea
H. odorata
69
H. helferi
Subsection Pierrea
H. apiculata
84
Hopea clade
H. bilitonensis
H. wightiana
Neobalanocarpus heimii
Outgroup
Upuna borneensis
Phylogeny based on the trnL-trnF, trnT-trnL and
atpB-rbcL sequences.