Plant Molecular SYstematics

• Plant Molecular Systematics


  The study of plant evolution and relationships using molecular data
• How are Plant Molecular Data Acquired?

  1. Plant collected

  2. Live samples e.g, allozymes analysis

  3. Dried or liquid-preserved samples, e.g., DNA analysis
• DNA sequence data


  The sequence of nucleotides in a particular region of the DNA of a given taxon
• PCR: Polymerase Chain Reaction

  1. DNA isolated, purified, heated to denature

  2. Primer used: Primer = short, conserved DNA region Complementary to ends of DNA to be amplified

  3. Taq polymerase, nucleotides, buffer/salts
• DNA Sequencing


  1. Small amount of Dideoxynucleotides used (along with higher concentration of nucleotides)

  2. Dideoxynucleotides, once joined to new DNA strand, terminate polymerase reaction

  3. Dideoxynucleotides identified by fluorescence pattern

  4. Length of DNA strands determined by electrophoresis
• Types of DNA sequence Data

  • Nuclear DNA (nDNA)
  • Chloroplasts DNA (cpDNA)
  • Mitochondrial DNA (mtDNA)
• Chloroplast DNA


  • Large single-copy region
  • Small single-copy region
  • Inverted repeats
• Nuclear DNA: ITS/ETS Sequence Data

  Used in lower-level analyses
• DNA alignment


  The process in which homologous nucleotide positions are arranged in corresponding columns
• Weighting of DNA sequence data

  • Transition: PY <—> PY or PU <—> PU
  • Transversion : PY <—> PU or PU <—> PY
• Restriction site


  A sequence of approximately 6-8 base pairs of DNA that binds to a given restriction enzyme
• RFLP: Restriction Fragment Length Polymorphism


  Refers to differences between taxa in restriction sites, and therefore the lengths of fragments of DNA following cleavage with restriction enzymes
• RFLP: Restriction Fragment Length Polymorphism

  • EcoR1 restriction enzyme
  • BamH1 restriction enzyme
• Allozyme


  Different molecular forms of an enzymes that correspond to different alleles of a common gene (locus)
• Allozyme


  • Used in the past frequently, rarely today
  • More difficult to code for phylogenetic study
• Allozyme


  Subjected to electrophoresis, identified with a stain specific to that enzyme and the bands marked by their relative position on the electrophoresis media
• Microsattellites


  Regions of DNA that contain short (usually 2-5) repeats of nucleotides, an example being TGTGTG, in which two base pairs repeat
• RAPDs: Random Amplified Polymorphic DNA


  Using randomly generated primers for the amplification of DNA to identify polymorphic DNA regions of different individuals or taxa
• RAPDs: Random Amplified Polymorphic DNA


  • Results are difficult to replicate (being very sensitive to PCR conditions)
  • Homology of similar bands in different taxa may be unclear
• Amplified Fragment Length Polymorphism (AFLPs)

  • A restriction enzyme is used to cut DNA into numerous, smaller pieces, each of which terminates in a characteristic nucleotide sequence
  • The numerous, cut DNA fragments are then modified by binding to each end (using DNA ligase) a synthesized, double- stranded pieces of DNA, known as a Primer adapter
• Amplified Fragment Length Polymorphism (AFLPs)


  Primers are constructed that bind to the primer adapters and amplify the DNA fragments using a polymerase chain reaction