ch14- Plant Molecular Systematics

Plant Molecular Systematics Notes

Types of Molecular Data

  • DNA sequences

  • DNA restriction sites: RFLPs

  • Allozymes: different forms of proteins

  • Microsatellites: DNA regions with tandem repeats

  • RAPDs: Random Amplification of Polymorphic DNA

  • AFLPs: Amplified Fragment Length Polymorphism

Acquisition of Plant Molecular Data

  • Collect plant samples and prepare vouchers

  • Use live samples, e.g., allozyme analysis

  • Use dried or liquid-preserved samples for DNA analysis

DNA Sequence Data

  • Components:

    • Adenine (A), Guanine (G), Cytosine (C), Thymine (T)

    • Purines: A, G

    • Pyrimidines: C, T

PCR: Polymerase Chain Reaction

  • Definition: Amplifies DNA to produce thousands of copies

  • Process:

    • Isolate and purify DNA, heat to denature

    • Use primers: short, conserved DNA regions

    • Include Taq polymerase and nucleotides

DNA Sequencing

  • Method: Similar to PCR but uses dideoxynucleotides which terminate synthesis.

  • Output: Length of DNA strands determined by electrophoresis

DNA Sequence Types

  • Chloroplast DNA (cpDNA)

  • Nuclear DNA (nDNA)

  • Mitochondrial DNA (mtDNA): less used in plants, more in animals

Chloroplast Coding Genes

  • atpB: ATP synthesis

  • rbcL: Photosynthesis (RUBISCO)

  • matK: Splicing type II introns

  • ndhF: NADH dehydrogenase

Internal Transcribed Spacers (ITS)

  • ITS Region: Involves nrDNA, used in phylogenetic studies

  • ETS Region: External transcribed spacer for additional data

DNA Alignment

  • Compare nucleotide sequences across taxa for variability

  • Character coding for differences

Models of Molecular Evolution

  • Different base substitution models affecting phylogenetic analysis

Restriction Fragment Length Polymorphism (RFLP)

  • Definition: Variation in the length of DNA fragments after digestion with restriction enzymes

  • E.g., using EcoRI enzyme

Allozymes

  • Definition: Variants of enzymes

  • Historically used but rarely today due to complexity in coding for phylogenetic studies

Next Generation Sequencing (NGS)

  • Description: High Throughput Sequencing allows massive data generation

  • Advantages: More data, lower costs per base, can sequence transcriptomes

  • Disadvantages: Requires advanced computing power for data assembly

Microsatellites and RAPDs

  • Microsatellites: Tandem repeats indicating genetic differences

  • RAPDs: Variability due to randomly generated primers leading to different lengths in amplicons

AFLP Technique

  • Steps: DNA cleavage by restriction enzymes, amplification via PCR with primers and adapters.