Week 5 Genetic Marker PDF

SB 33403 Molecular Biology in Conserva5on Lecturer: Dr. Si5 Fa5mah Md Isa (SFMI) Gene$c Markers v Revision on cell molecu...

SB 33403 Molecular Biology in Conserva5on Lecturer: Dr. Si5 Fa5mah Md Isa (SFMI) Gene$c Markers v Revision on cell molecular biology § Terminologies - Func5onal gene, coding DNA and non-coding DNA - Nuclear marker or organelle marker - Prokaryotes and Eukaryotes - Ribosomes, mictochondrial, chloroplast - DNA,rRna, RNA, protein - Large subunit, small subunit - ITS, 16s, rbcL, nrDNA, mtDNA, cpDNA  SB 33403 Molecular Biology in Conserva5on Lecturer: Dr. Si5 Fa5mah Md Isa (SFMI) Gene$c Markers cont. All cells: - store their hereditary informa5on in DNA - Replicate their DNA - Transcribe por5on of their DNA into RNA - Translate RNA into protein - Use proteins as catalysts - The fragments of DNA corresponding to one protein is one gene  SB 33403 Molecular Biology in Conserva5on Lecturer: Dr. Si5 Fa5mah Md Isa (SFMI) Gene$c Markers cont. Muta5on – altera5on in the nucleo5de sequence of the genome of an organisms due to mistakes when the DNA is copied or environmental factors (subs5tu5ons, dele5ons and inser5ons) Gene5c Varia5on – differences in DNA. Varia5on between individuals in their DNA is what makes them different. Non-coding DNA – doesn’t provide instruc5ons for making proteins - satellite DNA, telomeres, introns Coding DNA – contains informa5on for making proteins. Exons  SB 33403 Molecular Biology in Conserva5on Lecturer: Dr. Si5 Fa5mah Md Isa (SFMI) Gene$c Markers cont. v Gene5c markers à a gene or short sequence of DNA to locate other genes in a genome v PCR primers - Nuclear DNA (nrDNA) - Mitochondria DNA (mtDNA) - Chloroplast DNA (cpDNA) v Which marker is beXer? Mode of inheritance - mtDNA à uniparental and effec5vely haploid - cpDNA à uniparental and effec5vely haploid - nrDNA à recombina5on and diploid v Research ques5ons Popula5on-level Species-level Higher-level systema5c  SB 33403 Molecular Biology in Conserva5on Lecturer: Dr. Si5 Fa5mah Md Isa (SFMI) Gene$c Markers cont. v What is the difference between nrDNA and mtDNA? - mtDNA is encoded for generic informa5on required by mitochondria - nrDNA is encoded for the gene5c informa5on required by the en5re cell  SB 33403 Molecular Biology in Conserva5on Lecturer: Dr. Si5 Fa5mah Md Isa (SFMI) Gene$c Markers cont. trnL-F (intron v cpDNA gene - Plants and intergenic trnL (intron spacer gene) rbcL gene matK gene gene) (UAA) (GAA) Types of gene Plas5dial gene Plas5dial gene Transfer RNA gene Transfer RNA gene Func$on of Encodes the large Protein that splices Provides informa5on Provides informa5on gene subunit of ribulose Group II introns (in vivo on structures, on structures, bisphophate splicing) func5ons, and func5ons, and carboxylare (Rubisco) evolu5on in different evolu5on in different orders of flowering orders of flowering plants, in basal plants, in basal angiosperms, in land angiosperms, in land plants and in plants and in bryophytes bryophytes Applica$on in Can be contrasted with Universal matK Most widely used Widely used as phylogeney the rbcL genes of other primers can be used chloroplast markers for gene5c marker for plants in order to for DNA barcoding of phylogene5c analysis in phylogene5c analysis determine gene5c angiosperms plants of plants. similari5es and differences Provides a useful backbone to the barcode dataset  SB 33403 Molecular Biology in Conserva5on Lecturer: Dr. Si5 Fa5mah Md Isa (SFMI) Gene$c Markers cont. v Among the 4 genes men5oned, which genes are commonly / rarely used in the study of phylogene5c? Why? Types of genes rbcL gene matK gene trnL gene trnL-F gene The usage in Rare Rare Common Common phylogene5c analysis Explana5on Resolving Able to resolve Able to resolve Able to resolve phylogene5c phylogene5c phylogene5c phylogene5c rela5onships below reconstruc5on at rela5onship at rela5onship at the family level is subfamily and generic level generic level o]en poor since its family levels trnL intron evolves The non-coding rate of evolu5on is Rate of evolu5on at a rate that is the regions evolve slow higher than rbcL same as that of the faster (more than gene intergenic spacer three 5mes faster, on everage) than rbcL *Most cpDNA coding regions do not evolve rapidly enough to resolve rela5onships at these lower taxonomic levels  SB 33403 Molecular Biology in Conserva5on Lecturer: Dr. Si5 Fa5mah Md Isa (SFMI) Gene$c Markers cont. v Ques5ons 1. Which gene is protein coding gene and non-coding gene? 2. Differences between nrDNA, mtDNA, cpDNA 3. Give examples of marker / primer for nrDNA, mtDNA, cpDNA.