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BIOL V04 Lecture - Genomes & Their Evolution (Ch 21)
© copyright 2015 Marta D. de Jesus
I. How are genomes sequenced?
A. older method: 3-step process
B. Whole genome shotgun approach (pioneered by J. Craig Venter)
C. metagenome?
II. How is this information collected and accessed? Bioinformatics
A. databases
1. started with
2. GenBank
a. genomics
b. NCBI
http://researchguides.library.wisc.edu/bioinformatics_help
3. other databases as well
eg: proteomics
4. not all sequence information
B. programs & online tools
C. systems biology
D. genes, proteins & genomes can be compared
1. to help find
2. to help find
3. to help determine
a. when examining distant species
b. when examining close species
eg: FOXP2
4. compare between members of a species
a. single nucleotide polymorphisms
http://learn.genetics.utah.edu/content/pharma/snips/
b. copy number of genes (CNVs)
http://www.nature.com/scitable/topicpage/Copy-Number-Variation-445
http://www.nature.com/scitable/topicpage/Copy-Number-Variation-and-Genetic-Disease-911
III. Genome comparison
A. vary by total size
1. prokaryotes
viruses
2. eukaryotes
B. vary by # of genes
1. prokaryotes
2. eukaryotes
3. mismatch
4. helping to account for size mismatch
5. alternative splicing of RNAs
http://www.nature.com/scitable/topicpage/eukaryotic-genome-complexity-437
IV. Eukaryotic non-protein coding DNA
A. exons
B. repetitive DNA
1. transposable elements & related sequences
2. transposon vs. retrotransposon
eg: Alu elements
http://www.nature.com/scitable/topicpage/functions-and-utility-of-alu-jumping-genes-561
3. transposons can carry
4. Barbara McClintock
http://www.nature.com/scitable/topicpage/barbara-mcclintock-and-the-discovery-of-jumping-34083
5. transposable elements can
a. promote
b. change
c. modify
d. change
6. retrotransposons include ERVs
7. other repetitive DNA
a. large-segment duplication
b. simple sequence
http://www.vivo.colostate.edu/hbooks/genetics/medgen/dnatesting/satellites.html
1) satellites
2) minisatellites
3) microsatellites
= simple sequence repeats
= short tandem repeats
= variable number tandem repeats
C. other non-coding DNA
1. introns & regulatory sequences
2. unique non-coding DNA
V. Genes
A. most are
B. multigene families
pseudogenes
C. contributing to genome evolution
1. mutation
2. duplications
a. vertebrates
b. differences in chromosome structure
c. differences in gene copy number
3. once multiple copies exist
a. can be fine-tuned
b. can be modified
c. can become pseudogenes
4. exon shuffling
D. comparing genomes in development (Evo-Devo)
1. homeotic genes
2. in metazoans: one set are the Hox genes
eg: antennapedia complex
contain a homeobox
codes for a homeodomain
unusual arrangement
http://www.nature.com/scitable/topicpage/hox-genes-in-development-the-hox-code-41402
d. other model animals
for vertebrates
for mammals
3. in plants, there also are homeotic genes (Ch 35)
a. Hox-like: KNOTTED-1
b. closest analog: Mads-box family of genes
eg: flower organ identity
NCBI organization - simplified
(from: http://researchguides.library.wisc.edu/bioinformatics_help)
NCBI’s actual 04/15 sitemap on next page