1. It will help in preparing for the exam to read:
Chapter 19
p ,
Chapter 20 p

2. Comparative Genomics: The study of genome conservation
and variation among organisms
Chromosome number
Chromosome morphology
Gene number
Genome size
Gene order

3. Measures of Genome Size
C value : amount of DNA in the haploid
genome, generally measured in picograms
or in base pairs (Kb or Mb)

4. Range of C Values in Prokaryotes
Taxon Genome Size (Kb) Ratio
Bacteria ,
Mollicutes ,
Gram negatives ,
Gram positives , ,
Cyanobacteria , ,
Archaea , ,
~ 20 fold range in genome size

5. Gene Number and Genome Size in 12 Completely
Sequenced Bacterial Species
5000
4000
Gene
Number
3000
2000
1000
Genome Size (x 106 bp)

6. C value : So, what about eukaryotes?
In general, more DNA
Much greater variation in genome size
80,000 fold range across eukaryotes
Largest range observed among
unicellular protists (20,000 fold)
3,000 fold range in animals
No relationship between c value and
organismal complexity:
the c value paradox

7. C values from eukaryotic organisms ranked by genome size
Species C value (Kb)
Saccharomyces cerevisiae ,000
Caenorhabditi elegans ,000
Drosophila melanogaster ,000
Strongylocentrotus purpuratus ,000
Gallus domesticus 1,200,000
Canis familiaris ,900,000
Rattus norvegicus ,900,000
Xenopus laevis 3,100,000
Homo sapiens 3,600,000
Nicotiana tabacum 3,800,000
Ambystoma tigrinum ,000,000
Pinus resinosa ,000,000
Lepidosiren paradoxa ,000,000
Ophioglossum petiolatum ,000,000
Amoeba dubia ,000,000

8. Genome size and amount of heterochromatin
98% of variance explained

9. Genic Fraction vs Genome Size

10. Salamander Genome….BIG!
Human
Salamander
Reptile

11. Make BAC Library
36, 864 clones
PCR Screen for BACs
that contain genes
Clean
Assemble
Annotate
Sequence 16 BACs

12. Assembly Total Reads for Clustering (767,157) PaCE
Total PaCE Clusters (420,326)
Single Sequence Clusters (362,760)
Multi Sequence Clusters (57,566)
CAP3 Assembly
Contigs
(61,127)
Singlets
(5,199)
Total Contigs & Singletons : 429,086 (Contigs: 61,127 Singletons:367,959)

13. Annotation Total Sequences for Annotation (429,086) Human RefSeq
BLASTX
24,641 have a significant match
Remaining 404,445
Xenopus Laevis & Tropicalis Unigene
BLASTN
7130 have a significant match
Remaining 397,315 NR
BLASTX
3731* have a significant match
* BLAST not complete yet and is still running

14. Two Interesting Discoveries
Axolotl introns are large
Genic regions contain novel genes

15. Axolotl Introns are Large
Average orthologous intron size
Axolotl: bp
Human: bp
Chicken: 675 bp
Frog: bp

16. * *

17. Percentage of sequences identified as repetitive
Axolotl Human
BACs Introns Introns
Total interspersed:
Total retroelements:
SINEs:
LINEs:
L2/CR1/Rex
R1/LOA/Jockey 0 0 0
RTE/Bov-B
L1/CIN
LTR elements:
Gypsy/DIRS
Retroviral
DNA transposons:
hobo-Activator <
PiggyBac
Tourist/Harbinger

18. Number of predicted non-coding RNAs
Axolotl Human
miRNAs
snRNAs
% of intron bases: 2.7% %

19. So Why Are Axolotl Introns Large?
Nucleosome or matrix attachment sites?
Selection to moderate rates of biological processes?

20. Conclusions Genic regions of the axolotl genome appear to be
larger than they are in other vertebrates.
- Introns are larger
- Evidence of novel genes
- Next step: What does the non-genic portion look like?