It will help in preparing for the exam to read:

Chapter 19p.450-451, 456-472

Chapter 20p. 473-484

Comparative Genomics: The study of genome conservation

and variation among organisms

Chromosome numberChromosome morphology

Gene number

Genome sizeGene order

Measures of Genome Size

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

Range of C Values in Prokaryotes

Taxon Genome Size (Kb) Ratio

Bacteria 580 - 13,200 23 Mollicutes 580 - 2,200 4 Gram negatives 650 - 9,500 15 Gram positives 1,600 - 11,600 7 Cyanobacteria 3,100 - 13,200 4Archaea 1,600 - 4,100 3

~ 20 fold range in genome size

Genome Size (x 106 bp)

1000

2000

3000

4000

5000

GeneNumber

Gene Number and Genome Size in 12 CompletelySequenced Bacterial Species

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

Species C value (Kb)Saccharomyces cerevisiae 12,000Caenorhabditi elegans 80,000Drosophila melanogaster 180,000Strongylocentrotus purpuratus 870,000Gallus domesticus 1,200,000Canis familiaris 2,900,000Rattus norvegicus 2,900,000Xenopus laevis 3,100,000Homo sapiens 3,600,000Nicotiana tabacum 3,800,000Ambystoma tigrinum 32,000,000Pinus resinosa 68,000,000Lepidosiren paradoxa 120,000,000Ophioglossum petiolatum 160,000,000Amoeba dubia 690,000,000

C values from eukaryotic organisms ranked by genome size

Genome size and amount of heterochromatin

98% of variance explained

Genic Fraction vs Genome Size

Human

Reptile

Salamander

Salamander Genome….BIG!

Make BAC Library 36, 864 clones

PCR Screen for BACs that contain genes

Sequence 16 BACs

Clean

Assemble

Annotate

AssemblyTotal 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)

AnnotationTotal Sequences for Annotation (429,086)

BLASTX

24,641 have a significant match

7130 have a significant match

Remaining 404,445

Human RefSeq

BLASTNXenopus Laevis & Tropicalis Unigene

3731* have a significant match

Remaining 397,315

BLASTXNR

* BLAST not complete yet and is still running

Two Interesting Discoveries

- Axolotl introns are large

- Genic regions contain novel genes

Axolotl Introns are Large

Average orthologous intron size

Axolotl: 9454 bp

Human: 1938 bp

Chicken: 675 bp

Frog: 788 bp

*

*

Axolotl HumanBACs Introns Introns

Total interspersed: 2.32 1.77 0.38

Total retroelements: 2.24 1.67 0SINEs: 0 0 0LINEs: 0.29 0.24 0 L2/CR1/Rex 0.11 0.16 0 R1/LOA/Jockey 0 0 0 RTE/Bov-B 0.01 0.01 0 L1/CIN4 0.18 0.07 0

LTR elements: 1.95 1.43 0 Gypsy/DIRS1 1.42 0.76 0 Retroviral 0.24 0.36 0

DNA transposons: 0.08 0.10 0.38hobo-Activator <0.01 0.04 0PiggyBac 0 0 0.18Tourist/Harbinger 0.06 0.04 0

Percentage of sequences identified as repetitive

Number of predicted non-coding RNAs

Axolotl Human

miRNAs 86 6

snRNAs 26 1

% of intron bases: 2.7% 1.2%

So Why Are Axolotl Introns Large?

- Nucleosome or matrix attachment sites?

- Selection to moderate rates of biological processes?

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?