It will help in preparing for the exam to read: Chapter 19 p.450-451, 456-472 Chapter 20 p. 473-484

Comparative Genomics: The study of genome conservation and variation among organisms Chromosome number Chromosome morphology Gene number Genome size Gene 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 4 Archaea 1,600 - 4,100 3 ~ 20 fold range in genome size

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

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

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

Genome size and amount of heterochromatin 98% of variance explained

Genic Fraction vs Genome Size

Salamander Genome….BIG! Human Salamander Reptile

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

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)

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

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

* *

Percentage of sequences identified as repetitive Axolotl Human BACs Introns Introns Total interspersed: 2.32 1.77 0.38 Total retroelements: 2.24 1.67 0 SINEs: 0 0 0 LINEs: 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 0.38 hobo-Activator <0.01 0.04 0 PiggyBac 0 0 0.18 Tourist/Harbinger 0.06 0.04 0

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?