1. http://naturalsystems.uchicago.edu http://naturalsystems.uchicago.edu class web site /evolgenome Model system toolkit Genome sequences EST collections ORF clones interactomes cellular localizations metabolomes KO collections functional screens

2. Current Topics in Evolutionary Genomics Wen-Hsiung Li and Justin Borevitz Potential Topics: I. Evolution of Gene Expression II. Evolution of transcriptional regulatory code (cis- regulatory elements and circuits) III. Evolution of regulatory networks IV. Evolution of duplicate genes V. Emergence of new genes VI. Genetic variation within and between species VII. Effects of recombination and gene conversion on GC content and substitution rate

3. RNADNA Universal Whole Genome Tiling Array Transcriptome Atlas Expression levels Tissues specificity Transcriptome Atlas Expression levels Tissues specificity Gene Discovery Gene model correction Non-coding/ micro-RNA Antisense transcription Gene Discovery Gene model correction Non-coding/ micro-RNA Antisense transcription Alternative Splicing Comparative Genome Hybridization (CGH) Insertion/Deletions Comparative Genome Hybridization (CGH) Insertion/Deletions Methylation Chromatin Immunoprecipitation ChIP chip Chromatin Immunoprecipitation ChIP chip Polymorphism SFPs Discovery/Genotyping Polymorphism SFPs Discovery/Genotyping RNA binding protein Immunoprecipitation RNA binding protein Immunoprecipitation

4. Deletions

5. ChipViewer: Mapping of transcriptional units of ORFeome From 2000v At1g09750 (MIPS) to the latest AGI At1g09750 2000 v Annotation (MIPS) The latest AGI Annotation

6. SNP SFP MMMMMM MMMMMM Chromosome (bp) conservation SNP ORFa start AAAAA Transcriptome Atlas ORFb deletion

8. Natural Variation Sequence SNPs (other markers) –Allele frequencies (individual or pooled) Collections –Populations, related species –Mapping lines

9. http://www.ncbi.nlm.nih.gov/dbEST/ dbEST_summary.html dbEST release 091704 Summary by Organism - September 17, 2004 -------------------------------------------------------------------------------- Number of public entries: 23,683,506 Homo sapiens (human) 5,861,921 Mus musculus + domesticus (mouse) 4,246,846 Ciona intestinalis 684,280 Rattus sp. (rat) 683,256 Danio rerio (zebrafish) 575,250 Triticum aestivum (wheat) 561,786 Gallus gallus (chicken) 495,092 Bos taurus (cattle) 493,352 Xenopus laevis (African clawed frog) 432,424 Xenopus tropicalis 423,107 Zea mays (maize) 416,090 Drosophila melanogaster (fruit fly) 382,439 Hordeum vulgare + subsp. vulgare (barley) 367,798 Sus scrofa (pig) 358,930 Glycine max (soybean) 342,359 Arabidopsis thaliana (thale cress) 322,651 Caenorhabditis elegans (nematode) 302,074 Oryza sativa (rice) 284,234 Saccharum officinarum 246,301 Sorghum bicolor (sorghum) 190,949 Medicago truncatula (barrel medic) 187,763 Pinus taeda (loblolly pine) 173,680 Chlamydomonas reinhardtii 167,621 Malus x domestica (apple tree) 158,772 Solanum tuberosum (potato) 158,061 Oncorhynchus mykiss (rainbow trout) 158,020 Dictyostelium discoideum 155,032 Canis familiaris (dog) 154,722 Lycopersicon esculentum (tomato) 153,775 Schistosoma mansoni (blood fluke) 152,749 Anopheles gambiae (African malaria mosquito) 150,042 Oryzias latipes (Japanese medaka) 149,752 Vitis vinifera 143,423 Bombyx mori (domestic silkworm) 116,541 Hydra magnipapillata 112,517 Toxoplasma gondii 111,782 Lotus corniculatus var. japonicus 111,459 Salmo salar 91,093 Ciona savignyi 84,302 Physcomitrella patens subsp. patens 82,420 Lactuca sativa 68,188 Populus tremula x Populus tremuloides 65,981 Gossypium raimondii 63,577 Helianthus annuus 61,531 Cryptococcus neoformans var. neoformans 59,041 Picea glauca 55,108 Coccidioides posadasii 53,664 Magnaporthe grisea 53,101 Strongylocentrotus purpuratus (purple urchin) 52,661 Macaca mulatta (rhesus monkey) 46,571 Schistosoma japonicum (blood fluke) 45,902 Citrus sinensis 45,192 Hypocrea jecorina 42,917 Fundulus heteroclitus 40,533 Ascaris suum (pig roundworm) 39,242 Gossypium arboreum 39,007 Brassica napus (oilseed rape) 37,159 Ictalurus punctatus (channel catfish) 34,655 Ambystoma mexicanum 34,282 Paracoccidioides brasiliensis 33,230 Populus tremula 31,288 Capsicum annuum 30,149 Eimeria tenella 28,550 Phytophthora sojae 28,092 Neurospora crassa 28,089 Nicotiana benthamiana 26,925 Populus balsamifera subsp. trichocarpa 26,825 Pongo pygmaeus 26,301 Brugia malayi (parasitic nematode) 26,215 Ipomoea nil 25,899 Takifugu rubripes 25,850 Mesembryanthemum crystallinum (common ice plant) 25,803 Antirrhinum majus 25,310 Neospora caninum 25,064 Apis mellifera 24,643 Meloidogyne hapla 24,452 Heterodera glycines (soybean cyst nematode) 24,438 Hordeum vulgare subsp. spontaneum 24,150 Trichomonas vaginalis 22,488 Acyrthosiphon pisum 22,183 Haemonchus contortus 21,967 Haplochromis chilotes 21,652 Beta vulgaris (beet) 21,523 Glossina morsitans morsitans 21,427 Sorghum propinquum 21,387 Porphyra yezoensis 20,979 Tetrahymena thermophila 20,627 Boophilus microplus 20,560 Ambystoma tigrinum tigrinum 20,491 Aspergillus flavus 20,371 Plasmodium falciparum 3D7 20,176 Phaseolus coccineus 20,120