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Current Topics in Evolutionary Genomics Wen-Hsiung Li and Justin Borevitz Potential Topics : I. Evolution of Gene Expres

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. Current Topics in Evolutionary Genomics Wen-Hsiung Li and Justin Borevitz

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Current Topics in Evolutionary Genomics Wen-Hsiung Li and Justin Borevitz Potential Topics : I. Evolution of Gene Expres

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  1. http://naturalsystems.uchicago.edu class web site /evolgenomeModel system toolkitGenome sequencesEST collectionsORF clonesinteractomescellular localizationsmetabolomesKO collectionsfunctional 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. Universal Whole Genome Tiling Array RNA DNA Chromatin Immunoprecipitation ChIP chip Gene Discovery Gene model correction Non-coding/ micro-RNA Antisense transcription Methylation Transcriptome Atlas Expression levels Tissues specificity Polymorphism SFPs Discovery/Genotyping Comparative Genome Hybridization (CGH) Insertion/Deletions Alternative Splicing 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. ORFa Transcriptome Atlas ORFb start AAAAA deletion M M M M M M M M M M M M SFP SNP SNP SFP SFP conservation Chromosome (bp)

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

  8. 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

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