http://naturalsystems.uchicago.edu class web site /evolgenome

Model system toolkit

Genome sequencesEST collectionsORF clonesinteractomescellular localizationsmetabolomesKO collectionsfunctional screens

• 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

RNA DNA

Universal Whole Genome Tiling Array

Transcriptome AtlasExpression levelsTissues specificity

Transcriptome AtlasExpression levelsTissues specificity

Gene DiscoveryGene model correctionNon-coding/ micro-RNAAntisense transcription

Gene DiscoveryGene model correctionNon-coding/ micro-RNAAntisense transcription

Alternative SplicingAlternative Splicing Comparative GenomeHybridization (CGH)

Insertion/Deletions

Comparative GenomeHybridization (CGH)

Insertion/Deletions

MethylationMethylation

ChromatinImmunoprecipitation

ChIP chip

ChromatinImmunoprecipitation

ChIP chip

Polymorphism SFPsDiscovery/Genotyping

Polymorphism SFPsDiscovery/Genotyping

RNA binding proteinImmunoprecipitation

RNA binding proteinImmunoprecipitation

Deletions

ChipViewer: Mapping of transcriptional units of ORFeome

From 2000v At1g09750 (MIPS) to the latest AGI At1g09750

2000 v Annotation (MIPS)

The latest AGI Annotation

SNP SFP MMMMM MSFP

SFP

MMMMM M

Chromosome (bp)

con

serv

atio

n

SNP

ORFa

start AAAAA

Tra

nsc

ripto

me

Atla

s

ORFb

deletion

Natural Variation

• Sequence

• SNPs (other markers)– Allele frequencies (individual or pooled)

• Collections– Populations, related species– Mapping lines

http://www.ncbi.nlm.nih.gov/dbEST/dbEST_summary.html

• dbEST release 091704 • Summary by Organism - September 17, 2004

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• 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