Where does biological order come from?

Transcription

1 Where does biological order come from? Gavi Coat Bioiformatics Research Ceter Biological Scieces Program i Geetics gcoat@csu.edu coatlab.org

2 AA32G00445 Tp4g AT2G33430 DAL Tp1g AT1G04450 AA32G00441 Tp4g RIC1 AA19G00112 Tp1g AT1G Fixatio rate (γ): 0.17 Geome 2 fractioal preservatio rate (ε): 0.64 Trackig flip prob.: WGD AA19G00113 Tp1g AT1G04410 C-NAD-MDH1, AA32G00436 Tp2g AT5G43330 C-NAD-MDH2 Tp1g AT1G04400 AT-PHH1 AA32G00435 Tp2g Tp1g ERF14 AA32G00429 Tp2g ERF96 AA19G00116 Tp1g AA32G00428 Tp2g AT5G43420 AT5G43420 AA19G00118 Tp1g AT1G04340 AA32G00426 Tp2g AT5G43460 Tp1g AT1G04330 AA32G00423 Tp2g AT5G43540 Tp1g AT1G04300 MUSE13 AA32G00422 Tp2g AT5G43560 MUSE14 AA32G00420 Tp2g AT5G43600 ATAAH-2 AA19G00122 Tp1g AT1G04270 RPS15 AA32G00418 Tp2g AT5G43640 AT5G43640 AA19G00123 Tp1g AT1G04260 MPI7 AA32G00416 Tp2g AA19G00124 Tp1g AT1G04250 ATIAA17 AA32G AA19G00125 Tp1g IAA3 AA32G00413 Tp2g AT5G43700 ATAUX2-11 AA32G00412 Tp2g AT5G43710 MNS4 AT5G43720 AT1G04230 AA32G00411 Tp2g AT5G AA32G00410 Tp2g AT5G43745 AT5G43745 AA19G00126 Tp1g KCS2 AA32G00409 Tp2g KCS20 AT1G Tp1g03030 AA19G00128 Less fractioated paretal geome More fractioated paretal geome Arabidopsis thaliaa Arabidopsis lyrata Capsella rubella Thellugiella halophila Eutrema parvulum Aethioema arabicum Arabidopsis thaliaa Arabidopsis lyrata Capsella rubella Thellugiella halophila Eutrema parvulum Aethioema arabicum Origis of complexity Gee ad geome duplicatios All sigle copy from PG#1 All sigle copy from PG#2 Fully duplicated i all geomes Other Metageomics

3 Ope Project No-traditioal hardware for bioiformatics:

4 Approaches i the lab LINUX-based use of scripts for WGD ad metageomic aalysis Perl/Pytho programmig c/c++ tool developmet Parallel computig MPI OpeMP CUDA

5 3378±3386 Nucleic Acids Research, 2002, Vol. 30 No. 15 ã 2002 Oxford Uiversity Press GeomeHistory: a software tool ad its applicatio to fully sequeced geomes Gavi C. Coat* ad Adreas Wager Departmet of Biology, 167 Castetter Hall, The Uiversity of New Mexico, Albuquerque, NM 87131, USA ARTICLE IN PRESS J. Parallel Distrib. Comput. 63 (2003) Parallel Geehuter: implemetatio of a likage aalysis package for distributed-memory architectures Gavi C. Coat, a, Steve J. Plimpto, b William Old, c Adreas Wager, a Pamela R. Fai, d Theresa R. Pacheco, d ad Grat Heffelfiger b a Departmet of Biology, 167 Castetter Hall, The Uiversity of New Mexico, Albuquerque, NM , USA b Computatio, Computers, ad Mathematics Ceter, Sadia Natioal Laboratories, Albuquerque, NM, USA c Agilet Laboratories, Fort Collis, CO, USA d Health Scieces Ceter, The Uiversity of Colorado, Fort Collis, CO, USA Received 4 December 2002; revised 15 April 2003; accepted 16 May 2003 Copyright Ó 2008 by the Geetics Society of America DOI: /geetics Probabilistic Cross-Species Iferece of Orthologous Geomic Regios Created by Whole-Geome Duplicatio i Yeast Gavi C. Coat ad Keeth H. Wolfe 1 Smurfit Istitute of Geetics, Triity College, Dubli 2, Irelad Mauscript received April 12, 2007 Accepted for publicatio April 21, 2008

6 Box 1 Whole-geome duplicatios across the phylogey of eukaryotes Agiosperms Moss Aimals Fugi Ciliates Acorus americaus Musa spp. Triticum aestivum Hordeum vulgare Oryza sativa Sorghum bicolor Zea mays Eschscholzia califorica Solaum tuberosum Solaum lycopersicum Cetaurea solstitialis Lactuca sativa Vitis viifera Lotus japoicus Medicago trucatula Glycie max Populus trichocarpa Gossypium hirsutum Carica papaya Arabidopsis thaliaa Physcomitrella pates Bichir (Polypteriformes) Sturgeo (Acipeseriformes) Gar (Semiootiformes) Boy togues (Osteoglossiformes) Zebrafish Takifugu rubripes Medaka Mammals Birds Amphibia Lobe-fied fish Lampreys Hagfish Saccharomyces cerevisiae Cadida glabrata Saccharomyces spp. Kluyveromyces lactis Neurospora crassa Aspergillus fumigatus Paramecium spp. Tetrahymea spp. Va de Peer, Maere, & Meyer (2009) Nat Rev Geet 10:725 Ceozoic 65 mya Cretaceous 145 mya Moocots (Core) Eudicots Ascomycetes Jurassic 208 mya Triassic 245 mya Permia 290 mya 3R Teleosts Carboiferous 363 mya Devoia 409 mya Siluria 439 mya Fish Lad vertebrates Ordovicia 510 mya Agiosperms moss split Fish lad vertebrates split Cambria 542 mya Precambria >542 mya 2R 1R

7 5000 duplicates dow to Duplicate gee losses Geome duplicatio

8 A) B) ll= Fixatio rate (γ): Geome 2 fractioal preservatio rate (ε): Coverg. rate (δ): 0.37 Trackig flip prob.: TGD abhd spcs tgfb1b clda mettl cldj cal cal sdf supt6h rab34b rab34a ek traf4b traf4a Takifugu rubripes Tetraodo igroviridis Gasterosteus aculeatus Xiphophorus maculatus Oryzias latipes Oreochromis iloticus Daio rerio Astyaax mexicaus Takifugu rubripes Tetraodo igroviridis Gasterosteus aculeatus Xiphophorus maculatus Oryzias latipes Oreochromis iloticus Daio rerio Astyaax mexicaus Less fractioated paretal subgeome More fractioated paretal subgeome All sigle copy from PG#1 All sigle copy from PG#2 Fully duplicated i all geomes Other

9 Zygote Cleavage 0.7 Blastula Gastrula Segmetatio Pharygula Hatchig Expressio stage Larval Juveile Adult 1 Duplicates survive mostly from later i developmet Proportio of gees i a oholog pair Prop. ohologs I a stage Overall Post-zygote Prop. of root losses I a stage Overall Post-zygote Sig. diff from overall Sig. diff from post-zyg. Sig. diff from overall Sig. diff from post-zyg Time i hours Proportio of gees lost o root brach Biases toward various ervous tissues Especially the retia Teleosts have a specialized retial structure compared to other vertebrates

10 Box 1 Whole-geome duplicatios across the phylogey of eukaryotes Agiosperms Moss Aimals Fugi Ciliates Acorus americaus Musa spp. Triticum aestivum Hordeum vulgare Oryza sativa Sorghum bicolor Zea mays Eschscholzia califorica Solaum tuberosum Solaum lycopersicum Cetaurea solstitialis Lactuca sativa Vitis viifera Lotus japoicus Medicago trucatula Glycie max Populus trichocarpa Gossypium hirsutum Carica papaya Arabidopsis thaliaa Brassica Physcomitrella pates Bichir (Polypteriformes) Sturgeo (Acipeseriformes) Gar (Semiootiformes) Boy togues (Osteoglossiformes) Zebrafish Takifugu rubripes Medaka Mammals Birds Amphibia Lobe-fied fish Lampreys Hagfish Saccharomyces cerevisiae Cadida glabrata Saccharomyces spp. Kluyveromyces lactis Neurospora crassa Aspergillus fumigatus Paramecium spp. Tetrahymea spp. Va de Peer, Maere, & Meyer (2009) Nat Rev Geet 10:725 Ceozoic 65 mya Cretaceous 145 mya Moocots (Core) Eudicots Ascomycetes Jurassic 208 mya Triassic 245 mya Permia 290 mya 3R Teleosts Carboiferous 363 mya Devoia 409 mya Siluria 439 mya Ordovicia 510 mya Agiosperms moss split Arachids Fish Lad vertebrates Fish lad vertebrates split Meloidogye (ematodes) Cambria 2R 542 mya Precambria >542 mya 1R

11 Why study rume microbes?

12 NETWORK INTERFACE

13 A) B) 0.16 Node frequecy C) 0 Dowstream oly < >4.5 log 2 (Upstream/Dowstream) Upstream oly Dowstream oly -2 2 Upstream oly log 2 (Upstream/Dowstream) Cumulative weighted abudace Upstream Dowstream Node degree

14 coatlab.org THANKS!

15 Ackowledgemets Mariae Emery Maddie Willis Ke Wolfe Kevi Byre Jo Gordo Yue Hao Michela Becchi Jim Birchler Chris Pires Hua Truog Sara Wolff Tasia Taxis Melida Elliso Kristi Cammack Bill Lamberso Liz Ottese Ford Ballatye

16 AA32G00445 Tp4g AT2G33430 DAL RIC Fixatio rate (γ): 0.17 Geome 2 fractioal preservatio rate (ε): 0.64 Trackig flip prob.: WGD Arabidopsis thaliaa Arabidopsis lyrata Capsella rubella Thellugiella halophila Eutrema parvulum Aethioema arabicum Tp1g AT1G04450 AA32G00441 Tp4g AA19G00112 Tp1g AT1G AT5G43330 C-NAD-MDH2 AA19G00113 Tp1g AT1G04410 C-NAD-MDH1, AA32G00436 Tp2g Tp1g AT1G04400 AT-PHH1 AA32G00435 Tp2g ERF96 Tp1g ERF14 AA32G00429 Tp2g AT5G43420 AT5G43420 AA19G00116 Tp1g AA32G00428 Tp2g AT5G43460 AA19G00118 Tp1g AT1G04340 AA32G00426 Tp2g Tp1g AT1G04330 AA32G00423 Tp2g AT5G43540 AT5G43560 MUSE14 Tp1g AT1G04300 MUSE13 AA32G00422 Tp2g AA32G00420 Tp2g AT5G43600 ATAAH AT5G43640 AT5G43640 AA19G00122 Tp1g AT1G04270 RPS15 AA32G00418 Tp2g AA19G00123 Tp1g AT1G04260 MPI7 AA32G00416 Tp2g AA19G00124 Tp1g AT1G04250 ATIAA17 AA32G AT5G43700 ATAUX2-11 AA19G00125 Tp1g IAA3 AA32G00413 Tp2g AA32G00412 Tp2g AT5G43710 MNS4 AT5G43720 AT1G04230 AA32G00411 Tp2g AT5G AA32G00410 Tp2g AT5G43745 AT5G KCS20 AA19G00126 Tp1g KCS2 AA32G00409 Tp2g AA19G00128 Tp1g AT1G04210 Less fractioated paretal geome More fractioated paretal geome Arabidopsis thaliaa Arabidopsis lyrata Capsella rubella Thellugiella halophila Eutrema parvulum Aethioema arabicum Domiat subgeome Fractioated subgeome All sigle copy from PG#1 All sigle copy from PG#2 Fully duplicated i all geomes Other Biased fractioatio:

17 A) Arabidopsis thaliaa Key Arabidopsis lyrata Capsella rubella Eutrema salsugieum Shrekiella parvula Aethioema arabicum B) C) Pillar positio Geomes with shared paretal assigmets ML estimate of ε Ca reduce this WGD to a few large blocks Idetify geomic paret of origi for each block See hybridizatio i actio Full break i sytey betwee pillars Switch i paretal geome assigmet with P 85% Paretal geome assigmet cofidece <85% Shared sytey break i all geomes Trackig artifact (see captio) Paretal sytey blocks iferred with WGD-bf model Paretal sytey blocks iferred with WGD-f model (o biased fract.) Paretal geome assigmet cofidece <85%

18 Experimetal desig We sampled the rumes of 34 aimals: 2 steers o the same diet 8 sheep fed cor/grai 8 sheep fed alfalfa pellets 8 sheep with high RFI ad 8 with low RFI Sequeced the extracted microbial DNA i the Illumia HighSeq

19 0 1 Prop. of gees with ohologs

20 C) D) Node pairwise distace Forage/Forage Coce/Coce Forage/Coce FORG to FORG Pearso s r=0.23, P=>0.5 RFI: Low/Low High/Low High/High CONC to CONC Pearso s r=0.41, P=>0.5 RFI: Low/Low High/Low High/High FORG to CONC Grass-fed aimals have more similar 0.8 profiles tha Forage/Forage cor-fed Simulatio Coce/Coce Frequecy 0.4 Forage/Coce oes E) OTU pairwise distace