From: cmzmasek@gmail.com Date: Fri, 21 Jun 2013 17:04:53 +0000 (+0000) Subject: in progress X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=4dcd678fa5b503ced7ef9033827903953728bb6d;p=jalview.git in progress --- diff --git a/forester/data/tol_149.xml b/forester/data/tol_149.xml index e2327f3..9c6248e 100644 --- a/forester/data/tol_149.xml +++ b/forester/data/tol_149.xml @@ -2167,24 +2167,26 @@ - 5518 + 229533 GIBZE - Gibberella zeae + Gibberella zeae (strain PH-1 / ATCC MYA-4620 / FGSC 9075 / NRRL 31084) Wheat head blight fungus Fusarium graminearum - species + Gibberella zeae PH-1 + strain http://www.apsnet.org/publications/apsnetfeatures/PublishingImages/1999%20Features/Fusarium02sm.jpg - 29875 - HYPVI - Hypocrea virens - Gliocladium virens + 413071 + HYPVG + Hypocrea virens (strain Gv29-8 / FGSC 10586) Trichoderma virens Gliocladium flavofuscum - species + Trichoderma virens Gv29-8 + Gliocladium virens + strain http://www.ars.usda.gov/images/docs/10920_11114/Stroma1.jpg @@ -2244,21 +2246,21 @@ - 1029505 + 306901 CHAGB - Chaetomium globosum + Chaetomium globosum (strain ATCC 6205 / CBS 148.51 / DSM 1962 / NBRC 6347 / NRRL 1970) Kunze 1817 Soil fungus - species + strain - 5141 + 367110 NEUCR - Neurospora crassa - species + Neurospora crassa (strain ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGSC 987) + strain @@ -2277,22 +2279,22 @@ - 40559 - BOTFU - Botryotinia fuckeliana + 999810 + BOTF4 + Botryotinia fuckeliana (strain T4) Noble rot fungus Botrytis cinerea - species + strain - 5180 - SCLSC - Sclerotinia sclerotiorum + 665079 + SCLS1 + Sclerotinia sclerotiorum (strain ATCC 18683 / 1980 / Ss-1) White mold Whetzelinia sclerotiorum - species + strain @@ -2368,18 +2370,21 @@ 83344 - Mycosphaerella fijiensis + PFIXX + Pseudocercospora fijiensis + Mycosphaerella fijiensis species - 54734 - MYCGR - Mycosphaerella graminicola + 336722 + MYCGM + Mycosphaerella graminicola (strain CBS 115943 / IPO323) Speckled leaf blotch fungus - Septoria tritici - species + Zymoseptoria tritici IPO323 + Mycosphaerella graminicola IPO323 + strain @@ -2408,6 +2413,8 @@ 430998 BCOXX Baudoinia compniacensis + Angels' Share fungus + Torula compniacensis species http://www.botanicalgarden.ubc.ca/potd/images/2011/baudoinia-compniacensis2.jpg @@ -2466,29 +2473,13 @@ Cochliobolus & Setosphaeria - 5015 - Cochliobolus - genus + 45130 + COCSA + Cochliobolus sativus + Bipolaris sorokiniana + species + http://www.plantmanagementnetwork.org/pub/php/diagnosticguide/2003/rootrot/image/mathre6sm.jpg - - - 5016 - COCHE - Cochliobolus heterostrophus - Drechslera maydis - species - - - - - 45130 - COCSA - Cochliobolus sativus - Bipolaris sorokiniana - species - http://www.plantmanagementnetwork.org/pub/php/diagnosticguide/2003/rootrot/image/mathre6sm.jpg - - @@ -2510,17 +2501,18 @@ Pyrenophora tritici-repentis (strain Pt-1C-BFP) Wheat tan spot fungus Drechslera tritici-repentis + strain - 13684 + 321614 PHANO - Phaeosphaeria nodorum + Phaeosphaeria nodorum (strain SN15 / ATCC MYA-4574 / FGSC 10173) Glume blotch fungus Septoria nodorum - species + strain @@ -2540,22 +2532,21 @@ - 5059 - ASPFL - Aspergillus flavus - Link 1809 - Petromyces flavus - species + 332952 + ASPFN + Aspergillus flavus (strain ATCC 200026 / FGSC A1120 / NRRL 3357 / JCM 12722 / SRRC 167) + Aspergillus flavus NRRL3357 + strain http://www.schoolproject2.ewebsite.com/img/original/21/aspergillus-flavus.jpg - 5061 - ASPNG - Aspergillus niger - Tiegh - species + 425011 + ASPNC + Aspergillus niger (strain CBS 513.88 / FGSC A1513) + Aspergillus niger CBS 513.88 + strain http://www.vetmed.wisc.edu/students/vetmycology/15.jpg @@ -2572,12 +2563,12 @@ Neosartorya & Emericella - 195546 + 227321 EMENI - Emericella nidulans + Emericella nidulans (strain FGSC A4 / ATCC 38163 / CBS 112.46 / NRRL 194 / M139) Vuill. 1927 Aspergillus nidulans - species + strain @@ -2586,6 +2577,7 @@ NEOFI Neosartorya fischeri (strain ATCC 1020 / DSM 3700 / FGSC A1164 / NRRL 181) Aspergillus fischerianus + strain @@ -2604,8 +2596,6 @@ mitosporic Onygenales & Onygenaceae - - 246410 @@ -2620,6 +2610,7 @@ 336963 UNCRE Uncinocarpus reesii (strain UAMH 1704) + strain @@ -2641,6 +2632,7 @@ Tuber melanosporum (strain Mel28) Perigord black truffle Tuber melanosporum Mel28 + strain http://www.trufamania.com/trufas/Tuber%20melanosporum02.jpg @@ -2652,8 +2644,13 @@ budding yeasts order + + A fungal phylogeny based on 42 complete genomes derived from supertree and combined gene analysis + + + - Candida & Debaryomyces & Saccharomycetacea + mitosporic Saccharomycetales & Debaryomycetaceae & Saccharomycetaceae 4893 @@ -2661,63 +2658,38 @@ family - Saccharomyces_Pichia + Naumovozyma & Saccharomyces - Saccharomyces - - - 27288 - SACCA - Saccharomyces castellii - Yeast - Saccharomyces castellii - species - - - - - 4932 - YEAST - Saccharomyces cerevisiae - Baker's yeast - species - - + + 1064592 + NAUCC + Naumovozyma castellii (strain ATCC 76901 / CBS 4309 / NBRC 1992 / NRRL Y-12630) + Yeast + Saccharomyces castellii + strain + - 4905 - PICAN - Pichia angusta - Yeast - Hansenula polymorpha - species + 559292 + YEAST + Saccharomyces cerevisiae (strain ATCC 204508 / S288c) + Baker's yeast + strain - Kluyveromyces & Ashbya + Eremothecium & Kluyveromyces - Kluyveromyces - - - 284590 - KLULA - Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37) - Yeast - Candida sphaerica - Kluyveromyces lactis NRRL Y-1140 - - - - - 4914 - KLUWA - Kluyveromyces waltii - Yeast - species - - + + 284590 + KLULA + Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37) + Yeast + Candida sphaerica + Kluyveromyces lactis NRRL Y-1140 + @@ -2731,29 +2703,30 @@ - Candida & Debaryomyces + Debaryomyces & Candida 5475 Candida + Torulopsis genus - 5476 + 237561 CANAL - Candida albicans + Candida albicans (strain SC5314 / ATCC MYA-2876) Yeast - species + strain - 5482 - CANTR - Candida tropicalis + 294747 + CANTT + Candida tropicalis (strain ATCC MYA-3404 / T1) Yeast - species + strain @@ -2771,11 +2744,11 @@ - 4952 + 284591 YARLI - Yarrowia lipolytica + Yarrowia lipolytica (strain CLIB 122 / E 150) Candida lipolytica - species + strain @@ -2796,11 +2769,11 @@ - 4897 - SCHJP - Schizosaccharomyces japonicus + 402676 + SCHJY + Schizosaccharomyces japonicus (strain yFS275 / FY16936) Fission yeast - species + strain @@ -2815,11 +2788,11 @@ - 4896 + 284812 SCHPO - Schizosaccharomyces pombe + Schizosaccharomyces pombe (strain 972 / ATCC 24843) Fission yeast - species + strain @@ -2902,23 +2875,24 @@ 5346 - COPCI - Coprinopsis cinerea + COPC7 + Coprinopsis cinerea (strain Okayama-7 / 130 / ATCC MYA-4618 / FGSC 9003) Inky cap fungus Hormographiella aspergillata - species + strain http://upload.wikimedia.org/wikipedia/commons/e/e9/Coprinopsis.cinerea.-.lindsey.jpg - 29883 - LACBI + 486041 + LACBS Laccaria bicolor Bicoloured deceiver Laccaria laccata var. bicolor - species + Laccaria bicolor S238N-H82 + strain http://botit.botany.wisc.edu/toms_fungi/images/L_bicolor_NM.JPG @@ -2993,6 +2967,7 @@ 202697 + JARXX Jaapia argillacea species http://mycor.nancy.inra.fr/blogGenomes/wp-content/uploads/2012/08/IMG_21261.jpg @@ -3171,10 +3146,10 @@ - 5270 + 237631 USTMA - Ustilago maydis - Smut fungus + Ustilago maydis (strain 521 / FGSC 9021) + Corn smut fungus species @@ -3195,23 +3170,23 @@ - 156696 + 747676 MELLP - Melampsora laricis-populina + Melampsora larici-populina (strain 98AG31 / pathotype 3-4-7) Kleb. 1902 - Melampsora larici-populina - Melampsora laricipopulina - species + Poplar leaf rust fungus + Melampsora larici-populina 98AG31 + Melampsora laricis-populina 98AG31 + strain - 1029947 + 5297 PUCGR Puccinia graminis Pers. 1794 Black stem rust fungus - Wheat rust species @@ -3244,10 +3219,10 @@ - 148960 - WALSE - Wallemia sebi - species + 671144 + WALSC + Wallemia sebi (strain ATCC MYA-4683 / CBS 633.66) + strain @@ -3306,8 +3281,10 @@ 61392 + CREXX Coemansia reversa species + http://genome.jgi.doe.gov/public/Coere1/Coemansia.jpg @@ -3336,11 +3313,11 @@ - 109871 - BATDE - Batrachochytrium dendrobatidis + 684364 + BATDJ + Batrachochytrium dendrobatidis (strain JAM81 / FGSC 10211) Frog chytrid fungus - species + strain @@ -3377,27 +3354,60 @@ - 6033 - Encephalitozoon - genus + 6029 + Microsporidia + phylum - 6035 - ENCCU - Encephalitozoon cuniculi (strain GB-M1) - Microsporidian parasite - species - http://www.nature.com/modpathol/journal/v15/n5/images/3880566f7.jpg + 6032 + Apansporoblastina + suborder + + + 6033 + Encephalitozoon + genus + + + + 284813 + ENCCU + Encephalitozoon cuniculi (strain GB-M1) + Microsporidian parasite + strain + http://www.nature.com/modpathol/journal/v15/n5/images/3880566f7.jpg + + + + + 907965 + ENCHA + Encephalitozoon hellem (strain ATCC 50504) + Microsporidian parasite + strain + http://ruby.fgcu.edu/courses/davidb/50249/web/Encephalitozoonhellem91.jpg + + + + + + 993615 + VITCO + Vittaforma corneae (strain ATCC 50505) + Microsporidian parasite + Nosema corneum + + - 907965 - ENCHA - Encephalitozoon hellem (strain ATCC 50504) + 72359 + TRAHO + Trachipleistophora hominis Microsporidian parasite - http://ruby.fgcu.edu/courses/davidb/50249/web/Encephalitozoonhellem91.jpg + species