Computational Exploration of Virus Diversity on Transcriptomic Datasets Digitaler Anhang der Dissertation zur Erlangung des Doktorgrades (Dr. rer. nat.) der Mathematisch-Naturwissenschaftlichen Fakultät der Rheinischen Friedrich-Wilhelms-Universität Bonn vorgelegt von Simon Käfer aus Andernach Bonn 2019 Table of Contents 1 Table of Contents 1 Preliminary Work - Phylogenetic Tree Reconstruction 3 1.1 Non-segmented RNA Viruses ........................... 3 1.2 Segmented RNA Viruses ............................. 4 1.3 Flavivirus-like Superfamily ............................ 5 1.4 Picornavirus-like Viruses ............................. 6 1.5 Togavirus-like Superfamily ............................ 7 1.6 Nidovirales-like Viruses .............................. 8 2 TRAVIS - True Positive Details 9 2.1 INSnfrTABRAAPEI-14 .............................. 9 2.2 INSnfrTADRAAPEI-16 .............................. 10 2.3 INSnfrTAIRAAPEI-21 ............................... 11 2.4 INSnfrTAORAAPEI-35 .............................. 13 2.5 INSnfrTATRAAPEI-43 .............................. 14 2.6 INSnfrTBERAAPEI-19 .............................. 15 2.7 INSytvTABRAAPEI-11 .............................. 16 2.8 INSytvTALRAAPEI-35 .............................. 17 2.9 INSytvTBORAAPEI-47 .............................. 18 2.10 INSswpTBBRAAPEI-21 .............................. 19 2.11 INSeqtTAHRAAPEI-88 .............................. 20 2.12 INShkeTCLRAAPEI-44 .............................. 22 2.13 INSeqtTBNRAAPEI-11 .............................. 23 2.14 INSeqtTCJRAAPEI-20 .............................. 24 2.15 INSeqtTCZRAAPEI-47 .............................. 25 2.16 INSeqtTDXRAAPEI-19 .............................. 27 2.17 INSlupTBDRAAPEI-17 .............................. 28 2.18 INSlupTBKRAAPEI-31 .............................. 29 2.19 INSlupTBMRAAPEI-34 .............................. 30 2.20 INSlupTBURAAPEI-45 .............................. 31 2.21 INSlupTAFRAAPEI-44 .............................. 32 2.22 INSntgTABRAAPEI-216 ............................. 33 2.23 INSlupTASRAAPEI-89 .............................. 34 2.24 INSqiqTBFRAAPEI-61 .............................. 36 2.25 INSqiqTBLRAAPEI-83 .............................. 37 2.26 INSqiqTBNRABPEI-90 .............................. 38 2.27 INSqiqTCTRAAPEI-75 .............................. 40 2 Table of Contents 2.28 INSlupTATRAAPEI-90 .............................. 41 2.29 INSqiqTCXRAAPEI-90 .............................. 42 2.30 INSqiqTDLRAAPEI-72 .............................. 43 2.31 INSobdTDTRAAPEI-18 .............................. 44 2.32 INSobdTDYRAAPEI-30 .............................. 45 2.33 INSerlTCGRAAPEI-32 .............................. 47 2.34 INSkzdTABRAAPEI-136 ............................. 48 2.35 INSkzdTACRAAPEI-171 ............................. 49 2.36 INSofmTBLRAAPEI-71 .............................. 50 2.37 INSofmTCYRAAPEI-79 .............................. 51 2.38 INSqiqTDDRABPEI-136 ............................. 52 2.39 INSfkjTBIRAAPEI-202 .............................. 53 2.40 INSerlTAKRAAPEI-83 .............................. 54 2.41 INSfkjTBMRAAPEI-206 ............................. 55 2.42 INSofmTCERAAPEI-22 .............................. 57 2.43 INSofmTCFRAAPEI-26 .............................. 58 2.44 INSinlTAARABPEI-43 ............................... 59 2.45 INSinlTAPRAAPEI-33 ............................... 60 2.46 INSinlTAWRAAPEI-44 .............................. 61 2.47 RINSinlTCARAAPEI-55 .............................. 62 2.48 RINSinlTCNRAAPEI-33 .............................. 63 2.49 RINSymlTABRAAPEI-202 ............................ 64 2.50 RINSwvkTAURAAPEI-56 ............................. 65 2.51 ANIsrmTAAWRAAPEI-225 ............................ 66 2.52 WHANIsrmTMAFRAAPEI-14 .......................... 67 2.53 WHANIsrmTMCHRAAPEI-56 .......................... 68 2.54 INSeqtTBBRAAPEI-75 .............................. 69 2.55 INSobdTDIRAAPEI-84 .............................. 71 1. PRELIMINARY WORK - PHYLOGENETIC TREE RECONSTRUCTION 3 1 Preliminary Work - Phylogenetic Tree Reconstruction 1.1 Non-segmented RNA Viruses non-segmented RNA virus (-) 0.3 II 1KV_mono_000165 III KM817639-Shuangao_Insect_Virus... 1KV_mono_000207 1KV_mono_000169 1KV_mono_000166 1KV_mono_000067 1KV_mono_000135 1KV_mono_000172 1KV_mono_000223 1KV_mono_000138 1KV_mono_000020 1KV_mono_000109 KM817645-Wuhan_Ant_Virus_1KV_mono_000061 1KV_mono_000111 1KV_mono_000195 NC_025382-Spodoptera_frugiperd... NC_025253-Farmington_virus_(st... 1KV_mono_000179 1KV_mono_000117 KM817652-Wuhan_Insect_virus_6_... KM817649-Wuhan_House_Fly_Virus... 1KV_mono_000035 1KV_mono_000011 NC_007642-Lettuce_necrotic_yel... 1KV_mono_000123 KM817659-Wuhan_Mosquito_Virus_... KM817636-Shayang_Fly_Virus_3_(... 1KV_mono_000148 KM817650-Wuhan_Insect_virus_4_... KM817642-Tacheng_Tick_Virus_7_... NC_016136-Potato_yellow_dwarf_... KM817637-Shuangao_Bedbug_Virus... KM817647-Wuhan_Fly_Virus_3_(st... HM849039-Soybean_cyst_nematode... KM817651-Wuhan_Insect_virus_5_... 1KV_mono_000023 1KV_mono_000098 Rhabdoviridae 1KV_mono_000114 1KV_mono_000204 1KV_mono_000171 NC_002251-Northern_cereal_mosa... KM817634-Sanxia_Water_Strider_... 1KV_mono_000016 1KV_mono_000084 1KV_mono_000118 1KV_mono_000013 1KV_mono_000191 1KV_mono_000054 KM817631-Jingshan_Fly_Virus_2_... 1KV_mono_000027 KF823814-Fox_fecal_rhabdovirus... 1KV_mono_000150 1KV_mono_000039 1KV_mono_000201 NC_025401-Sunguru_virus_(strip... KM817638-Shuangao_Fly_Virus_2_... NC_025405-Niakha_virus_(stripp... 1KV_mono_000062 1KV_mono_000115 1KV_mono_000232 NC_025399-Oak-Vale_virus_ 1KV_mono_000102 1KV_mono_000040 1KV_mono_000063 1KV_mono_000139 NC_018629-Ikoma_lyssavirus_(st... 1KV_mono_000147 Anphevirus 1KV_mono_000002 IV 1KV_mono_000188 KM817643-Taishun_Tick_Virus_(s... 1KV_mono_000053 1KV_mono_000024 NC_001542-Rabies_virus_(stripp... 1KV_mono_000124 KM817661-Xincheng_Mosquito_Vir... NC_025393-Arboretum_virus 1KV_mono_000051 1KV_mono_000094 Lyssavirus 1KV_mono_000192 1KV_mono_000203 1KV_mono_000096 KM205018-Bahia_Grande_virus_(s... NC_025340-Long_Island_tick_rha... 1KV_mono_000177 1KV_mono_000164 NC_025359-Moussa_virus_(stripp... 1KV_mono_000043 NC_025354-Curionopolis_virus 1KV_mono_000031 1KV_mono_000092 1KV_mono_000095 1KV_mono_000030 KF360973-North_Creek_virus_(st... 1KV_mono_000082 1KV_mono_000091 NC_025384-Culex_tritaeniorhync... 1KV_mono_000007 1KV_mono_000209 1KV_mono_000228 JX297815-Bas-Congo_virus_ 1KV_mono_000036 KM817629-Bole_Tick_Virus_2_(st... 1KV_mono_000081 1KV_mono_000107 KM817640-Tacheng_Tick_Virus_3_... I 1KV_mono_000021 1KV_mono_000065 KM817660-Wuhan_Tick_Virus_1_(s... 1KV_mono_000048 1KV_mono_000100 NC_013135-Drosophila_melanogas... V KM817657-Wuhan_Louse_Fly_Virus... 1KV_mono_000042 KM817655-Wuhan_Louse_Fly_Virus... 1KV_mono_000060 KM817656-Wuhan_Louse_Fly_Virus...NC_007020-Tupaia_virus_(stripp... 1KV_mono_000106 1KV_mono_000200 1KV_mono_000058 1KV_mono_000224 NC_002526-Bovine_ephemeral_fev... KM817630-Huangpi_Tick_Virus_3_... KM817658-Wuhan_Louse_Fly_Virus... NC_020804-Tibrogargan_virus_(s... 1KV_mono_000012 NC_011639-Wongabel_virus_ 1KV_mono_000212 NC_025387-Scopthalmus_maximus_... NC_001560-Vesicular_stomatitis... 1KV_mono_000078 1KV_mono_000131 VI NC_002803-Spring_viraemia_of_c... KM817653-Wuhan_Insect_virus_7_... NC_020803-Perch_rhabdovirus NC_024702-Soybean_cyst_nematode... KM817654-Wuhan_Louse_Fly_Virus... KM350503-Santa_barbara_virus NC_012703-Nyamini_virusNC_024376-Sierra_Nevada_virus_... 1KV_mono_000167 1KV_mono_000077 KM817648-Wuhan_House_Fly_Virus... NC_025341-Fikirini_bat_rhabdov... NC_025362-Xiburema_virus KM817646-Wuhan_Fly_Virus_2 KM817646-Wuhan_Fly_Virus_2 KM817662-Yongjia_Tick_Virus 1KV_mono_000181 KM817635-Shayang_Fly_Virus_2 1KV_mono_000028 1KV_mono_000071 1KV_mono_000001 1KV_mono_000206 Nyamiviridae 1KV_mono_000068 1KV_mono_000052 NC_024296-Avian_Bornavirus. Vesiculovirus 1KV_mono_000009 1KV_mono_000015 1KV_mono_000004 1KV_mono_000198 1KV_mono_000199 NC_001607-Borna_disease_virus_... 1KV_mono_000180 1KV_mono_000162 1KV_mono_000044 1KV_mono_000006 NC_024778-Reptile_Bornavirus 1KV_mono_000059 1KV_mono_000152 1KV_mono_000116 1KV_mono_000174 1KV_mono_000149 KM817644-Wenzhou_Crab_Virus_1_... 1KV_mono_000156 Bornaviridae 1KV_mono_000194 1KV_mono_000141 VII 1KV_mono_000099 1KV_mono_000110 KM817598-Shayang_Fly_Virus_1_(... 1KV_mono_000022 Crustavirus 1KV_mono_000087 KM817613-Shuangao_Lacewing_Vir... KM817632-Lishi_Spider_Virus_2_... KM817614-Shuangao_Insect_Virus... 1KV_mono_000033 1KV_mono_000029 1KV_mono_000041 KM817641-Tacheng_Tick_Virus_6_... 1KV_mono_000101 1KV_mono_000154 KM817603-Wenzhou_Crab_Virus_3_... KM817633-Sanxia_Water_Strider_... VIII KM817599-Tacheng_Tick_Virus_4_... 1KV_mono_000113 Chengtivirus 1KV_mono_000057 1KV_mono_000047 1KV_mono_000190 Arlivirus KC601997-Sclerotinia_sclerotio... 1KV_mono_000046 1KV_mono_000049 Wastrivirus 1KV_mono_000055 1KV_mono_000225 1KV_mono_000142 Mymonaviridae KM817595-Changping_Tick_Virus_... KM817600-Tacheng_Tick_Virus_5_... 1KV_mono_000155 NC_001652-Infectious_hematopoi... 1KV_mono_000034 XIII 1KV_mono_000104 KJ746903-Deer_tick_mononegavir... KM817611-Wuhan_Tick_Virus_2_(s... KM817594-Changping_Tick_Virus_... 1KV_mono_000170 Novirhabdovirus KM817609-Wuhan_Louse_Fly_Virus... 1KV_mono_000090 1KV_mono_000076 1KV_mono_000050 1KV_mono_000132 KM817606-Wuhan_Louse_Fly_Virus... IX 1KV_mono_000227 KM817612-Shuangao_Fly_Virus_1_... 1KV_mono_000134 KM817597-Lishi_Spider_Virus_1_... NC_025403-Achimota_virus_1_(st... NC_025403-Achimota_virus_1_(st... 1KV_mono_000105 KM817601-Wenzhou_Crab_Virus_2_...KM817610-Wuhan_Mosquito_Virus_..