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Molecular Dating of the Emergence of Anaerobic Rumen Fungi and the Impact of Laterally Acquired Genes

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Molecular Dating of the Emergence of Anaerobic Rumen Fungi and the Impact of Laterally Acquired Genes Title: Molecular dating of the emergence of anaerobic rumen fungi and the impact of laterally acquired genes Short title: Molecular dating and HGT of anaerobic gut fungi Authors: Yan Wang*,†, Noha Youssef‡, M.B. Couger§, Radwa Hanafy‡, Mostafa Elshahed‡, Jason E. Stajich*,† Affiliations: * Department of Microbiology and Plant Pathology, University of California, Riverside, Riverside, California, 92521 USA. † Institute for Integrative Genome Biology, University of California, Riverside, Riverside, California, 92521 USA. ‡ Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, Oklahoma, 74074 USA. § High Performance Computing Center, Oklahoma State University, Stillwater, Oklahoma, 74074 USA. To whom correspondence may be addressed: Yan Wang, +1 951.386.5197, [email protected] Jason E. Stajich, +1 951.827.2363, [email protected] This Supplementary Materials PDF file includes: Figures S1-6 Tables S1-2 Supplementary figure legend: Fig. S1. Maximum likelihood phylogenetic tree of Neocallimastigomycota using Chytridiomycota as the outgroup. All bootstrap values (out of 100) are labeled on the branches. Fig. S2. Presence (dark gray) and absence (light gray) of the homologous gene families across the genomes (and transcriptomes) of Neocallimastigomycota and Chytridiomycota. The 4,824 gene families were selected as universal homologous genes that present at least 21 out of the 26 Neocallimastigomycota genomes (and transcriptomes) with missing no more than 1 of the 5 included Chytridiomycota genomes. In addition, it also includes the unique gene families that are strictly absence from all Chytridiomycota but encoded by the Neocallimastigomycota (missing no more than 5 out of the 26 taxa). Fig. S3. Mid-point rooted phylogenetic tree of the “Cthe_2159” domain encoded by the Neocallimastigomycota (red). All 126 Neocallimastigomycota (AGF) copies form a single clade (red) indicating the HGT donor, Clostridiales bacterium C5EMF8 (an obligate rumen bacterium), with strong support of maximum likelihood bootstrap (98/100). Fig. S4. Phylogenetic tree of the animal-like “Gal-Lectin” domain identified in Neocallimastigomycota. Clades are colored in consistence with the Figure 5 (Neocallimastigomycota in red, animals in blue, plants in green, and bacteria in brown). Fig. S5. Phylogenetic tree of the AGF “Gal-Lectin” flanking domain “Glyco_transf_34” (rooted with bacterium, in purple). AGF homologs are colored in red clustering with other fungal taxa (in black). Plant homologs are in green and protists in brown. Fig. S6. Mid-point rooted phylogenetic tree of the “Rhamnogal_lyase” domain encoded by the Neocallimastigomycota (red). Labels are consistent with the Figure 6. Pecoramyces sp. YC3 95 C1A 95 Pecoramyces ruminantium Pecoramyces sp. FS3C 100 Pecoramyces sp. S4B 95 sp. FX4B 100 Pecoramyces Orpinomyces sp. D3B 100 Orpinomyces sp. D3A 79 100 Orpinomyces sp. D4C Feramyces austinii WSF2c 100 100 Feramyces austinii WSF3a Neocallimastix californiae G1 100 sp. G3 100 Neocallimastix Neocallimastix frontalis Hef5 100 Anaeromyces sp. G3G 100 sp. NA 99 Anaeromyces Anaeromyces sp. C3G 100 Anaeromyces sp. C3J 100 100 Anaeromyces sp. O2 77 Anaeromyces robustus S4 Piromyces sp. B4 100 sp. B5 86 Piromyces 100 sp. A1 86 Piromyces sp. E2 77 Piromyces Piromyces finnis Caecomyces sp. Brit4 100 Caecomyces sp. Iso3 Chytriomyces sp. MP71 100 99 Rhizoclosmatium globosum 100 Entophlyctis helioformis JEL805 100 Gonapodya prolifera JEL478 Gaertneriomyces semiglobifer Barr43 0.3 Neocallimastigomycota Anaeromyces Piromyces Chytridiomycota Pecoramyces Neocallimastix Orpinomyces Caecomyces Feramyces Presence Absence 91 91 Anaeromyces_robustus_S4_305391 92 Anaeromyces_robustus_S4_330235 Anaeromyces_robustus_S4_330234 92 92 Anaeromyces_robustus_S4_295777 91 Anaeromyces_sp_C3G_6164 94 100 Anaeromyces_sp_C3J_33178 Anaeromyces_sp_NA_28982 99 Anaeromyces_sp_C3J_32903 Anaeromyces_robustus_S4_294801 100 Pecoramyces_sp_FS3C_28347 88 100Pecoramyces_ruminantium_C1A_1181724 92 Anaeromyces_sp_C3J_32897 89 Caecomyces_sp_Iso3_28243 98 80 Anaeromyces_robustus_S4_265696 Piromyces_sp_E2_13282 93 Piromyces_sp_E2_16996 88 Anaeromyces_sp_C3G_3365 78 Caecomyces_sp_Iso3_12816 100 Piromyces_sp_B4_57595 100 Piromyces_sp_B4_50542 Caecomyces_sp_Brit4_2790 92 100 Piromyces_finnis_356560 Piromyces_finnis_414173 99 100 Piromyces_sp_E2_5442 100 Piromyces_finnis_409988 100 Piromyces_sp_B4_55629 Piromyces_finnis_581087 100 100 Piromyces_sp_E2_5441 98 Pecoramyces_sp_FS3C_28354 100 Pecoramyces_ruminantium_C1A_1180421 98 Feramyces_austinii_WSF2c_44490 Feramyces_austinii_WSF3a_38604 94 100 100 Anaeromyces_robustus_S4_329210 Anaeromyces_sp_C3G_17122 100 Caecomyces_sp_Brit4_7458 94 Caecomyces_sp_Iso3_32479 100 Piromyces_sp_E2_5444 Piromyces_finnis_345772 Piromyces_sp_E2_248659 100 Pecoramyces_sp_FS3C_4471 95 100 Pecoramyces_sp_FS3C_18029 100 Pecoramyces_ruminantium_C1A_1186381 Pecoramyces_sp_YC3_16201 92 100Pecoramyces_ruminantium_C1A_1175978 100 Neocallimastix_californiae_G1_510108 100 100 Neocallimastix_californiae_G1_510110 100 Neocallimastix_californiae_G1_510107 97 Neocallimastix_californiae_G1_620865 91 Anaeromyces_robustus_S4_275012 94 Anaeromyces_robustus_S4_293955 59 Piromyces_sp_E2_15943 Pecoramyces_ruminantium_C1A_1179782 100 Pecoramyces_ruminantium_C1A_1179708 100 Pecoramyces_ruminantium_C1A_1187945 70 Neocallimastix_californiae_G1_640852 Neocallimastix_californiae_G1_640854100 100 Neocallimastix_californiae_G1_670432 43 Feramyces_austinii_WSF3a_27727 64 Pecoramyces_sp_YC3_20461 100 Anaeromyces_robustus_S4_330057 Piromyces_sp_E2_12499 92 Neocallimastix_californiae_G1_679316 74 Neocallimastix_californiae_G1_710198 55 74 Feramyces_austinii_WSF2c_15374 97 Feramyces_austinii_WSF2c_32250 100 Neocallimastix_frontalis_Hef5_44591 80 Neocallimastix_californiae_G1_638851 96 Neocallimastix_californiae_G1_679086 82 98 Piromyces_sp_B4_59147 Piromyces_finnis_585400 Piromyces_sp_E2_12505 90 Pecoramyces_ruminantium_C1A_1179702 67 Anaeromyces_robustus_S4_273069 92 Anaeromyces_robustus_S4_330058 58 59 Caecomyces_sp_Iso3_24744 Feramyces_austinii_WSF3a_47915 Piromyces_sp_E2_8821 100 100 Anaeromyces_robustus_S4_327961 100 Anaeromyces_sp_NA_2763 Piromyces_sp_E2_13245 97 100 Piromyces_finnis_584506 100 Anaeromyces_robustus_S4_270435 100 Anaeromyces_sp_C3J_47439 100 Anaeromyces_sp_C3G_16487 74 98 100 Piromyces_sp_A1_999 Piromyces_sp_E2_12494 48 Piromyces_finnis_585406 23 Neocallimastix_californiae_G1_710490 Piromyces_finnis_336161 100 Piromyces_sp_E2_5043 100 Pecoramyces_sp_FS3C_30089 33 100 Pecoramyces_sp_S4B_32602 100 Pecoramyces_ruminantium_C1A_1180902 99 Piromyces_finnis_588453 69 Piromyces_sp_E2_8199 Anaeromyces_sp_C3G_5587 39 100 Caecomyces_sp_Brit4_6442 91 Piromyces_sp_E2_12496 78 Piromyces_finnis_585407 Caecomyces_sp_Iso3_11920 100 Caecomyces_sp_Brit4_25893 100 Pecoramyces_sp_YC3_29771 100 Pecoramyces_sp_YC3_29772 100 Pecoramyces_sp_S4B_19211 100 100 Pecoramyces_ruminantium_C1A_1182088 82 Neocallimastix_californiae_G1_702986 69 Piromyces_sp_E2_12497 Feramyces_austinii_WSF2c_14310100 60 100 Piromyces_sp_B4_53914 98 Piromyces_sp_B4_53918 Piromyces_sp_B4_50142 98 100 Piromyces_sp_E2_10137 51 100 Piromyces_sp_A1_30720 Piromyces_sp_A1_30723 98 56 Piromyces_sp_E2_9301 53 74 Pecoramyces_ruminantium_C1A_1179584 57 Feramyces_austinii_WSF2c_1735_ 37 Feramyces_austinii_WSF3a_29255 Neocallimastix_californiae_G1_670430 58 Pecoramyces_sp_YC3_29332 50 Feramyces_austinii_WSF3a_11808 82 81 Caecomyces_sp_Brit4_6443 Piromyces_sp_E2_9302 Anaeromyces_robustus_S4_328840 100 Neocallimastix_frontalis_Hef5_24931 Neocallimastix_californiae_G1_508092 100 Clostridiales_bacterium_C5EMF8_149-397 92 Oribacterium_sinus_C2KW59_105-357 Oribacterium_sp._oral_taxon_D4CKY0_76-312 100 Hungatella_hathewayi_D3AMA3_63-315 87 Lachnospiraceae_bacterium_R9J5D6_73-323 84 Lachnospiraceae_bacterium_R9KQJ4_95-344 82 Clostridium_stercorarium_L7VQR5_90-387 Lachnospiraceae_bacterium_R9KF64_92-341 96 Lachnospiraceae_bacterium_R6NI92_55-302 68 100 Eubacterium_infirmum_H1PJH2_85-332 92 Butyrivibrio_proteoclasticus_E0S0X0_131-383 100 Slackia_heliotrinireducens_C7N1V3_112-364 Solobacterium_moorei_E7MPP4_87-336 93 100 Ruminococcus_albus_E6UH47_75-327 97 Ruminococcus_flavefaciens_W7UGE5_82-335 96 Shuttleworthia_satelles_C4GCI5_90-332 93 Olsenella_sp_G5F167_130-400 96 Firmicutes_bacterium_R6F067_70-304 68 71 95 Blautia_sp_R7JSW3_124-384 Peptostreptococcaceae_bacterium_J4TAQ5_87-323 94 Roseburia_inulinivorans_R5HY49_93-400 72 Desulfitobacterium_hafniense_Q24Y85_86-386 78 Marvinbryantia_formatexigens_C6LI05_95-382 97 Slackia_piriformis_K0YXK2_115-365 93 99 Adlercreutzia_equolifaciens_S6C770_119-338 97 Eggerthella_lenta_C8WKR1_151-371 Cryptobacterium_curtum_C7MME2_108-359 Methanocorpusculum_labreanum_A2SQ64_83-403 78 Syntrophobotulus_glycolicus_F0SYP4_82-361 100 Ruminococcus_albus_E6UH17_81-445 97 Cellulomonas_flavigena_WP_013116373.1 99 Cellulomonas_flavigena_WP_013116374.1 79 Xylanimonas_cellulosilytica_D1C0K7_108-371 100 99 Sanguibacter_keddieii_D1BCC2_100-367 94 Cellulomonas_fimi_F4H3C7_106-370 84 Gemmatimonas_aurantiaca_C1AAE0_125-385 83 Brachybacterium_phenoliresistens_Z9JUC2_86-337 78 91 Jonesia_denitrificans_C7QZY8_91-348 Pseudarthrobacter_chlorophenolicus_B8HFZ5_99-34596 83 100 Pseudoflavonifractor_capillosus_A6NRS6_135-438 Clostridium_lentocellum_F2JJB4_102-355 80 Holdemania_filiformis_B9YAY1_91-365 Anaerotruncus_sp._G3_R9LFA9_56-38799 100 Ruminococcus_flavefaciens_W7UM54_137-388 87 Ruminococcus_flavefaciens_W7UW60_139-390 94 Ruminococcus_champanellensis_D4L9K5_123-388 91 Turicibacter_sanguinis_D4W5L2_74-354 47 Clostridium_celatum_L1Q6H2_67-347
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