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Yeast-Species-GEM: The pan-GEM and strain specific GEMs for yeast species with whole-genome sequence.

  • Brief introduction:

As the unicellular fungi, the budding yeasts contain over 1000 different yeast species, which are widely distributed on our earth. Some yeast species, like Saccharomyces cerevisiae and Candida albicans, are very important to our human life and health. To further explore how different yeast species with interesting traits evolved in the long history, we built a pan-GEM for nearly all currently sequenced yeast species based on the latest research (Cell, 2018; DOI: 10.1016/j.cell.2018.10.023). With the advanced GEM of S.cerevisiae (Yeast8, https://github.com/SysBioChalmers/yeast-GEM) developed in our lab, the pan-GEM of for all these sequenced yeast species can be built by adding the new reactions with the gene association into Yeast8 through the detailed pan-genome annotation and mounts of physiological data mining. Next, with the gene function annotation of each yeast species, yeast species-specific GEMs of high quality can be built automatically. With the gap-filling and model test verified by the experimental data from different sources, the quality and prediction performances of species GEM will be improved continuously. We hope that this work could set a solid base in modelling simulation and systematic utilization of different yeast species for the wide research community.

  • Model KeyWords:

GEM Category: species; Utilisation: experimental data reconstruction, multi-omics integrative analysis, in silico strain design, model template, evolution analysis; Field: metabolic-network reconstruction; Type of Model: reconstruction, curated; Model Source: YeastMetabolicNetwork; Omic Source: genomics; Taxonomy: subphylum Saccharomycotina; Metabolic System: general metabolism; Strain: budding yeast species;

  • Contributing

Contributions are always welcome! Please firstly establish a new branch based on the dev branch (https://github.com/SysBioChalmers/Yeast-Species-GEMs/tree/dev) of this repo. You could also report an issue at https://github.com/SysBioChalmers/Yeast-Species-GEMs/issues if you have any question or idea about the content in this repo.

  • Citation

If you use yeast species GEMs, please cite this latest paper: Lu, H. et al. Yeast metabolic innovations emerged via expanded metabolic network and gene positive selection. Molecular Systems Biology 2021(17):e10427. https://www.embopress.org/doi/full/10.15252/msb.202110427.

  • Last update: 2021-10-25

  • Main Model Descriptors:

** Template Model | Yeast8.3 ** Generation date | 2020-06-25

Taxonomy Rxns Mets Genes
Alloascoidea_hylecoeti 3973 2755 1349
Ambrosiozyma_kashinagacola 3924 2700 1011
Ambrosiozyma_monospora 3931 2700 1223
Arthrobotrys_oligospora 3931 2874 1142
Arxula_adeninivorans 4045 2819 1085
Ascoidea_asiatica 3903 2688 1073
Ascoidea_rubescens 3856 2684 986
Ashbya_aceri 3623 2553 793
Aspergillus_nidulans 4053 2977 1613
Babjeviella_inositovora 3966 2736 1057
Botrytis_cinerea 4072 2940 1381
Brettanomyces_anomalus 3700 2665 946
Coccidioides_immitis 3922 2898 1159
Cyberlindnera_fabianii_JCM3601 3993 2740 1059
Cyberlindnera_jadinii 3957 2725 1051
Dekkera_bruxellensis 3681 2661 951
Eremothecium_coryli 3714 2572 807
Eremothecium_cymbalariae 3678 2561 799
Eremothecium_gossypii 3555 2556 795
Eremothecium_sinecaudum 3471 2549 748
Fusarium_graminearum 4098 2990 1612
Geotrichum_candidum 3886 2755 1171
Hanseniaspora_uvarum 3569 2464 782
Hanseniaspora_valbyensis 3583 2474 832
Hanseniaspora_vinae 3713 2531 857
Hyphopichia_burtonii 3728 2680 944
Kazachstania_africana 3830 2635 963
Kazachstania_naganishii 3859 2648 942
Kluyveromyces_lactis 3929 2688 954
Kluyveromyces_marxianus 3916 2683 995
Komagataella_pastoris 3806 2664 870
Kuraishia_capsulata 3959 2751 1056
Lachancea_cidri 3766 2686 965
Lachancea_dasiensis 3951 2686 982
Lachancea_fantastica 3837 2693 966
Lachancea_fermentati 3869 2695 1008
Lachancea_kluyveri 3961 2710 1040
Lachancea_lanzarotensis 3901 2689 942
Lachancea_meyersii 3886 2685 943
Lachancea_mirantina 3873 2674 930
Lachancea_nothofagi 3865 2698 967
Lachancea_quebecensis 3825 2659 919
Lachancea_thermotolerans 3934 2684 950
Lachancea_waltii 3839 2692 1008
Lipomyces_starkeyi 3869 2796 1150
Metschnikowia_aberdeeniae 3712 2656 869
Metschnikowia_arizonensis 3807 2681 911
Metschnikowia_bicuspidata 3807 2693 906
Metschnikowia_borealis 3780 2710 969
Metschnikowia_bowlesiae 3751 2677 917
Metschnikowia_cerradonensis 3845 2684 960
Metschnikowia_continentalis 3839 2711 952
Metschnikowia_dekortum 3791 2680 907
Metschnikowia_drakensbergensis 3762 2684 900
Metschnikowia_hamakuensis 3789 2695 945
Metschnikowia_hawaiiensis 3787 2695 937
Metschnikowia_hibisci 3823 2691 910
Metschnikowia_ipomoeae 3797 2706 961
Metschnikowia_kamakouana 3791 2704 936
Metschnikowia_kipukae 3813 2699 917
Metschnikowia_lockheadii 3824 2708 963
Metschnikowia_matae 3790 2703 961
Metschnikowia_matae_maris 3814 2703 980
Metschnikowia_mauinuiana 3816 2668 943
Metschnikowia_proteae 3804 2695 893
Metschnikowia_santaceciliae 3816 2685 952
Metschnikowia_shivogae 3787 2678 892
Metschnikowia_similis 3769 2686 901
Millerozyma_acaciae 3711 2676 891
Nadsonia_fulvescens_var_elongata 3770 2745 984
Nakaseomyces_bacillisporus 3764 2624 905
Nakaseomyces_bracarensis 3875 2643 973
Nakaseomyces_castellii 3761 2618 870
Nakaseomyces_delphensis 3845 2627 927
Nakaseomyces_nivariensis 3865 2637 962
Nakazawaea_peltata 3869 2679 1034
Naumovozyma_castellii 3806 2621 982
Naumovozyma_dairenensis 3881 2655 1009
Neurospora_crassa 3982 2934 1337
Ogataea_methanolica 3904 2690 1032
Ogataea_parapolymorpha 3654 2596 861
Ogataea_polymorpha 3618 2560 826
Pachysolen_tannophilus 3948 2715 1011
Pichia_membranifaciens 3819 2660 927
Priceomyces_haplophilus 3770 2699 885
Saccharomyces_arboricola 3801 2674 1037
Saccharomyces_cerevisiae 3992 2714 1211
Saccharomyces_eubayanus 3870 2654 1033
Saccharomyces_kudriavzevii 3774 2653 1001
Saccharomyces_mikatae 3834 2656 1000
Saccharomyces_paradoxus 3887 2687 1049
Saccharomyces_uvarum 3856 2664 1025
Saccharomycopsis_malanga 3961 2736 997
Saitoella_complicata 3969 2865 1043
Saprochaete_clavata 3891 2746 984
Scheffersomyces_lignosus 3991 2747 1077
Schizosaccharomyces_pombe 3330 2536 874
Sclerotinia_sclerotiorum 4065 2927 1278
Spathaspora_arborariae 3871 2701 990
Spathaspora_girioi 3802 2693 1029
Spathaspora_gorwiae 3893 2693 1030
Spathaspora_hagerdaliae 3915 2707 1033
Sporopachydermia_quercuum 4016 2800 1024
Stagonospora_nodorum 4091 2958 1449
Starmerella_bombicola_JCM9596 3735 2695 846
Sugiyamaella_lignohabitans 3959 2813 1052
Tetrapisispora_blattae 3847 2626 975
Tetrapisispora_phaffii 3847 2631 976
Tortispora_caseinolytica 3597 2693 831
Torulaspora_delbrueckii 3793 2639 905
Vanderwaltozyma_polyspora 3878 2641 1006
Wickerhamia_fluorescens 3798 2668 916
Wickerhamiella_domercqiae 3703 2679 828
Wickerhamomyces_anomalus 3988 2742 1115
Wickerhamomyces_ciferrii 4007 2755 1132
Xylona_heveae 3917 2886 1124
Yarrowia_deformans 3821 2771 1094
Yarrowia_keelungensis 3814 2769 1073
Yarrowia_lipolytica 3820 2765 1077
Zygosaccharomyces_bailii 3756 2662 900
Zygosaccharomyces_rouxii 3781 2650 906
yHAB132_Kazachstania_martiniae 3792 2636 1020
yHAB133_Kazachstania_unispora 3873 2662 1004
yHAB134_Kazachstania_turicensis 3831 2645 1040
yHAB136_Kazachstania_bromeliacearum 3649 2550 921
yHAB143_Kazachstania_siamensis 3758 2606 941
yHAB147_Kazachstania_taianensis 3767 2627 922
yHAB148_Kazachstania_intestinalis 3801 2615 918
yHAB153_Kazachstania_rosinii 3816 2628 977
yHAB154_Kazachstania_transvaalensis 3721 2598 856
yHAB155_Kazachstania_spencerorum 3684 2641 1071
yHAB158_Kazachstania_viticola 3795 2611 1002
yHAB159_Kazachstania_solicola 3827 2637 1005
yHAB160_Kazachstania_kunashirensis 3797 2630 979
yHAB164_Kazachstania_aerobia 3776 2623 936
yHAB166_Kazachstania_yakushimaensis 3769 2626 977
yHMPu5000026124_Ogataea_henricii 3821 2696 982
yHMPu5000026137_Ambrosiozyma_ambrosiae 3908 2675 1035
yHMPu5000026142_Citeromyces_matritensis 3870 2708 1162
yHMPu5000026145_Ambrosiozyma_vanderkliftii 3918 2703 1024
yHMPu5000026152_Torulaspora_franciscae 3754 2650 989
yHMPu5000026197_Brettanomyces_custersianus 3636 2582 901
yHMPu5000026256_Zygotorulaspora_mrakii 3824 2672 941
yHMPu5000026274_Komagataella_populi 3850 2662 885
yHMPu5000034594_Starmera_quercuum 3959 2736 1048
yHMPu5000034597_Candida_stellimalicola 3896 2697 975
yHMPu5000034604_Sporopachydermia_lactativora 3989 2770 994
yHMPu5000034605_Spencermartinsiella_europaea 3937 2818 1099
yHMPu5000034606_Priceomyces_medius 3881 2685 941
yHMPu5000034607_Saccharomycopsis_capsularis 3968 2737 1051
yHMPu5000034610_Saturnispora_hagleri 3499 2612 877
yHMPu5000034611_Saturnispora_mendoncae 3606 2625 853
yHMPu5000034612_Saturnispora_saitoi 3585 2599 874
yHMPu5000034613_Saturnispora_serradocipensis 3596 2564 862
yHMPu5000034614_Saturnispora_silvae 3666 2596 855
yHMPu5000034615_Saturnispora_zaruensis 3671 2634 893
yHMPu5000034622_Pichia_occidentalis 3845 2670 944
yHMPu5000034623_Pichia_norvegensis 3764 2641 884
yHMPu5000034624_Pichia_nakasei 3485 2594 805
yHMPu5000034625_Pichia_kudriavzevii 3625 2640 933
yHMPu5000034627_Pichia_heedii 3662 2592 895
yHMPu5000034629_Pichia_exigua 3685 2641 870
yHMPu5000034631_Martiniozyma_abiesophila 3757 2670 1167
yHMPu5000034632_Candida_athensensis 3609 2660 865
yHMPu5000034635_Nadsonia_fulvescens 3784 2747 1034
yHMPu5000034636_Ogataea_nitratoaversa 3880 2690 991
yHMPu5000034637_Ogataea_populiabae 3831 2708 980
yHMPu5000034643_Candida_schatavii 3841 2713 1002
yHMPu5000034646_Wickerhamiella_cacticola 3736 2701 940
yHMPu5000034648_Candida_restingae 3874 2708 967
yHMPu5000034654_Aciculoconidium_aculeatum 3931 2695 1051
yHMPu5000034655_Botryozyma_nematodophila 3750 2740 1048
yHMPu5000034660_Diddensiella_caesifluorescens 3918 2801 1098
yHMPu5000034661_Dipodascus_albidus 3982 2743 1115
yHMPu5000034665_Kodamaea_laetipori 3902 2679 1021
yHMPu5000034667_Blastobotrys_serpentis 3995 2801 1105
yHMPu5000034669_Blastobotrys_raffinofermentans 4040 2814 1134
yHMPu5000034670_Blastobotrys_proliferans 3943 2806 1120
yHMPu5000034671_Blastobotrys_peoriensis 4062 2839 1146
yHMPu5000034673_Blastobotrys_nivea 3960 2816 1225
yHMPu5000034674_Blastobotrys_muscicola 3883 2773 1024
yHMPu5000034675_Blastobotrys_mokoenaii 3931 2793 1043
yHMPu5000034681_Blastobotrys_americana 4032 2812 1045
yHMPu5000034709_Kluyveromyces_aestuarii 3898 2667 938
yHMPu5000034710_Kluyveromyces_dobzhanskii 3886 2683 952
yHMPu5000034742_Lipomyces_suomiensis 3875 2800 1049
yHMPu5000034748_Lipomyces_oligophaga 3735 2717 943
yHMPu5000034749_Lipomyces_mesembrius 3861 2762 1023
yHMPu5000034754_Lipomyces_arxii 3897 2782 1102
yHMPu5000034757_Lipomyces_doorenjongii 3778 2722 921
yHMPu5000034758_Lipomyces_japonicus 3768 2730 953
yHMPu5000034760_Lipomyces_kononenkoae 3874 2788 1077
yHMPu5000034761_Lipomyces_lipofer 3890 2792 1156
yHMPu5000034862_Zygotorulaspora_florentina 3789 2705 989
yHMPu5000034865_Zygosaccharomyces_kombuchaensis 3703 2654 882
yHMPu5000034866_Zygosaccharomyces_bisporus 3746 2644 919
yHMPu5000034875_Tetrapisispora_fleetii 3865 2635 963
yHMPu5000034876_Tetrapisispora_iriomotensis 3875 2637 1026
yHMPu5000034877_Tetrapisispora_namnaonensis 3876 2638 977
yHMPu5000034881_Torulaspora_pretoriensis 3897 2668 1114
yHMPu5000034883_Peterozyma_xylosa 3992 2751 1082
yHMPu5000034884_Peterozyma_toletana 3981 2743 1125
yHMPu5000034885_Ogataea_zsoltii 3889 2711 1016
yHMPu5000034886_Ogataea_trehalophila 3895 2694 969
yHMPu5000034887_Ogataea_trehaloabstinens 3900 2728 1052
yHMPu5000034890_Ogataea_ramenticola 3848 2716 1026
yHMPu5000034891_Ogataea_pini 3842 2715 977
yHMPu5000034892_Ogataea_pilisensis 3913 2689 1008
yHMPu5000034893_Ogataea_philodendra 3722 2591 870
yHMPu5000034897_Ogataea_glucozyma 3915 2713 1070
yHMPu5000034899_Ogataea_kodamae 3736 2641 843
yHMPu5000034901_Ogataea_methylivora 3928 2725 1108
yHMPu5000034902_Ogataea_minuta 3644 2614 840
yHMPu5000034903_Ogataea_naganishii 3918 2691 1000
yHMPu5000034904_Ogataea_nonfermentans 3835 2667 1048
yHMPu5000034918_Nakazawaea_holstii 3924 2714 1043
yHMPu5000034932_Kuraishia_ogatae 3966 2727 1024
yHMPu5000034933_Kuraishia_molischiana 3953 2731 1039
yHMPu5000034939_Komagataella_pseudopastoris 3712 2652 852
yHMPu5000034946_Ambrosiozyma_oregonensis 3910 2690 1092
yHMPu5000034947_Ambrosiozyma_philentoma 3923 2688 1205
yHMPu5000034950_Citeromyces_hawaiiensis 3857 2704 1069
yHMPu5000034952_Citeromyces_siamensis 3893 2731 1734
yHMPu5000034957_Hanseniaspora_osmophila 3691 2535 894
yHMPu5000034963_Hanseniaspora_clermontiae 3573 2464 770
yHMPu5000034967_Candida_freyschussii 3980 2749 1013
yHMPu5000034973_Danielozyma_ontarioensis 3936 2726 981
yHMPu5000034974_Deakozyma_indianensis 3878 2764 967
yHMPu5000034978_Cyberlindnera_mrakii 3916 2698 1053
yHMPu5000034979_Cyberlindnera_misumaiensis 3953 2730 1006
yHMPu5000034986_Candida_oregonensis 3934 2717 990
yHMPu5000034988_Candida_fructus 3869 2707 963
yHMPu5000034990_Candida_corydali 3728 2641 963
yHMPu5000034998_Cephaloascus_albidus 3968 2717 1084
yHMPu5000034999_Cephaloascus_fragrans 3974 2728 1040
yHMPu5000035011_Candida_pyralidae 3890 2684 921
yHMPu5000035018_Candida_canberraensis 3944 2710 1012
yHMPu5000035022_Candida_emberorum 3849 2692 960
yHMPu5000035031_Candida_kruisii 3835 2686 1051
yHMPu5000035032_Candida_gatunensis 3793 2686 909
yHMPu5000035033_Candida_cretensis 3887 2678 969
yHMPu5000035037_Candida_montana 3658 2731 1005
yHMPu5000035040_Ambrosiozyma_maleeae 3842 2676 950
yHMPu5000035041_Ambrosiozyma_pseudovanderkliftii 3924 2700 1016
yHMPu5000035044_Barnettozyma_californica 3971 2739 1060
yHMPu5000035045_Barnettozyma_hawaiiensis 3949 2732 976
yHMPu5000035046_Barnettozyma_populi 3951 2732 1011
yHMPu5000035047_Barnettozyma_pratensis 3981 2742 1038
yHMPu5000035048_Barnettozyma_salicaria 3826 2723 1010
yHMPu5000035242_Zygoascus_ofunaensis 3976 2780 1005
yHMPu5000035243_Zygoascus_meyerae 4004 2792 1000
yHMPu5000035244_Candida_incommunis 3895 2757 995
yHMPu5000035252_Yamadazyma_nakazawae 3798 2664 959
yHMPu5000035261_Candida_ponderosae 4014 2767 1133
yHMPu5000035268_Wickerhamomyces_hampshirensis 3996 2755 1091
yHMPu5000035271_Wickerhamomyces_bovis 3958 2722 1013
yHMPu5000035274_Wickerhamomyces_alni 3989 2735 1065
yHMPu5000035279_Tortispora_starmeri 3815 2697 891
yHMPu5000035282_Trigonopsis_vinaria 3946 2769 966
yHMPu5000035286_Candida_azyma 3997 2753 1074
yHMPu5000035296_Priceomyces_carsonii 3809 2716 1025
yHMPu5000035297_Priceomyces_castillae 3883 2708 923
yHMPu5000035301_Pichia_terricola 3759 2662 925
yHMPu5000035302_Candida_fragi 3832 2699 971
yHMPu5000035318_Hyphopichia_heimii 3815 2738 1053
yHMPu5000035325_Cyberlindnera_petersonii 3936 2736 1037
yHMPu5000035335_Candida_blattae 3938 2758 1077
yHMPu5000035629_Yueomyces_sinensis 3787 2613 923
yHMPu5000035633_Candida_hispaniensis 3768 2743 954
yHMPu5000035639_Wickerhamomyces_canadensis 3982 2736 1060
yHMPu5000035640_Yamadazyma_philogaea 3743 2663 900
yHMPu5000035641_Yamadazyma_scolyti 3608 2634 974
yHMPu5000035643_Yarrowia_bubula 3809 2762 1095
yHMPu5000035645_Yarrowia_divulgata 3820 2770 1104
yHMPu5000035650_Trigonopsis_variabilis 3956 2775 964
yHMPu5000035651_Torulaspora_microellipsoides 3965 2704 1046
yHMPu5000035652_Torulaspora_maleeae 3792 2634 858
yHMPu5000035654_Tortispora_ganteri 3737 2718 903
yHMPu5000035658_Starmera_amethionina 3865 2691 962
yHMPu5000035659_Saturnispora_dispora 3378 2598 823
yHMPu5000035662_Meyerozyma_caribbica 3764 2701 952
yHMPu5000035665_Middelhovenomyces_tepae 3979 2824 1104
yHMPu5000035667_Kurtzmaniella_cleridarum 3854 2715 969
yHMPu5000035670_Phaffomyces_opuntiae 3843 2711 1007
yHMPu5000035671_Phaffomyces_antillensis 3865 2720 996
yHMPu5000035672_Phaffomyces_thermotolerans 3797 2687 995
yHMPu5000035673_Candida_orba 3773 2667 980
yHMPu5000035674_Kregervanrija_delftensis 3781 2694 961
yHMPu5000035675_Kregervanrija_fluxuum 3811 2702 1012
yHMPu5000035677_Kodamaea_ohmeri 3935 2731 975
yHMPu5000035679_Candida_rhagii 3932 2748 1033
yHMPu5000035681_Candida_gotoi 3978 2747 1040
yHMPu5000035684_Kloeckera_hatyaiensis 3582 2465 785
yHMPu5000035686_Cyberlindnera_saturnus 3988 2737 1110
yHMPu5000035687_Cyberlindnera_suaveolens 3974 2732 1025
yHMPu5000035688_Cyberlindnera_xylosilytica 3990 2738 1134
yHMPu5000035689_Candida_mycetangii 3983 2749 1055
yHMPu5000035690_Candida_vartiovaarae 3986 2742 992
yHMPu5000035691_Candida_salmanticensis 3937 2798 1035
yHMPu5000035695_Hanseniaspora_pseudoguilliermondii 3559 2476 779
yHMPu5000035696_Hanseniaspora_singularis 3534 2460 786
yHMPu5000035699_Cyberlindnera_maclurae 3844 2668 980
yHMPu5000035703_Cyberlindnera_americana 3979 2746 1066
yHMPu5000035707_Candida_heveicola 3859 2711 965
yHMPu5000041678_Debaryomyces_prosopidis 3843 2719 1092
yHMPu5000041693_Debaryomyces_nepalensis 3956 2755 1022
yHMPu5000041713_Debaryomyces_maramus 3881 2736 997
yHMPu5000041743_Candida_hawaiiana 3811 2709 910
yHMPu5000041818_Magnusiomyces_tetrasperma 3873 2727 1285
yHMPu5000041822_Dipodascus_geniculatus 3893 2734 1091
yHMPu5000041824_Debaryomyces_subglobosus 3939 2735 1005
yHMPu5000041829_Debaryomyces_fabryi 3955 2746 1041
yHMPu5000041833_Candida_tammaniensis 3918 2718 1000
yHMPu5000041840_Candida_wancherniae 3791 2672 893
yHMPu5000041855_Candida_ascalaphidarum 3834 2709 925
yHMPu5000041862_Candida_golubevii 3771 2693 947
yHMPu5000041863_Candida_gorgasii 3834 2727 969

Installation

Required Software - User:

Required Software - Contributor:

Dependencies - Recommended Software:

Installation Instructions

  • For users: Clone it from master in the Github repo, or just download the latest release.
  • For contributors: Fork it to your Github account, and create a new branch from dev.

Model Files

The model is available in .xml, .txt. All model files can be found in: ModelFiles

Contributors