Table 1.
List of rRNA genes used in phylogenetic analysis.
| Taxon | Isolate number | GenBank accession no. |
Cumulative length (%) | ||
|---|---|---|---|---|---|
| 18S | 5.8S | 28S | |||
| Outgroup: aphelids and rozellids | |||||
| Amoeboaphelidium protococcarum | CALU X-5 | JX507298 | JX507298 | JX507298 | 99 |
| Rozella allomycis | UCB 47-054 (AFTOL-ID 297) | AY635838 | AY997087 | DQ273803 | 99 |
| Rozella sp. | JEL347 (AFTOL-ID 16) | AY601707 | AY997086 | DQ273766 | 98 |
| Blastocladiomycota | |||||
| Blastocladiella emersonii | M54937 | AY997032 | X90411 | 98 | |
| Allomyces arbuscula | AFTOL-ID 300 | AY552524 | AY997028 | AY552525 | 98 |
| Physoderma maydis | AFTOL-ID 19 | AY601708 | AY997072 | DQ273768 | 96 |
| Neocallimastigomycota | |||||
| Neocallimastix sp. | GE13 (AFTOL-ID 638) | DQ322625 | AY997064 | DQ273822 | 97 |
| Orpinomyces sp. | OUS1 | AJ864616, AJ864475 | AJ864475 | AJ864475 | 98 |
| Cyllamyces aberensis | EO14 (AFTOL-ID 846) | DQ536481 | AY997042 | DQ273829 | 100 |
| D3 | uncultured | EU910609 | 36 | ||
| Monoblepharidomycetes | |||||
| Monoblepharella mexicana | BK 78-1 (AFTOL-ID 33) | AF164337 | AY997061 | DQ273777 | 98 |
| Gonapodya prolifera | JEL478 | JGI v. 1.0 | JGI v. 1.0 | JGI v. 1.0 | 100 |
| Oedogoniomyces sp. | CR84 (AFTOL-ID 298) | AY635839 | AY997066 | DQ273804 | 99 |
| Hyaloraphidium curvatum | SAG 235-1 (AFTOL-ID 26) | Y17504 | AY997055 | DQ273771 | 91 |
| PFE7AU2004 | uncultured | DQ244008 | 36 | ||
| L73_ML_156 | uncultured | FJ354068 | 22 | ||
| Elev_18S_563 | uncultured | EF024210 | 36 | ||
| Gromochytriales, ord. nov. | |||||
| Gromochytrium mamkaevae | CALU X-51 | KF586842 | KF586842 | KF586842 | 99 |
| kor_110904_17 | uncultured | FJ157331 | 33 | ||
| IIN1-34 | uncultured | EU516964 | EU516964 | 15 | |
| Mesochytriales, ord. nov. | |||||
| Mesochytrium penetrans | CALU X-10 | FJ804149 | FJ804153 | 37 | |
| WS 10-E02 | uncultured | AJ867629 | 34 | ||
| WS 10-E14 | uncultured | AJ867630 | 36 | ||
| WS 10-E15 | uncultured | AJ867631 | 36 | ||
| Spring_08 | uncultured | JX069031 | 11 | ||
| Spring_37 | uncultured | JX069054 | 11 | ||
| Spring_57 | uncultured | JX069067 | 11 | ||
| Spring_71 | uncultured | JX069077 | 11 | ||
| T2P1AeB05 | uncultured | GQ995415 | 36 | ||
| T2P1AeF04 | uncultured | GQ995412 | 36 | ||
| T3P1AeC03 | uncultured | GQ995413 | 36 | ||
| T5P2AeC07 | uncultured | GQ995414 | 36 | ||
| SAPA5_E7 | uncultured | FJ483310 | 15 | ||
| P60E-9 | uncultured | DQ104060 | 13 | ||
| P60E-29 | uncultured | DQ104068 | 14 | ||
| Clones from a lake in China | uncultured | JX426910, JX426918, JX426923, JX426937, JX426998, JX427002, JX427011 | 7 | ||
| Clones from Lake Bourget (BI74, B1, B43, B44, B46-138, B49, B52, B56, BI78, BI88, BI100, BI104, BI107, BI121, BI123, BI15, BI72, BI76, B86-161, BI5) | uncultured | EF196711, EF196713, EF196728, EF196729, EF196731, EF196734, EF196735, EF196738, EF196745, EF196749, EF196751, EF196753, EF196755, EF196762, EF196763, EF196765, EF196775, EF196776, EF196786, EF196799 | 20 | ||
| PFF5SP2005 | uncultured | EU162641 | 36 | ||
| PFD6SP2005 | uncultured | EU162637 3’-end | 30 | ||
| PFA12SP2005 | uncultured | EU162643 | 36 | ||
| Pa2007C10 | uncultured | JQ689425 | 35 | ||
| F08_SE1B | uncultured | FJ592495 3’-end | 17 | ||
| ThJAR2B-48 | uncultured | JF972676 | 33 | ||
| 528-O25 | uncultured | EF586095 | 17 | ||
| GA069 | uncultured | HM486988 | 28 | ||
| GF29312 | uncultured | JX417945 | 16 | ||
| PFG9SP2005 | uncultured | EU162638 | 36 | ||
| PA2009C3 | uncultured | HQ191369 | HQ191369 | 40 | |
| PA2009B6 | uncultured | HQ191400 | HQ191400 | 40 | |
| PA2009D8 | uncultured | HQ191406 | HQ191406 | 40 | |
| PA2009E7 | uncultured | HQ191286 | HQ191286 | 40 | |
| Va2007BB6 | uncultured | JQ689445 | 35 | ||
| FV23_1H5 | uncultured | DQ310332 | 29 | ||
| Order Lobulomycetales | |||||
| Lobulomyces angularis | JEL45 (AFTOL-ID 630) | AF164253 | AY997036 | DQ273815 | 100 |
| Lobulomyces angularis | PL70 | EF443138 | EU352774 | EF443143 | 53 |
| Gen. sp. | AF011 | EF432819 | EF432819 | EF432819 | 57 |
| Maunachytrium keaense | AF021 | EF432822 | EF432822 | EF432822 | 54 |
| CCW64 | uncultured | AY180029 | 35 | ||
| RSC-CHU-20 | uncultured | AJ506002 | 32 | ||
| D2P03D7 | uncultured | EF100268 | 29 | ||
| AY2009B4 | uncultured | HQ219419 | HQ219419 | 40 | |
| IIS1-20 | uncultured | EU517013 | EU517013 | 14 | |
| Family Synchytriaceae | |||||
| Synchytrium decipiens | AFTOL-ID 634 | DQ536475 | AY997094 | DQ273819 | 91 |
| Synchytrium macrosporum | DUH0009363 (AFTOL-ID 635) | DQ322623 | AY997095 | DQ273820 | 99 |
| Synchytrium endobioticum | P-58 and Sluknov | AJ784274, AY854021 | 36 | ||
| Synchytrium endobioticum | AS-1 | JF795580 | JF795579 | 16 | |
| OTU97-188 | uncultured | JQ310927 | 11 | ||
| OTU97-621 | uncultured | JQ311409 | 11 | ||
| Order Polychytriales | |||||
| Polychytrium aggregatum | JEL109 (AFTOL-ID 24) | AY601711 | AY997074 | AY546686 | 100 |
| Lacustromyces hiemalis | JEL31 | AH009039 | HQ901700 | 49 | |
| Arkaya lepida | JEL93 (AFTOL-ID 629) | AF164278 | AY997056 | DQ273814 | 100 |
| Neokarlingia chitinophila | JEL510 | HQ901766 | HQ901703 | 52 | |
| Karlingiomyces asterocystis | JEL572 | HQ901769 | HQ901708 | 52 | |
| Order Cladochytriales | |||||
| Cladochytrium replicatum | JEL180 (AFTOL-ID 27) | AY546683 | AY997037 | AY546688 | 98 |
| Endochytrium sp. | JEL325 | AY349046 | AY349081 | 33 | |
| Allochytridium luteum | JEL324 (AFTOL-ID 631) | AY635844 | AY997044 | DQ273816 | 97 |
| Nephrochytrium sp. | JEL125 | AH009049 | EU828511 | 41 | |
| Diplochytridium lagenarium | JEL72 | AH009044 | AY349109 | AY349083 | 50 |
| Nowakowskiella sp. | JEL127 (AFTOL-ID 146) | AY635835 | AY997065 | DQ273798 | 98 |
| Order Chytridiales | |||||
| Podochytrium dentatum | JEL30 (AFTOL-ID 1539) | AH009055 | DQ53650 | DQ273838 | 95 |
| Chytriomyces sp. | JEL378 (AFTOL-ID 1532) | DQ536483 | DQ273832 | 73 | |
| Rhizoclosmatium sp. | JEL347-h (AFTOL-ID 20) | AY601709 | AY997076 | DQ273769 | 98 |
| Chytriomyces spinosus | JEL59 (AFTOL-ID 1540) | AH009063 | DQ273839 | 86 | |
| Chytridiales sp. | JEL187 (AFTOL-ID 39) | AY635825 | AY997035 | DQ273783 | 98 |
| Chytriomyces sp. | WB235A (AFTOL-ID 1536) | DQ536486 | DQ536498 | DQ536493 | 98 |
| Chytriomyces hyalinus | AFTOL-ID 1537 | DQ536487 | DQ536499 | DQ273836 | 98 |
| Chytriomyces sp. | JEL341 (AFTOL-ID 1531) | DQ536482 | DQ273831 | 92 | |
| Rhizidium endosporangiatum | JEL221 (AFTOL-ID 1534) | DQ536484 | DQ536496 | DQ273834 | 100 |
| «Rhizophydium» sp. | JEL354 (AFTOL-ID 41) | AY635827 | AY997083 | DQ273785 | 100 |
| Phlyctochytrium planicorne | JEL47 (AFTOL-ID 628) | DQ536473 | AY997070 | DQ273813 | 99 |
| Order Spizellomycetales | |||||
| Spizellomyces punctatus | ATCC 48900 (AFTOL-ID 182) | AY546684 | AY997092 | AY546692 | 92 |
| Powellomyces sp. | JEL95 (AFTOL-ID 32) | AF164245 | AY997075 | DQ273776 | 98 |
| Triparticalcar arcticum | AFTOL-ID 696 | DQ536480 | AY997096 | DQ273826 | 100 |
| Gaertneriomyces semiglobiferus | BK91-10 | AF164247 | |||
| Gaertneriomyces semiglobiferus | AFTOL-ID 34 | AY997051 | DQ273778 | 99 | |
| Order Rhizophlyctidales | |||||
| Rhizophlyctis rosea | JEL 318 (AFTOL-ID 43) | AY635829 | AY997078 | DQ273787. | 99 |
| Catenomyces sp. | JEL342 (AFTOL-ID 47) | AY635830 | AY997033 | DQ273789 | 99 |
| Blyttiomyces helicus | AFTOL-ID 2006 | DQ536491 | 34 | ||
| P34.43 | uncultured | AY642701 | 36 | ||
| Order Rhizophydiales | |||||
| ‘Rhizophlyctis’ harderi | JEL171 (AFTOL-ID 31) | AF164272 | AY997077 | DQ273775 | 98 |
| Rhizophydium sp. | JEL316 (AFTOL-ID 1535) | DQ536485 | DQ536497 | DQ273835 | 99 |
| Rhizophydium sp. | JEL317 (AFTOL-ID 35) | AY635821 | AY997081 | DQ273779 | 98 |
| Rhizophydium brooksianum | JEL136 (AFTOL-ID 22) | AY601710 | AY997079 | DQ273770 | 99 |
| Boothiomyces macrosporum | PL AUS 21 (AFTOL-ID 689) | DQ322622 | AY997084 | DQ273823 | 99 |
| Kappamyces laurelensis | AFTOL-ID 690 | DQ536478 | DQ536494 | DQ273824 | 99 |
| Rhizophydium sphaerotheca | AFTOL-ID 37 | AY635823 | AY997082 | DQ273781 | 97 |
| Rhizophydium sp. | JEL151 (AFTOL-ID 30) | AF164270 | AY997080 | DQ273774 | 96 |
| Entophlyctis sp. | JEL174 (AFTOL-ID 38) | AY635824 | AY997049 | DQ273782 | 93 |
| Entophlyctis sp. DU-DC1 | DU-DC1 | AF164255 | 20 | ||
| Entophlyctis helioformis | JEL326 (AFTOL-ID 40) | AY635826 | AY997048 | DQ273784 | 97 |
| Homoloaphlyctis polyrhiza | JEL142 | AFSM01005055 | AFSM01005055 | AFSM01005055 | 99 |
| Batrachochytrium dendrobatidis | AAHL-97-845 | AF051932 | |||
| Batrachochytrium dendrobatidis | JEL197 (AFTOL-ID 21) | AY997031 | AY546693 | 96 | |
| incertae sedis | |||||
| 18s1-47 | uncultured | EU733554 | 21 | ||
| 18s3 24 | uncultured | EU733608 | 21 | ||
| LLSG10_1 PML-2011t | uncultured | JN049552 | 13 | ||