TABLE 4.
List of powdery mildew specimens included in the genome-scale and nuclear ribosomal (nrDNA) phylogenetic analyses.
| Powdery mildew species | Isolate/specimen ID | GenBank assembly accession | Databasea | nrDNA accession no. |
||
| 28S | 5.8S | 18S | ||||
| Blumeria hordei (formerly B. graminis f. sp. hordei) | DH14 | GCA_900239735.1 | NCBI | OENG01000016.1 b | OENG01000016.1 b | OENG01000016.1 b |
| RACE1 | GCA_900237765.1 | NCBI | UNSH01000070.1 c | UNSH01000070.1 c | UNSH01000070.1 c | |
| B. graminis f. sp. triticale | THUN-12 | GCA_905067625.1 | NCBI | CAJHIT010000009.1 d | CAJHIT010000009.1 d | CAJHIT010000009.1 d |
| B. graminis f. sp. tritici | 70 | GCA_000441875.1 | NCBI | ASJN01035784.1 | ASJN01035784.1 | ASJN01035784.1 |
| 96224 | GCA_900519115.1 | NCBI | LR026992.1 e | LR026992.1 e | LR026992.1 e | |
| Erysiphe alphitoides | MS_42D | – | –f | Contig 84 | Contig 84 | Contig 84 |
| E. necator | C | GCA_000798715.1 | NCBI | JNVN01000032 h | JNVN01000032 h | JNVN01000032 h |
| e1-101 | GCA_000798795.1 | NCBI | JOKO01000133 | JOKO01000133 | JOKO01000133 | |
| Lodi | GCA_000798775.1 | NCBI | JNUU01000055 | JNUU01000055 | JNUU01000055 | |
| E. neolycopersici (formerly Oidium neolycopersici) | UMSG2 | GCA_003610855.1 | NCBI | n.d.i | KX776199 | KX776199 |
| E. pisi | Palampur-1 | – | JGI | scaffold_125 j | scaffold_125 j | scaffold_125 j |
| E. pulchra | TENN-F-071826 | GCA_002918395.1 | NCBI | PEDP01018202.1 k | MH766898 | n.d.i |
| E. quercicola (formerly Oidium heveae) | HO-73 | GCA_003957845.1 | NCBI | KJ868175 g | KJ868176 g | KP171512 g |
| Golovinomyces cichoracearum | UCSC1 | GCA_003611215.1 | NCBI | n.d.i | AF031282 | AF031282 |
| UMSG3 | GCA_003611195.1 | NCBI | n.d.i | KR611314 | KR611314 | |
| G. magnicellulatus | FPH2017-1 | GCA_006912115.1 | NCBI | n.d.i,l | n.d.i,l | n.d.i,l |
| Leveillula taurica | HNHM-MYC-006405 | PRJEB36538 | ENA | OM906815* | MT125856 | OM906851* |
| Parauncinula polyspora | – | PRJEB29715 | ENA | OM906816* | OM906197* | OM906852* |
| Phyllactinia moricola | HMJAU-PM91933 | GCA_019455665.1 | NCBI | MZ540403 | MZ541088 | JAHYSQ010042711.1 m |
| Pleochaeta shiraiana | HAL3440 F | GCA_019455505.1 | NCBI | OM906817* | MZ661116 | OM906853* |
| Podosphaera cerasi | MH | GCA_018398735.1 | NCBI | JAGTUB010000840.1 n | JAGTUB010000840.1 n | JAGTUB010000840.1 n |
| Po. leucotricha | PuE-3 | GCA_013170925.1 | NCBI | n.d.i | MT180425 | n.d.i |
| Po. xanthii | 2086 | GCA_014884795.1 | NCBI | MK225554 | JACSEY010000300 | MK225523 |
| Wanju2017 | GCA_010015925.1 | NCBI | JAAAXZ010001060 | JAAAXZ010001060 | JAAAXZ010001060 | |
If available as a result of Sanger sequencing, 28S, 5.8S and 18S nrDNA sequences were obtained from the NCBI GenBank nucleotide database (accession numbers shown in bold). Some loci were determined by Sanger sequencing in this work (indicated by asterisk, *). If nrDNA sequences of some specimens were not available in the nucleotide database of GenBank, and could not be determined in this study, sequences of the corresponding regions were extracted from the published genomes (contig/scaffold numbers harboring the respective nrDNA regions underlined).
aENA, European Nucleotide Archive; JGI, Joint Genome Institute; and NCBI, National Centre for Biotechnology Information.
bIdentical copies of nrDNA sequences were also detected in contig OENG01000318.1.
cIdentical copies of nrDNA sequences were also detected in contigs UNSH01000068.1 and UNSH01000069.1.
dIdentical copies of nrDNA sequences were also detected in contigs CAJHIT010000019.1, CAJHIT010000020.1, CAJHIT010000022.1, CAJHIT010000023.1, CAJHIT010000025.1, and CAJHIT010000030.1.
eIdentical copies of nrDNA sequences were also detected in contig LR026995.1.
fGenome of Erysiphe alphitoides specimen MS-42D is available from http://arachne.pierroton.inra.fr/AlphiGeno/.
gContigs QVIK01005055.1, QVIK01001208.1, QVIK01002109.1, and QVIK01007960.1 in the E. quercicola genome included nrDNA sequences, which were not included in the nrDNA analysis, as these were identical or highly similar to multiple other fungi and plant species.
hnrDNA sequences extracted from this contig showed high similarity to those of Erysiphe species, however, the 5.8S sequence was only partial, with 45 bp missing in the middle. Additional nrDNA sequences were detected in Contig JNVN01005878.1 in E. necator genome (GCA_000798715.1), which were identical to the nrDNA sequences of multiple Penicillium spp.
in.d., not detected; the sequence of the corresponding region was not found in NCBI GenBank database or the published genome.
jScaffold_34 also includes copies of nrDNA sequences that are identical or highly similar to those in Scaffold_125.
kThis contig showed high similarity to 28S sequence of Erysiphe pulchra reference sequences on GenBank. Additional nrDNA sequences were detected in Contig PEDP01005487.1, which were identical to the nrDNA sequences of Cladosporium spp. Also, contig PEDP01002611.1 harbors partial 18S (609 bp) and 28S (1,291 bp) sequences identical and highly similar (99.8%) to those of Neohydatothrips annulipes.
lContigs VCMJ01009734 and VCMJ01035023 in G. magnicellulatus genome harbor nrDNA sequences, which were not included in the analysis, as these showed high similarity to nrDNA sequences from Pseudozyma, Moesziomyces, and Acremonium spp.
mThis contig included a very small fragment of 18S sequence (135 bp).
nContig JAGTUB010000459.1 in Po. cerasi genome harbored nrDNA sequences identical to Aureobasidium pullulans and other ascomycetes.