TABLE 5.

Comparison of 28S, ITS and 18S sequences extracted from whole genome sequencing (WGS) datasets (genome assembly accession numbers shown in Table 4) to sequences determined by Sanger sequencing available at NCBI GenBank database.

Powdery mildew species	Isolate/specimen ID	Sanger sequencing (GenBank accession numbers)a			WGS (Contigs/scaffolds containing nrDNA sequence fragments)b			Number of nucleotide position differencesc/alignment length
		28S	ITS	18S	28S	ITS	18S	28S	ITS	18S
Erysiphe quercicola (formerly Oidium heveae)	HO-73	KJ868175	KJ868176	KP171512	QVIK010007 45.1d	QVIK01007 960.1e	QVIK010012 08.1f	0/328	–	–
					and QVIK010012 08.1f		and QVIK010021 09.1g	–	–	–
					and QVIK010050 55.1h		and QVIK010112 55.1i	–	–	–
E. neolycopersici	UMSG2	n.a.	KX776199	KX776199	n.d.j	n.d.	n.d.	–	–	–
E. pulchra	TENN-F-071826	n.a.	MH766898	n.a.	n.d.	PEDP01005487.1k	n.d.	–	–	–
G. cichoracearum	UCSC1	n.a.	AF031282	AF031282	n.d.	n.d.	n.d.	–	–	–
	UMSG3	n.a.	KR611314	KR611314	n.d.	n.d.	n.d.	–	–	–
Leveillula taurica	HNHM-MYC-006405	OM906815	MT125856	OM906851	scaffold_175 59l	scaffold_04895m	scaffold_04895m	–	41/585	894/1,797
							and scaffold_17559l	–	–	–
Parauncinula polyspora	-	OM906816	OM906197	OM906852	NODE_26095n	NODE_26095n	NODE_26095n	3/813	0/566	0/423
Phyllactinia moricola	HMJAU-PM91933	MZ540403	MZ541088	n.a.	JAHY SQ010042711.1	JAHYSQ010042711.1	n.d.	0/721	0/563	–
Pleochaeta shiraiana	HAL3440 F	OM906817	MZ661116	OM906853	JAHY SP010014424.1	JAHYSP010014424.1	JAHYSP010014424.1	0/241	0/445	0/1,736
							and JAHYSP010004388.1o	–	–	32/427
Podosphaera leucotricha	PuE-3	n.a.	MT180425	n.a.	n.d.	n.d.	n.d.	–	–	–
Po. xanthii	2086	MK225554	n.a.	MK225523	JACSEY010000300.1	n.d.	JACSEY010000300.1	28/3,019	–	4/899

^an.a., not available.

^bThe nrDNA sequences obtained from NCBI GenBank database were used as BLAST queries to extract similar sequences from the corresponding genomes in Geneious Prime using Megablast. Contigs/scaffolds were only reported to contain nrDNA sequence fragments if they had a query coverage of 100% or BLAST hit length of at least 300 bp.

^cNumber of nucleotide positions with variable characters, i.e., positions with single nucleotide polymorphisms or indels, between nrDNA sequences from WGS versus Sanger sequencing. This information is provided only when the detected contig was identified as nrDNA fragments belonging to powdery mildew species. Dashes (‘–’) indicate that comparisons were meaningless, due to lack of data or because the nrDNA sequences did not come from the respective powdery mildew isolate.

^dA 328 bp sequence extracted from this contig was identical to the 28S sequence of Oidium heveae (E. quercicola) (KJ868175).

^eA 369 bp fragment from this contig was identical to the ITS region of Curvularia spp.

^fTwo fragments of 666 bp and 353 bp from this contig were highly similar (>98%) and identical to 28S and 18S sequences of multiple plant species.

^gA 500 bp fragment from this contig showed high similarity (>99%) to species belonging to the class Arachnida.

^hA 490 bp fragment from this contig showed high similarity (99.8%) to Cladosporium spp.

ⁱThis contig is 320 bp and identical to 18S sequence of multiple Cladosporium spp.

^jn.d., not detected; the sequence of the corresponding region was not detected in the published genome.

^kA 611 bp fragment from this contig is identical to the ITS sequence of multiple Cladosporium spp.

^lTwo 786 bp and 1,747 bp fragments from this contig were identical and highly similar (99.7%) to 28S and 18S sequences of multiple Penicillium spp.

^mThis contig harbored 18S and ITS sequences with similarity to Leveillula spp., however, large areas of dissimilarity were also identified (Figure 3).

ⁿThe Parauncinula polyspora contig NODE_26095, which harbors the nrDNA region (Frantzeskakis et al., 2019a), was missing from the genome that was retrieved from ENA and was obtained from Lamprinos Frantzeskakis (personal communication).

^oThis contig also included a partial 18S sequence with only 94% similarity to the 18S sequence of Pleochaeta shiraiana HAL3440 F.