Alternaria alternata
Alternaria abutilonis
Alternaria arborescens
Alternaria astragali
Alternaria azukiae
Alternaria bokurai
Alternaria brassicae
Alternaria citri
Alternaria compacta
Alternaria destruens
Alternaria gaisen
Alternaria lini
Alternaria longipes
Alternaria mali
Alternaria pomicola
Alternaria solani
Alternaria tenuis
Alternaria tenuissima
Aspergillus fumigatus
Bionectria ochroleuca
Cladosporium funiculosum
Cladosporium uredinicola
Cladosporium vignae
Colletotrichum gloeosporioides
Coniothyrium concentricum
Macrophomina phaseolina
Pleurotus ostreatus
Septoria lycopersici
Stagonosporopsis cucurbitacearum
Fraction of sequence
Yamamoto et al., Identification accuracy and diversity reproducibility
associated with ITS-based fungal taxonomic library preparation
(2.1%)
(0.1%)
(0.1%)
(0.1%)
(96.7%)
(0.1%)
(0.3%)
(0.1%)
(0.1%)
(0.1%)
BLASTn output
Fig. S1. Fractions of Alternaria alternata sequences by types of taxonomic placements. The
full-length ITS sequences were used for BLSATn. The categories labeled Aa1 through Aa10
each correspond to a fraction of the total Alternaria alternata sequences and the taxa that
represent top BLASTn hit(s) to this fraction are listed in the adjacent map. Nearly all (99.6%)
of the sequences were assigned to A. alternata either solely or ambiguously (Aa1-Aa6). At the
genus rank, 99.9% of the sequences were assigned correctly (Aa1-Aa8). The truly identified
sequences that were assigned solely to A. alternata constitute 2.1% of the sequences (Aa1).
S1
Fraction of sequence
Aspergillus fumigatus
Aspergillus arvii
Aspergillus fumigatiaffinis
Aspergillus fumisynnematus
Aspergillus lentulus
Aspergillus novofumigatus
Aspergillus ochraceus
Aspergillus ustus
Aspergillus viridinutans
Emericella quadrilineata
Neosartorya coreana
Neosartorya fischeri
Penicillium griseofulvum
Yamamoto et al., Identification accuracy and diversity reproducibility
associated with ITS-based fungal taxonomic library preparation
(30.9%)
(11.9%)
(12.3%)
(1.7%)
(15.0%)
(4.2%)
(0.2%)
(0.2%)
(0.2%)
(0.2%)
(2.3%)
(0.8%)
(1.0%)
(1.5%)
(0.8%)
(5.2%)
(0.2%)
(5.8%)
(5.8%)
BLASTn output
Fig. S2. Fractions of Aspergillus fumigatus sequences by types of taxonomic placements. The
full-length ITS sequences were used for BLASTn. The categories labeled Af1 through Af19
each correspond to a fraction of the total Aspergillus fumigatus sequences and the taxa that
represent top BLASTn hit(s) to this fraction are listed in the adjacent map. 76.6% of the
sequences were assigned to A. fumigatus either solely or ambiguously (Af1-Af9). At the
genus rank, 99.8% of the sequences were assigned correctly either to Aspergillus or
Neosartorya (Af1-Af16, Af18 and Af19). The truly identified sequences that were assigned
solely to A. fumigatus constitute 30.9% of the sequences (Af1).
S2
Cladosporium cladosporioides
Cladophialophora minourae
Cladosporium acalyphae
Cladosporium angustisporum
Cladosporium antarcticum
Cladosporium asperulatum
Cladosporium australiense
Cladosporium basiinflatum
Cladosporium bruhnei
Cladosporium chalastosporoides
Cladosporium chubutense
Cladosporium colocasiae
Cladosporium coralloides
Cladosporium cucumerinum
Cladosporium delicatulum
Cladosporium exasperatum
Cladosporium exile
Cladosporium flabelliforme
Cladosporium funiculosum
Cladosporium gamsianum
Cladosporium globisporum
Cladosporium gossypiicola
Cladosporium herbaroides
Cladosporium hillianum
Cladosporium inversicolor
Cladosporium iranicum
Cladosporium laxicapitulatum
Cladosporium licheniphilum
Cladosporium lycoperdinum
Cladosporium macrocarpum
Cladosporium magnusianum
Cladosporium myrtacearum
Cladosporium ossifragi
Cladosporium oxysporum
Cladosporium paracladosporioides
Cladosporium perangustum
Cladosporium phyllactiniicola
Cladosporium phyllophilum
Cladosporium piniponderosae
Cladosporium pseudocladosporioides
Cladosporium ramotenellum
Cladosporium rectoides
Cladosporium scabrellum
Cladosporium sinuosum
Cladosporium sphaerospermum
Cladosporium spinulosum
Cladosporium subinflatum
Cladosporium subtilissimum
Cladosporium subuliforme
Cladosporium tenellum
Cladosporium tenuissimum
Cladosporium variabile
Cladosporium varians
Cladosporium velox
Cladosporium verrucocladosporioides
Cladosporium vignae
Cladosporium xylophilum
Davidiella dianthi
Davidiella macrospora
Davidiella tassiana
Glomerella cingulata
Passalora robiniae
Phacellium veronicae
Pleurotus ostreatus
Ramularia didyma
Sphaerulina polyspora
Fraction of sequence
Yamamoto et al., Identification accuracy and diversity reproducibility
associated with ITS-based fungal taxonomic library preparation
(0.3%)
(0.1%)
(0.0%)
(0.0%)
(98.8%)
(0.0%)
(0.7%)
(0.0%)
(0.0%)
BLASTn output
Fig. S3. Fractions of Cladosporium cladosporioides sequences by types of taxonomic placements. The full-length ITS sequences were used for
BLASTn. The categories labeled Cc1 through Cc9 each correspond to a fraction of the total Cladosporium cladosporioides sequences and the
taxa that represent top BLASTn hit(s) to this fraction are listed in the adjacent map. 99.2% of the sequences were assigned to C. cladosporioides
either solely or ambiguously (Cc1-Cc6). At the genus rank, 99.9% of the sequences were assigned correctly (Cc1-Cc7). The truly identified
sequences that were assigned solely to C. cladosporioides constitute 0.3% of the sequences (Cc1). 98.8% of the sequences were ambiguous with
Cladosporium cucumerinum (Cc5).
S3
Epicoccum nigrum
Pycnopeziza sympodialis
Dacryopinax spathularia
Guepinia spathularia
Fraction of sequence
Yamamoto et al., Identification accuracy and diversity reproducibility
associated with ITS-based fungal taxonomic library preparation
(99.9%)
(0.0%)
(0.0%)
BLASTn output
Fig. S4. Fractions of Epicoccum nigrum sequences by types of taxonomic placements. The
full-length ITS sequences were used for BLASTn. The categories labeled En1 through En3
each correspond to a fraction of the total Epicoccum nigrum sequences and the taxa that
represent top BLASTn hit(s) to this fraction are listed in the adjacent map. The truly identified
sequences that were assigned solely to E. nigrum constitute 99.9% of the sequences (En1).
S4
Fraction of sequence
Penicillium chrysogenum
Botryosphaeria dothidea
Cryptococcus chernovii
Cryptococcus stepposus
Eupenicillium baarnense
Eupenicillium crustaceum
Eupenicillium egyptiacum
Eupenicillium molle
Filobasidium globisporum
Hypocrea lixii
Paecilomyces variotii
Penicillium aethiopicum
Penicillium allii
Penicillium atramentosum
Penicillium aurantiogriseum
Penicillium brevistipitatum
Penicillium camemberti
Penicillium citrinum
Penicillium clavigerum
Penicillium commune
Penicillium concentricum
Penicillium coprobium
Penicillium coprophilum
Penicillium crustosum
Penicillium dipodomyicola
Penicillium dipodomyis
Penicillium echinulatum
Penicillium expansum
Penicillium gladioli
Penicillium glandicola
Penicillium granulatum
Penicillium griseofulvum
Penicillium griseoroseum
Penicillium hirsutum
Penicillium janthinellum
Penicillium lanosum
Penicillium nalgiovense
Penicillium oxalicum
Penicillium sclerotigenum
Penicillium solitum
Penicillium turbatum
Penicillium urticae
Penicillium venetum
Penicillium verrucosum
Penicillium vinaceum
Penicillium viridicatum
Penicillium vulpinum
Scopulariopsis brevicaulis
Talaromyces leycettanus
Yamamoto et al., Identification accuracy and diversity reproducibility
associated with ITS-based fungal taxonomic library preparation
(8.2%)
(0.2%)
(0.4%)
(0.3%)
(1.7%)
(0.5%)
(2.7%)
(0.3%)
(1.2%)
(0.2%)
(9.7%)
(0.2%)
(0.4%)
(0.1%)
(14.0%)
(14.3%)
(0.9%)
(0.5%)
(0.1%)
(0.1%)
(5.8%)
(0.5%)
(21.2%)
(0.1%)
(0.9%)
(9.8%)
(0.2%)
(1.4%)
(0.1%)
(0.1%)
(0.2%)
(0.3%)
(0.1%)
(0.4%)
(0.1%)
(0.2%)
(0.3%)
(0.1%)
(0.1%)
(0.1%)
(0.1%)
(0.1%)
(0.1%)
(0.1%)
(0.2%)
(0.1%)
(1.2%)
(0.4%)
BLASTn output
Fig. S5. Fractions of Penicillium chrysogenum sequences by types of taxonomic placements.
The full-length ITS sequences were used for BLASTn. The categories labeled Pc1 through
Pc48 each correspond to a fraction of the total Penicillium chrysogenum sequences and the
taxa that represent top BLASTn hit(s) to this fraction are listed in the adjacent map. 95.8% of
the sequences were assigned to P. chrysogenum either solely or ambiguously (Pc1-Pc29). At
the genus rank, 99.8% of the sequences were assigned correctly to either Penicillium or
Eupenicillium (Pc1-Pc29, Pc31-Pc45, Pc47 and Pc48). The truly identified sequences that
were assigned solely to P. chrysogenum constitute 8.2% of the sequences (Pc1).
S5
Yamamoto et al., Identification accuracy and diversity reproducibility
associated with ITS-based fungal taxonomic library preparation
Table S1. Summary statistics of fungal ITS sequences obtained with ITS1F and ITS4 primers
by 454 pyrosequencing.
Length of sequences (bp)
Number of
Sample
sequences
50th percentile
90th percentile
Standard
A. alternata
1778
491
497
A. fumigatus
521
514
538
C. cladosporioides
3025
533
545
E. nigrum
2070
496
510
P. chrysogenum
1058
535
557
Total
8452
501
543
Environmental sample
N0
N0 dup
N1
N1 dup
N2
N2 dup
N3
N3 dup
N4
N4 dup
Total
875
671
749
467
501
498
777
354
311
410
5613
488
492
488
472
479
470
443
407
467
449
472
519
513
538
525
521
532
505
503
505
504
518
Total
14065
492
543
S6
Yamamoto et al., Identification accuracy and diversity reproducibility
associated with ITS-based fungal taxonomic library preparation
Table S2. Diversity parameters for sampled atmospheric fungi based on 97% OTU similarity without normalizing the number of sequence reads
among the libraries.
Sample
Number of observed OTUs
Chao1
Shannon index
Dup 1
Dup 2
%RSD
Dup 1
Dup 2
%RSD
Dup 1
Dup 2
%RSD
N0
256
179
5157
1307
5.2
4.5
25.0
84.2
10.2
N1
359
222
3320
3357
6.8
6.2
33.3
0.8
6.5
N2
280
288
1650
2999
7.4
7.3
2.0
41.0
1.0
N3
545
249
3579
1989
8.7
7.8
52.7
40.4
7.7
N4
195
316
1010
1818
7.4
8.2
33.5
40.4
7.3
S7
Yamamoto et al., Identification accuracy and diversity reproducibility
associated with ITS-based fungal taxonomic library preparation
Table S3. Diversity parameters for sampled atmospheric fungi based on 97% OTU similarity with normalizing the number of sequences to 250
reads for each library.
Sample
Number of observed OTUs
Chao1
Shannon index
Dup 1
Dup 2
%RSD
Dup 1
Dup 2
%RSD
Dup 1
Dup 2
%RSD
N0
97
92
3.7
863
756
9.3
4.6
4.2
6.8
N1
150
143
3.4
2068
2404
10.6
6.1
5.8
3.2
N2
178
185
2.7
1042
2023
45.3
6.9
6.8
1.3
N3
215
221
1.9
2778
2912
3.3
7.5
7.6
1.2
N4
191
228
12.5
968
1932
47.0
7.3
7.8
4.2
S8
Yamamoto et al., Identification accuracy and diversity reproducibility
associated with ITS-based fungal taxonomic library preparation
Table S4. Number of fungal taxa identified by 454 pyrosequencing.
Number of sequences determined to each taxonomic level (no. of taxa identified)
Number of
Sample
sequences
Class a
Order a
Genus
Species
N0
875
840 (10)
712 (27)
661 (100)
522 (127)
N0 dup
671
651 (12)
542 (30)
517 (99)
451 (123)
N1
749
703 (10)
655 (32)
587 (142)
465 (201)
N1 dup
467
449 (11)
409 (27)
356 (112)
281 (133)
N2
501
485 (10)
475 (28)
439 (121)
384 (168)
N2 dup
498
484 (8)
464 (23)
415 (114)
338 (151)
N3
777
762 (11)
751 (26)
729 (124)
627 (180)
N3 dup
354
348 (8)
340 (20)
326 (86)
292 (114)
N4
311
309 (7)
299 (15)
294 (56)
280 (64)
N4 dup
410
407 (8)
397 (17)
389 (66)
358 (79)
Total
5613
5438 (16)
5044 (54)
4713 (371)
3998 (642)
a
Fungi that are categorized as incertae sedis at these taxonomic levels are excluded from counting the numbers of identified taxa.
S9