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. 2026 Jun 12;191(4):59. doi: 10.1007/s11046-026-01085-2

Long-Read Sequencing and Comparative Genome Analyses of Seven Emergomyces Type-Strains

Ilan S Schwartz 1, Bert Gerrits van den Ende 2, Ferry Hagen 2,3,4,✉
PMCID: PMC13263191  PMID: 42286369

Abstract

Emergomyces (Ajellomycetaceae, Onygenales) is a genus of dimorphic fungal pathogens that cause severe, opportunistic infections around the world. We used long-read nanopore sequencing to generate de novo genome assemblies followed by comparative analyses for the type-strains of Emergomyces africanus, Emergomyces canadensis, Emergomyces crescens, Emergomyces europaeus, Emergomyces orientalis, Emergomyces pasteurianus, and Emergomyces soli. The average Emergomyces genome was found to be 32,965,087 bp in size (range 28,687,700–35,863,369 bp) with GC%-contents of 42.01–45.72%. Average Nucleotide Identity analysis of the seven type-strain genomes with the publicly available Emergomyces and Blastomyces genomes was performed, showing values of 85–100% similarity between genomes and 85–91% between the twelve species tested. Furthermore, we formally validate the species descriptions for Emergomyces crescens and Emergomyces soli.

Keywords: Emergomyces, Emergomycosis, Comparative genomics, Nanopore sequencing, Average nucleotide identity

Emergomyces is a genus of thermally dimorphic human fungal pathogens that belongs to the order Onygenales (family Ajellomycetaceae) alongside better-known taxa of human and animal pathogens including Blastomyces, Coccidioides, Histoplasma, and Paracoccidioides [1]. Emergomyces species have emerged as causes of clinical disease, primarily in immunocompromised patients, around the world [1]. The genus was proposed less than a decade ago to accommodate several pathogens isolated from immunocompromised patients with systemic infections that resembled Emmonsia parva (since reclassified as Blastomyces parvus) in the mould phase, but which transformed to small yeast-like cells in host tissues, rather than the swollen, sessile “adiaspores” of E. parva. Specifically, the genus initially included Emmonsia pasteuriana (= Emergomyces pasteurianus), Emmonsia orientalis (= Emergomyces orientalis) and Emergomyces africanus [1, 2], and were joined soon thereafter by Emergomyces canadensis and Emergomyces europaeus [3–6]. Lastly, Jiang and colleagues transferred to the genus two non-pathogenic species, Emmonsia soli and Emmonsia crescens, as Emergomyces soli and Emergomyces crescens, respectively, based on genetic relatedness [7]. These taxa are outliers in that E. soli is a non-pathogen that has been isolated only from soil, and E. crescens transforms to swollen adiaspores rather than yeasts, and causes a localized pulmonary disease known as adiaspiromycosis in small mammals [7]. While the geographical distribution of Emergomyces appears to be widespread, emergomycosis remains a relatively rare disease, except for E. africanus which is among the most common clinically encountered dimorphic fungal pathogens in South Africa, where it causes severe, disseminated infections in persons with advanced HIV disease [8, 9].

With the increasing application of molecular diagnostics to detect and identify fungal pathogens directly from clinical material there is a need for reference genomes. Especially with the rapidly developing applications of metabarcoding and metagenomics in clinical diagnostics [10, 11]. At present, few highly fragmented genomes of Emergomyces species have been made publicly available via NCBI Genome. Here, we aim to provide high-quality reference genomes for the type-strains of all seven Emergomyces species.

The type-strains of E. africanus (CBS 136260T), E. canadensis (CBS 139872T), E. crescens (CBS 177.60T), E. europaeus (CBS 102456T), E. orientalis (CBS 124587T), E. pasteurianus (CBS 101426T), and E. soli (CBS 142607T) were obtained from the CBS Culture Collection (hosted at the Westerdijk Fungal Biodiversity Institute, Utrecht, Netherlands). The strains were sub-cultured on Malt-Extract agar (MEA; Oxoid, Basingstoke, United Kingdom) and incubated at 25 °C for 2 weeks to obtain enough biomass for genomic DNA purification using the manual cetyltrimethylammonium bromide extraction protocol [12]. Genomic DNA quality and quantity was assessed by Qubit Broad Range kit (ThermoFisher, Waltham, MA, U.S.A.), 2% agarose gel electrophoresis and by TapeStation using the Genomic DNA Screentape (Agilent, Santa Clara, CA, U.S.A.).

One microgram of genomic DNA was used as input for long-read nanopore sequencing for which the library preparation was performed with the SQK-NBD114.24 kit that enables multiplex sequencing by ligation of unique barcodes per sample (Oxford Nanopore Technologies, ONT; Oxford, United Kingdom). The library was loaded onto R10.4.1 flow cells and raw sequence data was generated with the MinION Mk1D platform (ONT). Raw sequence data was basecalled using the super-accurate mode with dorado v7.8.3 model dna_r10.4.1_e8.2_400bps_sup@v4.3.0 implemented in the MinKNOW v25.03.9 standalone software (ONT). Ultimately, all sequence data per strain was collected into a single FASTQ file and subsequently quality-controlled prior further downstream analysis. For this, FASTQ files were filtered using chopper v0.8.0 for reads of ≥ 1100 bp and a Q-value of ≥ 10, followed by 50 bp removal of the 5′- and 3′-ends of each read [13]. NanoComp v1.12.0 was used to create filtered sequence statistics as listed in Table 1 [13].

Table 1.

Genome assembly information of the seven sequenced Emergomyces type-strains

General summary E. africanus
CBS 136260 T 		E. canadensis
CBS139872T 		E. crescens
CBS 177.60 T 		E. europaeus
CBS 102456 T 		E. orientalis
CBS 124587 T 		E. pasteurianus
CBS 101426 T 		E. soli
CBS 142607 T
General sequence statistics
Mean read length 3497.6 7002.9 4118.7 4079.1 3176.8 6616.8 5213.6
Mean read quality 20.1 18.9 18.8 18.5 20.3 18.6 19.1
Median read length 2093 4100 2349 2040 2010 3523 3382
Median read quality 23.0 21.0 20.8 20.3 23.2 20.6 21.3
Number of reads 703,855 107,200 242,230 389,145 464,413 173,376 254,962
Read length N50 5139 12,614 6756 7601 4234 12,736 8200
S.D. read length 3735.6 7326.0 4496.5 5214.9 3319.2 7150.5 5046.8
Total bases 2,461,785,846 750,711,355 997,675,177 1,587,347,577 1,475,361,397 1,147,197,235 1,329,266,616
Reads with quality > Q10 703,693 (100.0%) 2461.5Mbp 107,183 (100.0%) 750.7Mbp 242,192 (100.0%) 997.6Mbp 389,088 (100.0%) 1587.3Mbp 464,336 (100.0%) 1475.2Mbp 173,362 (100.0%) 1147.2Mbp 254,938 (100.0%) 1329.2Mbp
Reads with quality > Q15 660,833 (93.9%) 2312.8Mbp 98,452 (91.8%) 689.6Mbp 221,846 (91.6%) 915.2Mbp 353,263 (90.8%) 1447.7Mbp 436,857 (94.1%) 1389.5Mbp 157,749 (91.0%) 1047.9Mbp 235,228 (92.3%) 1220.8Mbp
Reads with quality > Q20 525,407 (74.6%) 1839.9Mbp 66,491 (62.0%) 472.9Mbp 142,520 (58.8%) 604.3Mbp 209,207 (53.8%) 899.1Mbp 351,961 (75.8%) 1123.6Mbp 98,203 (56.6%) 674.7Mbp 166,683 (65.4%) 876.4Mbp
Reads with quality > Q25 218,803 (31.1%) 703.8Mbp 8219 (7.7%) 30.4Mbp 20,072 (8.3%) 51.5Mbp 24,514 (6.3%) 58.4Mbp 152,881 (32.9%) 463.2Mbp 11,270 (6.5%) 39.1Mbp 25,081 (9.8%) 84.5Mbp
Reads with quality > Q30 35,880 (5.1%) 69.1Mbp 543 (0.5%) 0.9Mbp 1386 (0.6%) 2.1Mbp 1555 (0.4%) 2.2Mbp 23,006 (5.0%) 44.0Mbp 692 (0.4%) 1.1Mbp 1601 (0.6%) 2.8Mbp
Genome statistics
Total genome size 32,435,257 bp 33,509,182 bp 32,560,084 bp 35,863,369 bp 34,295,918 bp 33,404,102 bp 28,687,700 bp
GC% 42.01% 44.69% 44.46% 42.27% 45.72% 43.91% 45.46%
Fragments 9 13 22 10 42 9 12
Fragments N50 4,239,726 bp 3,738,050 bp 4,473,560 bp 5,096,094 bp 1,452,906 bp 4,469,582 bp 3,738,837 bp
Largest fragment 9,500,345 bp 5,418,418 bp 7,332,920 bp 6,469,515 bp 4,517,116 bp 9,833,851 bp 6,844,355 bp
Mean coverage 76X 21X 30X 43X 22X 32X 45X
Mitochondrial genome size 22,061 bp 33,725 bp 31,265 bp 42,028 bp 30,657 bp 27,220 bp 24,969 bp
Mitochondrial genome coverage 5117X 1045X 978X 876X 1264X 1197X 1341X
Predicted genes 8390 9763 9788 9792 10,899 9421 8716
BUSCO analysis using the onygenales_odb10 dataset (4,862 BUSCOs included)
Single BUSCOs 4,847 (99.69%) 4,857 (99.90%) 4,852 (99.79%) 4,851 (99.77%) 4,846 (99.67%) 4,850 (99.75%) 4,850 (99.75%)
Duplicated BUSCOs 3 (0.06%) 4 (0.08%) 2 (0.04%) 2 (0.04%) 10 (0.21%) 4 (0.08%) 5 (0.10%)
Fragmented BUSCOs 3 (0.06%) 0 (0.00%) 1 (0.02%) 1 (0.02%) 3 (0.06%) 0 (0.00%) 0 (0.00%)
Missing BUSCOs 9 (0.19%) 1 (0.02%) 7 (0.14%) 8 (0.16%) 3 (0.06%) 8 (0.16%) 7 (0.14%)
Data availability via NCBI BioProject PRJNA1285980
NCBI BioSample SAMN50881230 SAMN49785778 SAMN49785779 SAMN49785776 SAMN50881229 SAMN49785780 SAMN49785777
NCBI Sequence Read Archive SRR35194778 SRR34394616 SRR34394615 SRR34394618 SRR35194779 SRR34394614 SRR34394617
NCBI Genome JBRATR000000000 JBVPGW000000000 JBRATP000000000 JBVPGX000000000 JBTGNQ000000000 JBRATQ000000000 JBVPGV000000000
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De novo genome assemblies were generated using Flye v2.9.5-b1801 followed by manual curation, which includes (i) removal of short contigs that have low coverage compared to the nuclear content (< 10kbp) are caused by barcode-leakage which is a known phenomenon with the library kit used; ii) checking the circularity of mitochondrial genomes as this software package usually places multiple copies of circular fragments in tandem [14]. The average Emergomyces genome was found to be 32,965,087 bp in size with a range of 28,687,700 bp (E. soli genome) to 35,863,369 bp (E. europaeus genome). The assembled genome sequences in this study of E. africanus CBS 136260T and E. pasteurianus CBS 101426T consisted each of 9 fragments (Table 1). This is a significant improvement as for both type-strains the genome sequences have been deposited a decade ago in NCBI Genome (GCA_001660665.1 and GCA_001883825.1, respectively) which are highly fragmented with 4444 and 1643 scaffolds, respectively. The genome sequences of E. europaeus CBS 102456T, E. soli CBS 142607T, and E. canadensis CBS 139872T were assembled into slightly more fragments, being 10, 12 and 13 fragments, respectively (Table 1). The genome sequence of E. crescens CBS 177.60T consists of 22 fragments, from the same strain a decade old NCBI deposited genome sequence (GCA_001008285.1) is available that consists of 1734 scaffolds, while that of another strain (UAMH 4076; GCA_002572855.1) is also highly fragmented with 1288 scaffolds. The genome sequence of E. orientalis CBS 124587T was the most fragmented with 42 fragments (Table 1). However, this long-read nanopore based assembled genome sequence is an improvement compared to the two publicly available E. orientalis genomes deposited in NCBI (GCA_002110485.1 and GCA_020085055.1) which were assembled with 108 and 2,498 scaffolds, respectively. The most accurate number of chromosomes has only been determined for Histoplasma capsulatum and Paracoccidioides brasiliensis using various karyotyping tools, which demonstrated 5–7 chromosomes for H. capsulatum and 4–5 chromosomes in P. brasiliensis [15, 16]. There are no karyotyping data available for Blastomyces and Emergomyces species. To investigate the level of genome completeness we used TeloVision v0.3.2 to detect telomeric regions in the Emergomyces genome assemblies [17]. This revealed that the genome of E. pasteurianus was nearly fully telomere-to-telomere assembled, as of the 8 nuclear fragments 4 had telomeric regions at both ends. This suggests that E. pasteurianus CBS 101426T has 6 chromosomes (Supplementary Data). Two fragments in the genomes of E. africanus CBS 136260T, E. europaeus CBS 102456T and E. canadensis CBS 139872T had telomeric regions at both ends, while this was only seen for one fragment in the genomes of E. crescens CBS 177.60T and E. soli CBS 142607T, and no telomere-to-telomere assembled fragments in E. orientalis CBS 124587T (Supplementary Data). Given this analysis it is expected that, like other closely related genera, Emergomyces species have 5–7 chromosomes. Genome completeness was investigated using compleasm v0.2.7 that assesses the genome sequence against a benchmarking dataset of lineage-specific single-copy orthologs, in this case the onygenales_odb10 dataset [18, 19]. All 7 genome sequences were found to be highly complete, with 4846–4857 BUSCO’s present among the 4862 BUSCO assessed (Table 1). Subsequently, ab initio gene prediction was performed using the Helixer v0.3.4 webtool [20]. The range of predicted genes was found to be 8390–10,899, with the highest number of predicted genes for E. orientalis CBS 124587T (Table 1).

The GC% was assessed using the EZBioCloud webtool [21] resulting in values between 42.01–45.72%, which is closely to previously reported GC% values of other Onygenales species. Earlier performed DNA-DNA hybridization experiments showed that E. crescens CBS 177.60T had a nuclear DNA GC% of 46.8%, and E. pasteurianus CBS 101426T (cited as IP 2310.95) a nuclear DNA GC% of 47.3% [22]. The same study reported overall nuclear DNA GC% of 46.1–47.3% for species belonging to other Onygenales genera. As the in silico GC% calculation is more accurate than the DNA-DNA hybridization method, this explains the overestimation of GC% for the latter approach.

Finally, we compared the nanopore long-read based genome sequences of the 7 Emergomyces type-strains to publicly available genome sequences available from NCBI Genomes. For this, we applied an Average Nucleotide Identity (ANI) calculation using pyani v0.2.13.1 which determines the percentage similarity between genomes by arbitrarily generating k-mer fragments (usually 1024 bp) and compare them all against all for every pair of genomes [23]. Other publicly available Emergomyces and Blastomyces genome sequences at NCBI Genomes were included in this analysis, the strain details and genomic data are presented in Fig. 1 [1, 24, 25]. The two E. pasteurianus strains (CBS 101426T and UAMH 9510) had an ANI-value of 100%, this also applies to the two genome sequences of E. africanus CBS 136260T (Fig. 1) and to that of both E. orientalis strains (5z489 and CBS 124587T). This could be expected for these three species as the genome pairs per species are the same strain that has been deposited in different culture collections. However, given the differences in used next-generation sequencing technology (viz. short-read versus long-read), different assemblers used, and the large difference in fragments per genome it was unexpected that the ANI-values were in all three cases 100%. For example, two different strains of E. crescens (CBS 177.60T and UAMH 4076) have an ANI-value of 93%. All other Emergomyces genome sequences have ANI-values of 85–89% when compared to any of the other genome sequences in this analysis, even those from Blastomyces species and vice versa. This percentage is more in the expected range for different species.

Fig. 1.

Fig. 1

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Average Nucleotide Identity (ANI) analysis using pyani v0.2.13.1 which determines the percentage similarity between every pair of genomes. [20] Other publicly available Emergomyces and Blastomyces genome sequences from NCBI Genomes were included in this analysis. Species names are followed by the (type-)strain accession number and NCBI Genomes accession number (between brackets). Information presented in bold identifies the here described and analysed de novo genome assemblies. Raw sequence reads and de novo genome assemblies are available via the NCBI BioProject database under accession number PRJNA1285980. Additionally, the de novo genome assemblies can be accessed via the DANS-KNAW Data Station Life Sciences (https://doi.org/10.17026/LS/SXUBNO)

Lastly, we observed that the descriptions of the new combinations for E. crescens and E. soli were in 2019 not validly described by Jiang and colleagues [7]. Hence, we here take the opportunity to formally validating these names:

Emergomyces crescens (C.W. Emmons & Jellison) Y.P. Jiang & de Hoog, comb. nov.—Mycobank MB862275.

Basionym: Emmonsia crescens C.W. Emmons & Jellison, Ann. New York Acad. Sci. 89: 98, 1960.

Synonyms: Chrysosporium parvum var. crescens (C.W. Emmons & Jellison) J.W. Carmich., Canad. J. Bot. 40: 1164, 1962.

Emmonsia parva var. crescens (C.W. Emmons & Jellison) Oorschot, Stud. Mycol. 20: 59, 1980.

Emergomyces crescens (C.W. Emmons & Jellison) Y.P. Jiang & de Hoog, Mycopathologia 185: 626, 2020, nom. inval.

Ajellomyces crescens Sigler, J. Med. Vet. Mycol. 34: 305, 1996.

Emergomyces soli (Y.P. Jiang, Borman & de Hoog) Y.P. Jiang & de Hoog, comb. nov.—MycoBank MB862276.

Basionym: Emmonsia soli Y.P. Jiang, Borman & de Hoog [as ‘sola’], Fungal Diversity 90: 262, 2018.

Synonym: Emergomyces soli (Y.P. Jiang, Borman & de Hoog) Y.P. Jiang & de Hoog, Mycopathologia 185: 626, 2020, nom. inval.

Acknowledgements

We thank Konstanze Bensch for her valuable contribution to formalizing the previously invalidly described species Emergomyces crescens and Emergomyces soli.

Author Contributions

Ilan S. Schwartz: Conceptualization, Data curation, Writing—original draft, Writing – review & editing; Bert Gerrits van den Ende: Data curation, Investigation, Methodology, Resources, Writing—review & editing; Ferry Hagen: Conceptualization, Data curation, Formal analysis, Funding acquisition, Investigation, Methodology, Project administration, Resources, Software, Supervision, Validation, Visualization, Writing—original draft,Writing—review & editing.

Funding

The authors declare that no funds, grants, or other support were received during the preparation of this manuscript.

Data Availability

Emergomyces type-strains are available via the CBS Culture Collection (Westerdijk Institute, Utrecht, The Netherlands). The basecalled and quality controlled FASTQ reads and the genome sequences are available via the NCBI BioProject database under accession number PRJNA1285980. Additionally, the de novo genome assemblies can be accessed via the DANS-KNAW Data Station Life Sciences (https:/doi.org/10.17026/LS/SXUBNO).

Declarations

Conflict of interests

The authors declare no competing interests.

Footnotes

Publisher's Note

Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

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Associated Data

This section collects any data citations, data availability statements, or supplementary materials included in this article.

Data Availability Statement

Emergomyces type-strains are available via the CBS Culture Collection (Westerdijk Institute, Utrecht, The Netherlands). The basecalled and quality controlled FASTQ reads and the genome sequences are available via the NCBI BioProject database under accession number PRJNA1285980. Additionally, the de novo genome assemblies can be accessed via the DANS-KNAW Data Station Life Sciences (https:/doi.org/10.17026/LS/SXUBNO).

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