Phyllosticta paracitricarpa is synonymous with the EU quarantine fungus P. citricarpa based on phylogenomic analyses

Valerie A. van Ingen-Buijs; Anouk C. van Westerhoven; Petros Skiadas; Xander C.L. Zuijdgeest; Sajeet Haridas; Christopher Daum; Kecia Duffy; Jie Guo; Hope Hundley; Kurt LaButti; Anna Lipzen; Jasmyn Pangilinan; Robert Riley; Jie Wang; Mi Yan; Francis Martin; Kerrie Barry; Igor V. Grigoriev; Johannes Z. Groenewald; Pedro W. Crous; Michael F. Seidl

doi:10.1016/j.fgb.2024.103925

Phyllosticta paracitricarpa is synonymous with the EU quarantine fungus P. citricarpa based on phylogenomic analyses

Valerie A. van Ingen-Buijs, Anouk C. van Westerhoven, Petros Skiadas, Xander C.L. Zuijdgeest, Sajeet Haridas, Christopher Daum, Kecia Duffy, Jie Guo, Hope Hundley, Kurt LaButti, Anna Lipzen, Jasmyn Pangilinan, Robert Riley, Jie Wang, Mi Yan, Francis Martin, Kerrie Barry, Igor V. Grigoriev, Johannes Z. Groenewald, Pedro W. CrousMichael F. Seidl

Onderzoeksoutput: Bijdrage aan wetenschappelijk tijdschrift/periodieke uitgave › Artikel › Wetenschappelijk › peer review

Samenvatting

Phyllosticta citricarpa is an important citrus-pathogen and a quarantine organism in the European Union. Its recently described relative, P. paracitricarpa, is very closely related and not listed as a quarantine organism. P. paracitricarpa is very difficult to distinguish from P. citricarpa, since its morphological features overlap and the barcoding gene sequences that were originally used to delimit them as distinct species have a low number of species-specific polymorphisms that have subsequently been shown to overlap between the two clades. Therefore, we performed extensive genomic analyses to determine whether the genetic variation between P. citricarpa and P. paracitricarpa strains should be considered to represent infraspecific variation within P. citricarpa, or whether it is indicative of distinct species. Using a phylogenomic analysis with 3,000 single copy ortholog genes and whole-genome comparisons, we determined that the variation between P. citricarpa and P. paracitricarpa can be considered as infraspecies variation within P. citricarpa. We also determined the level of variation in mitochondrial assemblies of several Phyllosticta species and concluded there are only minimal differences between the assemblies of P. citricarpa and P. paracitricarpa. Thus, using several orthogonal approaches, we here demonstrate that variation within the nuclear and mitochondrial genomes of other Phyllosticta species is larger than variation between genomes obtained from P. citricarpa and P. paracitricarpa strains. Thus, P. citricarpa and P. paracitricarpa should be considered as conspecific.

Originele taal-2	Engels
Pagina's (van-tot)	103925
Aantal pagina's	1
Tijdschrift	Fungal Genetics and Biology
Volume	175
DOI's	https://doi.org/10.1016/j.fgb.2024.103925
Status	Gepubliceerd - 13 sep. 2024

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10.1016/j.fgb.2024.103925

Citeer dit

Ingen-Buijs, V. A. V., Westerhoven, A. C. V., Skiadas, P., Zuijdgeest, X. C. L., Haridas, S., Daum, C., Duffy, K., Guo, J., Hundley, H., LaButti, K., Lipzen, A., Pangilinan, J., Riley, R., Wang, J., Yan, M., Martin, F., Barry, K., Grigoriev, I. V., Groenewald, J. Z., ... Seidl, M. F. (2024). Phyllosticta paracitricarpa is synonymous with the EU quarantine fungus P. citricarpa based on phylogenomic analyses. Fungal Genetics and Biology, 175, 103925. https://doi.org/10.1016/j.fgb.2024.103925

@article{04eba8acda69497f91e72e349355109b,

title = "Phyllosticta paracitricarpa is synonymous with the EU quarantine fungus P. citricarpa based on phylogenomic analyses",

abstract = "Phyllosticta citricarpa is an important citrus-pathogen and a quarantine organism in the European Union. Its recently described relative, P. paracitricarpa, is very closely related and not listed as a quarantine organism. P. paracitricarpa is very difficult to distinguish from P. citricarpa, since its morphological features overlap and the barcoding gene sequences that were originally used to delimit them as distinct species have a low number of species-specific polymorphisms that have subsequently been shown to overlap between the two clades. Therefore, we performed extensive genomic analyses to determine whether the genetic variation between P. citricarpa and P. paracitricarpa strains should be considered to represent infraspecific variation within P. citricarpa, or whether it is indicative of distinct species. Using a phylogenomic analysis with 3,000 single copy ortholog genes and whole-genome comparisons, we determined that the variation between P. citricarpa and P. paracitricarpa can be considered as infraspecies variation within P. citricarpa. We also determined the level of variation in mitochondrial assemblies of several Phyllosticta species and concluded there are only minimal differences between the assemblies of P. citricarpa and P. paracitricarpa. Thus, using several orthogonal approaches, we here demonstrate that variation within the nuclear and mitochondrial genomes of other Phyllosticta species is larger than variation between genomes obtained from P. citricarpa and P. paracitricarpa strains. Thus, P. citricarpa and P. paracitricarpa should be considered as conspecific.",

keywords = "Citrus black spot, Comparative genomics, Fungal taxonomy, Quarantine plant pathogen",

author = "Ingen-Buijs, {Valerie A. van} and Westerhoven, {Anouk C. van} and Petros Skiadas and Zuijdgeest, {Xander C.L.} and Sajeet Haridas and Christopher Daum and Kecia Duffy and Jie Guo and Hope Hundley and Kurt LaButti and Anna Lipzen and Jasmyn Pangilinan and Robert Riley and Jie Wang and Mi Yan and Francis Martin and Kerrie Barry and Grigoriev, {Igor V.} and Groenewald, {Johannes Z.} and Crous, {Pedro W.} and Seidl, {Michael F.}",

year = "2024",

month = sep,

day = "13",

doi = "10.1016/j.fgb.2024.103925",

language = "English",

volume = "175",

pages = "103925",

journal = "Fungal Genetics and Biology",

issn = "1087-1845",

publisher = "Academic Press",

}

Ingen-Buijs, VAV, Westerhoven, ACV, Skiadas, P, Zuijdgeest, XCL, Haridas, S, Daum, C, Duffy, K, Guo, J, Hundley, H, LaButti, K, Lipzen, A, Pangilinan, J, Riley, R, Wang, J, Yan, M, Martin, F, Barry, K, Grigoriev, IV, Groenewald, JZ , Crous, PW & Seidl, MF 2024, 'Phyllosticta paracitricarpa is synonymous with the EU quarantine fungus P. citricarpa based on phylogenomic analyses', Fungal Genetics and Biology, vol. 175, blz. 103925. https://doi.org/10.1016/j.fgb.2024.103925

Phyllosticta paracitricarpa is synonymous with the EU quarantine fungus P. citricarpa based on phylogenomic analyses. / Ingen-Buijs, Valerie A. van; Westerhoven, Anouk C. van; Skiadas, Petros et al.
In: Fungal Genetics and Biology, Vol. 175, 13.09.2024, blz. 103925.

Onderzoeksoutput: Bijdrage aan wetenschappelijk tijdschrift/periodieke uitgave › Artikel › Wetenschappelijk › peer review

TY - JOUR

T1 - Phyllosticta paracitricarpa is synonymous with the EU quarantine fungus P. citricarpa based on phylogenomic analyses

AU - Ingen-Buijs, Valerie A. van

AU - Westerhoven, Anouk C. van

AU - Skiadas, Petros

AU - Zuijdgeest, Xander C.L.

AU - Haridas, Sajeet

AU - Daum, Christopher

AU - Duffy, Kecia

AU - Guo, Jie

AU - Hundley, Hope

AU - LaButti, Kurt

AU - Lipzen, Anna

AU - Pangilinan, Jasmyn

AU - Riley, Robert

AU - Wang, Jie

AU - Yan, Mi

AU - Martin, Francis

AU - Barry, Kerrie

AU - Grigoriev, Igor V.

AU - Groenewald, Johannes Z.

AU - Crous, Pedro W.

AU - Seidl, Michael F.

PY - 2024/9/13

Y1 - 2024/9/13

N2 - Phyllosticta citricarpa is an important citrus-pathogen and a quarantine organism in the European Union. Its recently described relative, P. paracitricarpa, is very closely related and not listed as a quarantine organism. P. paracitricarpa is very difficult to distinguish from P. citricarpa, since its morphological features overlap and the barcoding gene sequences that were originally used to delimit them as distinct species have a low number of species-specific polymorphisms that have subsequently been shown to overlap between the two clades. Therefore, we performed extensive genomic analyses to determine whether the genetic variation between P. citricarpa and P. paracitricarpa strains should be considered to represent infraspecific variation within P. citricarpa, or whether it is indicative of distinct species. Using a phylogenomic analysis with 3,000 single copy ortholog genes and whole-genome comparisons, we determined that the variation between P. citricarpa and P. paracitricarpa can be considered as infraspecies variation within P. citricarpa. We also determined the level of variation in mitochondrial assemblies of several Phyllosticta species and concluded there are only minimal differences between the assemblies of P. citricarpa and P. paracitricarpa. Thus, using several orthogonal approaches, we here demonstrate that variation within the nuclear and mitochondrial genomes of other Phyllosticta species is larger than variation between genomes obtained from P. citricarpa and P. paracitricarpa strains. Thus, P. citricarpa and P. paracitricarpa should be considered as conspecific.

AB - Phyllosticta citricarpa is an important citrus-pathogen and a quarantine organism in the European Union. Its recently described relative, P. paracitricarpa, is very closely related and not listed as a quarantine organism. P. paracitricarpa is very difficult to distinguish from P. citricarpa, since its morphological features overlap and the barcoding gene sequences that were originally used to delimit them as distinct species have a low number of species-specific polymorphisms that have subsequently been shown to overlap between the two clades. Therefore, we performed extensive genomic analyses to determine whether the genetic variation between P. citricarpa and P. paracitricarpa strains should be considered to represent infraspecific variation within P. citricarpa, or whether it is indicative of distinct species. Using a phylogenomic analysis with 3,000 single copy ortholog genes and whole-genome comparisons, we determined that the variation between P. citricarpa and P. paracitricarpa can be considered as infraspecies variation within P. citricarpa. We also determined the level of variation in mitochondrial assemblies of several Phyllosticta species and concluded there are only minimal differences between the assemblies of P. citricarpa and P. paracitricarpa. Thus, using several orthogonal approaches, we here demonstrate that variation within the nuclear and mitochondrial genomes of other Phyllosticta species is larger than variation between genomes obtained from P. citricarpa and P. paracitricarpa strains. Thus, P. citricarpa and P. paracitricarpa should be considered as conspecific.

KW - Citrus black spot

KW - Comparative genomics

KW - Fungal taxonomy

KW - Quarantine plant pathogen

U2 - 10.1016/j.fgb.2024.103925

DO - 10.1016/j.fgb.2024.103925

M3 - Article

SN - 1087-1845

VL - 175

SP - 103925

JO - Fungal Genetics and Biology

JF - Fungal Genetics and Biology

ER -