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

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

doi:10.1016/j.fgb.2024.103925

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

Journal Article · Thu Sep 05 00:00:00 UTC 2024 · Fungal Genetics and Biology

DOI: https://doi.org/10.1016/j.fgb.2024.103925 · OSTI ID:2479726

van Ingen-Buijs, Valerie A. ^[1]; van Westerhoven, Anouk C. ^[2]; Skiadas, Petros ^[3]; Zuijdgeest, Xander C.L. ^[4]; Haridas, Sajeet ^[5]; Daum, Christopher ^[5]; Duffy, Kecia ^[5]; Guo, Jie ^[5]; Hundley, Hope ^[5]; LaButti, Kurt ^[5]; Lipzen, Anna ^[5]; Pangilinan, Jasmyn ^[5]; Riley, Robert ^[5]; Wang, Jie ^[5]; Yan, Mi ^[5]; Martin, Francis ^[6]; Barry, Kerrie ^[5]; Grigoriev, Igor V. ^[7]; Groenewald, Johannes Z. ^[8]; Crous, Pedro W. ^[8] more »

Westerdijk Fungal Biodiversity Institute, Utrecht (Netherlands); Netherlands Food and Consumer Product Safety Authority (NVWA) (Netherlands)
Westerdijk Fungal Biodiversity Institute, Utrecht (Netherlands); Utrecht University (Netherlands)
Utrecht University (Netherlands)
Univ. of Tubingen (Germany)
USDOE Joint Genome Institute (JGI), Berkeley, CA (United States)
Universite de Lorraine, Champenoux (France)
USDOE Joint Genome Institute (JGI), Berkeley, CA (United States); University of California, Berkeley, CA (United States)
Westerdijk Fungal Biodiversity Institute, Utrecht (Netherlands)

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.

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Research Organization:: Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)

Sponsoring Organization:: USDOE Office of Science (SC), Biological and Environmental Research (BER). Biological Systems Science (BSS)

Grant/Contract Number:: AC02-05CH11231

OSTI ID:: 2479726

Journal Information:: Fungal Genetics and Biology, Journal Name: Fungal Genetics and Biology Vol. 175; ISSN 1087-1845

Publisher:: ElsevierCopyright Statement

Country of Publication:: United States

Language:: English

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59 BASIC BIOLOGICAL SCIENCES
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Phyllosticta citricarpa
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Quarantine plant pathogen

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

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