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ORIGINAL RESEARCH article

Front. Microbiol.
Sec. Microbe and Virus Interactions with Plants
Volume 16 - 2025 | doi: 10.3389/fmicb.2025.1515894
This article is part of the Research Topic Advancing Crop Disease Resistance Through Microbial-Assisted Breeding View all 7 articles

Genomic Insights and Comparative Analysis of Colletotrichum Species Associated with Anthracnose Fruit Rot and Crown Rot of Strawberry in North Carolina

Provisionally accepted
Tika Adhikari Tika Adhikari 1*Norman Muzhinji Norman Muzhinji 2Ashley N. Philbrick Ashley N. Philbrick 1Frank J. Louws Frank J. Louws 1
  • 1 North Carolina State University, Raleigh, North Carolina, United States
  • 2 University of the Free State, Bloemfontein, Free State, South Africa

The final, formatted version of the article will be published soon.

    Colletotrichum is a large genus of fungal phytopathogens responsible for significant economic losses in numerous crops globally. These pathogens exhibit varying host specificities; some have a broad host range, while others are more limited. To explore the genetic composition and underlying factors of fungal virulence and pathogenicity, we sequenced the genomes of seven isolates of Colletotrichum spp.: three from the C. acutatum complexC. acutatum and four from the C. gloeosporioides complexC. gloeosporioides. These isolates were sourced from anthracnose fruit rot and crown rot of strawberriesstrawberry in North Carolina. Phylogenetic and phylogenomic analyses classified the isolates within the C. acutatum complexC. acutatum as C. nymphaeae, while those in the C. gloeosporioides complexC. gloeosporioides were identified as C. siamense. The genome sizes of the C. nymphaeae isolates ranged from 50.3Mb to 50.7 Mb, with 14,235 to 14, 260 predicted protein-coding gene models. In contrast, the genome sizes of the C. siamense isolates ranged from 55.7 Mb to 58.6 Mb, with predicted protein-coding gene models ranging from 17,420 to 17,729. The GC content across all genomes spanned from 51.9% to 53.7%. The predicted gene models included effectors (339 to 480), secondary metabolic gene clusterssm (67 to 90), and carbohydrate-active enzymes (800 to 1060), with C. siamense isolates exhibiting the highest numbers in these categories. The genomic resources from this study will aid in resolving taxonomic challenges associated with Colletotrichum spp., elucidate their evolutionary history, and enhance the understanding of fungal biology and ecology, which is crucial for developing effective disease management strategies.

    Keywords: Anthracnose, Crown rot, Colletotrichum, whole genome sequencing, comparative genomics; fruit rot, strawberry

    Received: 23 Oct 2024; Accepted: 23 Jan 2025.

    Copyright: © 2025 Adhikari, Muzhinji, Philbrick and Louws. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

    * Correspondence: Tika Adhikari, North Carolina State University, Raleigh, 27695, North Carolina, United States

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