Skip to content
1887

Microbial Genomics logo Microbial Genomics

Volume 10, Issue 8

Complete genome of the Medicago anthracnose fungus, , reveals a mini-chromosome-like region within a core chromosome Open Access

Abstract

() is a phytopathogenic fungus causing significant economic losses on forage legume crops ( and species) worldwide. To gain insights into the genetic basis of fungal virulence and host specificity, we sequenced the genome of an isolate from using long-read (PacBio) technology. The resulting genome assembly has a total length of 51.7 Mb and comprises ten core chromosomes and two accessory chromosomes, all of which were sequenced from telomere to telomere. A total of 15, 631 gene models were predicted, including genes encoding potentially pathogenicity-related proteins such as candidate-secreted effectors (484), secondary metabolism key enzymes (110) and carbohydrate-active enzymes (619). Synteny analysis revealed extensive structural rearrangements in the genome of relative to the closely related Brassicaceae pathogen, . In addition, a 1.2 Mb species-specific region was detected within the largest core chromosome of that has all the characteristics of fungal accessory chromosomes (transposon-rich, gene-poor, distinct codon usage), providing evidence for exchange between these two genomic compartments. This region was also unique in having undergone extensive intra-chromosomal segmental duplications. Our findings provide insights into the evolution of accessory regions and possible mechanisms for generating genetic diversity in this asexual fungal pathogen.

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): accessory chromosome , chromosome rearrangements , fungal genomics , M. truncatula , phytopathogenic fungus and SD
Funding
This study was supported by the:
  • Agence Nationale de la Recherche (Award ANR-17-EUR-0007)
    • Principal Award Recipient: NotApplicable
  • Agence Nationale de la Recherche (Award ANR-17-CAPS-0004)
    • Principal Award Recipient: RichardJ O'Connell
© 2024 The Authors
  • This is an open-access article distributed under the terms of the Creative Commons Attribution License. This article was made open access via a Publish and Read agreement between the Microbiology Society and the corresponding author’s institution.
Loading

Article metrics loading...

/content/journal/mgen/10.1099/mgen.0.001283
2024-08-21
2025-11-12

Metrics

Loading full text...

Full text loading...

/deliver/fulltext/mgen/10/8/mgen001283.html?itemId=/content/journal/mgen/10.1099/mgen.0.001283&mimeType=html&fmt=ahah

References

  1. Frayssinet S. Colletotrichum destructivum: a new lucerne pathogen in Argentina. Australas Plant Dis Notes 2008; 3:68 [View Article]
     [Google Scholar]
  2. Latunde-Dada AO, Bailey JA, Lucas JA. Infection process of Colletotrichum destructivum O’Gara from lucerne (Medicago sativa L.). Eur J Plant Pathol 1997; 103:35–41 [View Article]
     [Google Scholar]
  3. Damm U, O’Connell RJ, Groenewald JZ, Crous PW. The Colletotrichum destructivum species complex - hemibiotrophic pathogens of forage and field crops. Stud Mycol 2014; 79:49–84 [View Article] [PubMed]
     [Google Scholar]
  4. Sun HY, Liang Y. First report of anthracnose on sunflower caused by Colletotrichum destructivumin China. Plant Dis 2018; 102:245 [View Article]
     [Google Scholar]
  5. Manandhar JB. Colletotrichum destructivum, the anamorph of Glomerella glycines. Phytopathology 1986; 76:282 [View Article]
     [Google Scholar]
  6. Tiffany LH, Gilman JC. Species of Colletotrichum from legumes. Mycologia 1954; 46:52–75 [View Article]
     [Google Scholar]
  7. Damm U, Sato T, Alizadeh A, Groenewald JZ, Crous P. The Colletotrichum dracaenophilum C. magnum and C. orchidearum species complexes. Stud Mycol 2019; 92: [View Article]
     [Google Scholar]
  8. Gan P, Tsushima A, Hiroyama R, Narusaka M, Takano Y et al. Colletotrichum shisoi sp. nov., an anthracnose pathogen of Perilla frutescens in Japan: molecular phylogenetic, morphological and genomic evidence. Sci Rep 2019; 9: [View Article]
     [Google Scholar]
  9. Dallery J-F, Lapalu N, Zampounis A, Pigné S, Luyten I et al. Gapless genome assembly of Colletotrichum higginsianum reveals chromosome structure and association of transposable elements with secondary metabolite gene clusters. BMC Genom 2017; 18:667 [View Article] [PubMed]
     [Google Scholar]
  10. Tsushima A, Gan P, Kumakura N, Narusaka M, Takano Y et al. Genomic plasticity mediated by transposable elements in the plant pathogenic fungus Colletotrichum higginsianum. Genome Biol Evol 2019; 11:1487–1500 [View Article] [PubMed]
     [Google Scholar]
  11. Lelwala RV, Korhonen PK, Young ND, Scott JB, Ades PK et al. Comparative genome analysis indicates high evolutionary potential of pathogenicity genes in Colletotrichum tanaceti. PLoS One 2019; 14:e0212248 [View Article] [PubMed]
     [Google Scholar]
  12. Bhadauria V, MacLachlan R, Pozniak C, Cohen-Skalie A, Li L et al. Genetic map-guided genome assembly reveals a virulence-governing minichromosome in the lentil anthracnose pathogen Colletotrichum lentis. New Phytol 2019; 221:431–445 [View Article] [PubMed]
     [Google Scholar]
  13. Wang H, Huang R, Ren J, Tang L, Huang S et al. The evolution of mini-chromosomes in the fungal genus Colletotrichum. mBio 2013; 14:e00629-23 [View Article]
     [Google Scholar]
  14. Plaumann P-L, Koch C. The many questions about mini chromosomes in Colletotrichum spp. Plants 2020; 9:641 [View Article]
     [Google Scholar]
  15. Ma L-J, van der Does HC, Borkovich KA, Coleman JJ, Daboussi M-J et al. Comparative genomics reveals mobile pathogenicity chromosomes in Fusarium. Nature 2010; 464:367–373 [View Article]
     [Google Scholar]
  16. Liu S, Lin G, Ramachandran SR, Daza LC, Cruppe G et al. Rapid mini‐chromosome divergence among fungal isolates causing wheat blast outbreaks in Bangladesh and Zambia. New Phytol 2024; 241:1266–1276 [View Article]
     [Google Scholar]
  17. Plaumann P-L, Schmidpeter J, Dahl M, Taher L, Koch C. A dispensable chromosome is required for virulence in the hemibiotrophic plant pathogen Colletotrichum higginsianum. Front Microbiol 2018; 9:1005 [View Article] [PubMed]
     [Google Scholar]
  18. O’Connell R, Herbert C, Sreenivasaprasad S, Khatib M, Esquerré-Tugayé M-T et al. A novel Arabidopsis-Colletotrichum pathosystem for the molecular dissection of plant-fungal interactions. Mol Plant Microbe Interact 2004; 17:272–282 [View Article] [PubMed]
     [Google Scholar]
  19. Stiehler F, Steinborn M, Scholz S, Dey D, Weber APM et al. Helixer: cross-species gene annotation of large eukaryotic genomes using deep learning. Bioinformatics 2021; 36:5291–5298 [View Article] [PubMed]
     [Google Scholar]
  20. Koren S, Walenz BP, Berlin K, Miller JR, Bergman NH et al. Canu: scalable and accurate long-read assembly via adaptive k-mer weighting and repeat separation. Genom Res 2017; 27:722–736 [View Article]
     [Google Scholar]
  21. Seppey M, Manni M, Zdobnov EM. BUSCO: assessing genome assembly and annotation completeness. Methods Mol Biol 2019; 1962:227–245 [View Article] [PubMed]
     [Google Scholar]
  22. Rehmeyer C, Li W, Kusaba M, Kim Y-S, Brown D et al. Organization of chromosome ends in the rice blast fungus, Magnaporthe oryzae. Nucleic Acids Res 2006; 34:4685–4701 [View Article] [PubMed]
     [Google Scholar]
  23. Soorni A, Haak D, Zaitlin D, Bombarely A. Organelle_PBA, a pipeline for assembling chloroplast and mitochondrial genomes from PacBio DNA sequencing data. BMC Genom 2017; 18:49 [View Article] [PubMed]
     [Google Scholar]
  24. Bolger AM, Lohse M, Usadel B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 2014; 30:2114–2120 [View Article] [PubMed]
     [Google Scholar]
  25. Dobin A, Davis CA, Schlesinger F, Drenkow J, Zaleski C et al. STAR: ultrafast universal RNA-seq aligner. Bioinformatics 2013; 29:15–21 [View Article] [PubMed]
     [Google Scholar]
  26. Flutre T, Duprat E, Feuillet C, Quesneville H. Considering transposable element diversification in de novo annotation approaches. PLoS One 2011; 6:e16526 [View Article] [PubMed]
     [Google Scholar]
  27. Amselem J, Lebrun M-H, Quesneville H. Whole genome comparative analysis of transposable elements provides new insight into mechanisms of their inactivation in fungal genomes. BMC Genom 2015; 16:141 [View Article] [PubMed]
     [Google Scholar]
  28. Hoede C, Arnoux S, Moisset M, Chaumier T, Inizan O et al. PASTEC: an automatic transposable element classification tool. PLoS One 2014; 9:e91929 [View Article] [PubMed]
     [Google Scholar]
  29. Wicker T, Sabot F, Hua-Van A, Bennetzen JL, Capy P et al. A unified classification system for eukaryotic transposable elements. Nat Rev Genet 2007; 8:973–982 [View Article] [PubMed]
     [Google Scholar]
  30. Sallet E, Gouzy J, Schiex T. EuGene: An Automated Integrative Gene Finder for Eukaryotes and Prokaryotes New York, NY: Humana; 2019 pp 97–120 [View Article]
     [Google Scholar]
  31. Min B, Grigoriev IV, Choi I-G. FunGAP: fungal genome annotation pipeline using evidence-based gene model evaluation. Bioinformatics 2017; 33:2936–2937 [View Article] [PubMed]
     [Google Scholar]
  32. Eilbeck K, Moore B, Holt C, Yandell M. Quantitative measures for the management and comparison of annotated genomes. BMC Bioinform 2009; 10:67 [View Article] [PubMed]
     [Google Scholar]
  33. Valach M, Burger G, Gray MW, Lang BF. Widespread occurrence of organelle genome-encoded 5S rRNAs including permuted molecules. Nucleic Acids Res 2014; 42:13764–13777 [View Article] [PubMed]
     [Google Scholar]
  34. Bernt M, Donath A, Jühling F, Externbrink F, Florentz C et al. MITOS: improved de novo metazoan mitochondrial genome annotation. Mol Phylogenet Evol 2013; 69:313–319 [View Article] [PubMed]
     [Google Scholar]
  35. Drillon G, Carbone A, Fischer G. SynChro: a fast and easy tool to reconstruct and visualize synteny blocks along eukaryotic chromosomes. PLoS One 2014; 9:e92621 [View Article] [PubMed]
     [Google Scholar]
  36. Gilchrist CLM, Chooi YH. Clinker & clustermap.js: automatic generation of gene cluster comparison figures. Bioinformatics 2021; 37:2473–2475 [View Article] [PubMed]
     [Google Scholar]
  37. Jones P, Binns D, Chang H-Y, Fraser M, Li W et al. InterProScan 5: genome-scale protein function classification. Bioinformatics 2014; 30:1236–1240 [View Article] [PubMed]
     [Google Scholar]
  38. Camacho C, Coulouris G, Avagyan V, Ma N, Papadopoulos J et al. BLAST+: architecture and applications. BMC Bioinform 2009; 10:421 [View Article] [PubMed]
     [Google Scholar]
  39. Gene Ontology Consortium The gene ontology (GO) database and informatics resource. Nucleic Acids Res 2004; 32:D258–D261 [View Article] [PubMed]
     [Google Scholar]
  40. Götz S, García-Gómez JM, Terol J, Williams TD, Nagaraj SH et al. High-throughput functional annotation and data mining with the Blast2GO suite. Nucleic Acids Res 2008; 36:3420–3435 [View Article] [PubMed]
     [Google Scholar]
  41. Zhang H, Yohe T, Huang L, Entwistle S, Wu P et al. dbCAN2: a meta server for automated carbohydrate-active enzyme annotation. Nucleic Acids Res 2018; 46:W95–W101 [View Article] [PubMed]
     [Google Scholar]
  42. Petersen TN, Brunak S, von Heijne G, Nielsen H. SignalP 4.0: discriminating signal peptides from transmembrane regions. Nat Methods 2011; 8:785–786 [View Article] [PubMed]
     [Google Scholar]
  43. Emanuelsson O, Nielsen H, Brunak S, von Heijne G. Predicting subcellular localization of proteins based on their N-terminal amino acid sequence. J Mol Biol 2000; 300:1005–1016 [View Article] [PubMed]
     [Google Scholar]
  44. Krogh A, Larsson B, von Heijne G, Sonnhammer EL. Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes. J Mol Biol 2001; 305:567–580 [View Article] [PubMed]
     [Google Scholar]
  45. Sperschneider J, Dodds PN, Gardiner DM, Singh KB, Taylor JM. Improved prediction of fungal effector proteins from secretomes with EffectorP 2.0. Mol Plant Pathol 2018; 19:2094–2110 [View Article] [PubMed]
     [Google Scholar]
  46. Blin K, Shaw S, Steinke K, Villebro R, Ziemert N et al. antiSMASH 5.0: updates to the secondary metabolite genome mining pipeline. Nucleic Acids Res 2019; 47:W81–W87 [View Article] [PubMed]
     [Google Scholar]
  47. Zhou P, Silverstein KAT, Ramaraj T, Guhlin J, Denny R et al. Exploring structural variation and gene family architecture with De Novo assemblies of 15 Medicago genomes. BMC Genom 2017; 18:261 [View Article] [PubMed]
     [Google Scholar]
  48. Moll KM, Zhou P, Ramaraj T, Fajardo D, Devitt NP et al. Strategies for optimizing BioNano and Dovetail explored through a second reference quality assembly for the legume model, Medicago truncatula. BMC Genom 2017; 18:578 [View Article] [PubMed]
     [Google Scholar]
  49. O’Connell RJ, Thon MR, Hacquard S, Amyotte SG, Kleemann J et al. Lifestyle transitions in plant pathogenic Colletotrichum fungi deciphered by genome and transcriptome analyses. Nat Genet 2012; 44:1060–1065 [View Article] [PubMed]
     [Google Scholar]
  50. Coleman JJ, Rounsley SD, Rodriguez-Carres M, Kuo A, Wasmann CC et al. The genome of Nectria haematococca: contribution of supernumerary chromosomes to gene expansion. PLOS Genet 2009; 5:e1000618 [View Article] [PubMed]
     [Google Scholar]
  51. Hu J, Chen C, Peever T, Dang H, Lawrence C et al. Genomic characterization of the conditionally dispensable chromosome in Alternaria arborescens provides evidence for horizontal gene transfer. BMC Genom 2012; 13:1–13 [View Article] [PubMed]
     [Google Scholar]
  52. Vollger MR, Dishuck PC, Sorensen M, Welch AE, Dang V et al. Long-read sequence and assembly of segmental duplications. Nat Methods 2019; 16:88–94 [View Article] [PubMed]
     [Google Scholar]
  53. Liu F, Ma ZY, Hou LW, Diao YZ, Wu WP et al. Updating species diversity of Colletotrichum, with a phylogenomic overview. Stud Mycol 2022; 101:1–56 [View Article]
     [Google Scholar]
  54. Rogério F, Boufleur TR, Ciampi-Guillardi M, Sukno SA, Thon MR et al. Genome sequence resources of Colletotrichum truncatum, C. plurivorum, C. musicola, and C. sojae: four species pathogenic to soybean (glycine max). Phytopathology 2020; 110:1497–1499
     [Google Scholar]
  55. Langner T, Harant A, Gomez-Luciano LB, Shrestha RK, Win J et al. Genomic rearrangements generate hypervariable mini-chromosomes in host-specific lineages of the blast fungus. GenomicsbioRxiv [View Article]
     [Google Scholar]
  56. Langner T, Harant A, Gomez-Luciano LB, Shrestha RK, Malmgren A et al. Genomic rearrangements generate hypervariable mini-chromosomes in host-specific isolates of the blast fungus. PLOS Genet 2021; 17:e1009386 [View Article] [PubMed]
     [Google Scholar]
  57. Vanheule A, Audenaert K, Warris S, van de Geest H, Schijlen E et al. Living apart together: crosstalk between the core and supernumerary genomes in a fungal plant pathogen. BMC Genom 2016; 17:670 [View Article] [PubMed]
     [Google Scholar]
  58. Condon BJ, Leng Y, Wu D, Bushley KE, Ohm RA et al. Comparative genome structure, secondary metabolite, and effector coding capacity across Cochliobolus pathogens. PLoS Genet 2013; 9:e1003233 [View Article] [PubMed]
     [Google Scholar]
  59. Yang G, Turgeon BG, Yoder OC, Bronson CR, Yoder OC. Toxin-deficient mutants from a toxin-sensitive transformant of Cochliobolus heterostrophus. Genetics 1994; 137:751–757 [View Article] [PubMed]
     [Google Scholar]
  60. Klosterman SJ, Subbarao KV, Kang S, Veronese P, Gold SE et al. Comparative genomics yields insights into niche adaptation of plant vascular wilt pathogens. PLoS Pathog 2011; 7:e1002137 [View Article] [PubMed]
     [Google Scholar]
  61. Gan P, Hiroyama R, Tsushima A, Masuda S, Shibata A et al. Telomeres and a repeat-rich chromosome encode effector gene clusters in plant pathogenic Colletotrichum fungi. Environ Microbiol 2021; 23:6004–6018 [View Article] [PubMed]
     [Google Scholar]
  62. Croll D, Zala M, McDonald BA. Breakage-fusion-bridge cycles and large insertions contribute to the rapid evolution of accessory chromosomes in a fungal pathogen. PLoS Genet 2013; 9:e1003567 [View Article] [PubMed]
     [Google Scholar]
  63. Bertazzoni S, Williams AH, Jones DA, Syme RA, Tan K-C et al. Accessories make the outfit: accessory chromosomes and other dispensable DNA regions in plant-pathogenic fungi. Mol Plant Microbe Interact 2018; 31:779–788 [View Article] [PubMed]
     [Google Scholar]
  64. Francis A, Ghosh S, Tyagi K, Prakasam V, Rani M et al. Evolution of pathogenicity-associated genes in Rhizoctonia solani AG1-IA by genome duplication and transposon-mediated gene function alterations. BMC Biol 2023; 21:15 [View Article] [PubMed]
     [Google Scholar]
  65. Fraser JA, Huang JC, Pukkila-Worley R, Alspaugh JA, Mitchell TG et al. Chromosomal translocation and segmental duplication in Cryptococcus neoformans. Eukaryot Cell 2005; 4:401–406 [View Article] [PubMed]
     [Google Scholar]
  66. van Westerhoven AC, Aguilera-Galvez C, Nakasato-Tagami G, Shi-Kunne X, Martinez de la Parte E et al. Segmental duplications drive the evolution of accessory regions in a major crop pathogen. New Phytol 2024; 242:610–625 [View Article] [PubMed]
     [Google Scholar]
  67. Wilson AM, Lelwala RV, Taylor PWJ, Wingfield MJ, Wingfield BD. Unique patterns of mating pheromone presence and absence could result in the ambiguous sexual behaviors of Colletotrichum species. G3 Genes Genom Genet 2021; 11:jkab187 [View Article] [PubMed]
     [Google Scholar]
  68. Bhunjun CS, Phukhamsakda C, Jeewon R, Promputtha I, Hyde KD. Integrating different lines of evidence to establish a novel Ascomycete genus and family (Anastomitrabeculia, Anastomitrabeculiaceae) in Pleosporales. J Fungi 2021; 7:94 [View Article]
     [Google Scholar]
  69. Manners JM, He C. Slow-growing heterokaryons as potential intermediates in supernumerary chromosome transfer between biotypes of Colletotrichum gloeosporioides. Mycol Progress 2011; 10:383–388 [View Article]
     [Google Scholar]
  70. He C, Rusu AG, Poplawski AM, Irwin JAG, Manners JM. Transfer of a supernumerary chromosome between vegetatively incompatible biotypes of the fungus Colletotrichum gloeosporioides. Genetics 1998; 150:1459–1466 [View Article] [PubMed]
     [Google Scholar]
  71. Roca MG, Davide LC, Davide LMC, Mendes-Costa MC, Schwan RF et al. Conidial anastomosis fusion between Colletotrichum species. Mycol Res 2004; 108:1320–1326 [View Article] [PubMed]
     [Google Scholar]
  72. Ishikawa FH, Souza EA, Shoji J-Y, Connolly L, Freitag M et al. Heterokaryon incompatibility is suppressed following conidial anastomosis tube fusion in a fungal plant pathogen. PLoS One 2012; 7:e31175 [View Article] [PubMed]
     [Google Scholar]
  73. Mehta N, Baghela A. Quorum sensing-mediated inter-specific conidial anastomosis tube fusion between Colletotrichum gloeosporioides and C. siamense. IMA Fungus 2021; 12: [View Article]
     [Google Scholar]
  74. Schmidt SM, Houterman PM, Schreiver I, Ma L, Amyotte S et al. MITEs in the promoters of effector genes allow prediction of novel virulence genes in Fusarium oxysporum. BMC Genom 2013; 14:1–21 [View Article] [PubMed]
     [Google Scholar]
  75. van der Does HC, Fokkens L, Yang A, Schmidt SM, Langereis L et al. Transcription factors encoded on core and accessory chromosomes of Fusarium oxysporum induce expression of effector genes. PLOS Genet 2016; 12:e1006401 [View Article] [PubMed]
     [Google Scholar]
  76. Mould MJR, Boland GJ, Robb J. Ultrastructure of the Colletotrichum trifolii-Medicago sativa pathosystem. I. Pre-penetration events. Physiol Mol Plant Pathol 1991; 38:179–194 [View Article]
     [Google Scholar]
  77. Damm U, Cannon PF, Liu F, Barreto RW, Guatimosim E et al. The Colletotrichum orbiculare species complex: important pathogens of field crops and weeds. Fungal Diversity 2013; 61:29–59 [View Article]
     [Google Scholar]
  78. Ameline-Torregrosa C, Wang B-B, O’Bleness MS, Deshpande S, Zhu H et al. Identification and characterization of nucleotide-binding site-leucine-rich repeat genes in the model plant Medicago truncatula. Plant Physiol 2008; 146:5–21 [View Article]
     [Google Scholar]
/content/journal/mgen/10.1099/mgen.0.001283
Loading
Complete genome of the Medicago anthracnose fungus, Colletotrichum destructivum, reveals a mini-chromosome-like region within a core chromosome
M Gen 10, 001283 (2024); https://doi.org/10.1099/mgen.0.001283
/content/journal/mgen/10.1099/mgen.0.001283
/content/journal/mgen/10.1099/mgen.0.001283
Loading

Data & Media loading...

Supplements

Supplementary material 1

PDF

Supplementary material 2

EXCEL

Supplementary material 3

EXCEL

Most cited Most Cited RSS feed

This is a required field
Please enter a valid email address
Approval was a Success
Invalid data
An error occurred
Approval was partially successful, following selected items could not be processed due to error