Subtelomeric regions and a repeat-rich chromosome harbor multicopy effector gene clusters with variable conservation in multiple plant pathogenic Colletotrichum species

Members of the Colletotrichum gloeosporioides species complex are causal agents of anthracnose in a wide range of commercially important plants. To provide an in-depth overview of its diversity, we sequenced the genomes of fungi belonging to this group, including multiple strains of C. fructicola (C...

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Published inbioRxiv
Main Authors Gan, Pamela, Hiroyama, Ryoko, Tsushima, Ayako, Masuda, Sachiko, Shibata, Arisa, Ueno, Akiko, Kumakura, Naoyoshi, Narusaka, Mari, Trinh Xuan Hoat, Narusaka, Yoshihiro, Takano, Yoshitaka, Shirasu, Ken
Format Paper
LanguageEnglish
Published Cold Spring Harbor Cold Spring Harbor Laboratory Press 29.04.2020
Subjects
Anthracnose
Chromosomes
Colletotrichum
Copy number
Evolutionary conservation
Fungi
Gene clusters
Gene expression
Gene transfer
Genomes
Species
Synteny
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Summary:Members of the Colletotrichum gloeosporioides species complex are causal agents of anthracnose in a wide range of commercially important plants. To provide an in-depth overview of its diversity, we sequenced the genomes of fungi belonging to this group, including multiple strains of C. fructicola (Cf) and C. siamense (Cs), as well as representatives of three previously unsequenced species, C. aenigma (Ca), C. tropicale and C. viniferum. Comparisons between multiple Cf and Cs strains led to the identification of accessory regions that show variable conservation in both lineages. These accessory regions encode effector candidate genes, including homologs of previously characterized effectors, organized in clusters of conserved synteny with copy number variations in different strains of Cf, Cs and Ca. Analysis of highly contiguous assemblies of Cf, Cs and Ca strains revealed the association of such accessory effector gene clusters with subtelomeric regions and repeat-rich minichromosomes and provided evidence of gene transfer between these two genomic compartments. In addition, expression analysis indicated that paralogs associated with clusters of conserved synteny showed a tendency for correlated gene expression. These data highlight the importance of subtelomeric regions and repeat-rich chromosomes to the genome plasticity of Colletotrichum fungi. Competing Interest Statement The authors have declared no competing interest.
DOI:10.1101/2020.04.28.061093