Telomeres and a repeat‐rich chromosome encode effector gene clusters in plant pathogenic Colletotrichum fungi

Abstract

Members of the Colletotrichum gloeosporioides species complex are causal agents of anthracnose in many commercially important plants. Closely related strains have different levels of pathogenicity on hosts despite their close phylogenetic relationship. To gain insight into the genetics underlying these differences, we generated and annotated whole-genome assemblies of multiple isolates of C. fructicola (Cf) and C. siamense (Cs), as well as three previously unsequenced species, C. aenigma (Ca), C. tropicale and C. viniferum with different pathogenicity on strawberry. Based on comparative genomics, we identified accessory regions with a high degree of conservation in strawberry-pathogenic Cf, Cs and Ca strains. These regions encode homologs of pathogenicity-related genes known as effectors, organized in syntenic gene clusters, with copy number variations in different strains of Cf, Cs and Ca. Analysis of highly contiguous assemblies of Cf, Cs and Ca revealed the association of related accessory effector gene clusters with telomeres and repeat-rich chromosomes and provided evidence of exchange between these two genomic compartments. In addition, expression analysis indicated that orthologues in syntenic gene clusters showed a tendency for correlated gene expression during infection. These data provide insight into mechanisms by which Colletotrichum genomes evolve, acquire and organize effectors.

Transposable Elements Contribute to Genome Dynamics and Gene Expression Variation in the Fungal Plant PathogenVerticillium dahliae

“…In many filamentous pathogens, effector genes are enriched in TE-rich and gene-sparse compartments, whereas they are typically underrepresented in TE-poor and gene-dense genomic regions that typically harbor housekeeping genes ( Seidl and Thomma 2014 ; Dong et al 2015 ; Frantzeskakis et al 2020 ). TE-rich compartments are often characterized by increased substitution rates and increased occurrence of SVs and presence/absence polymorphisms ( Raffaele et al 2010 ; Croll and McDonald 2012 ; de Jonge et al 2012 , 2013 ; Dutheil et al 2016 ; Hartmann and Croll 2017 ; Hartmann et al 2017 ; Wang et al 2017 ; Fokkens et al 2018 ; Plissonneau et al 2018 ; Grandaubert et al 2019 ; Gan et al 2021 ; Wyka et al 2021 ). Notably, a similar association of TEs with genes involved in immune responses has also been observed in plant hosts ( Leister 2004 ; Kawakatsu et al 2016 ; Mascher et al 2017 ; Seidl and Thomma 2017 ).…”

The Conserved Colletotrichum spp. Effector Candidate CEC3 Induces Nuclear Expansion and Cell Death in Plants

“…To investigate whether the function of CEC3 genes is conserved across Colletotrichum species pathogenic on different host plants, we cloned the cDNAs of CEC3 homologs from C. higginsianum (ChCEC3), C. orbiculare (CoCEC3-1 and CoCEC3-2), C. fructicola (CfCEC3-1 and CfCEC3-2), and C. graminicola (CgCEC3) into pGWB5 for expression under the control of the 35S CaMV promoter with a C-terminal GFP-tag (Supplementary Figure 4). ChCEC3, CoCEC3-1, CoCEC3-2, CfCEC3-1, and CfCEC3-2 were identical to the previously predicted CDSs (Gan et al, 2019(Gan et al, , 2021Tsushima et al, 2019a). However, CgCEC3 from C. graminicola MAFF 244463 had a 30 bp insertion encoding 10 extra amino acid sequences, and a missense mutation compared to the predicted CDS of C. graminicola M1.001 (GLRG_05522; O'Connell et al, 2012) (Supplementary Figure 5).…”

“…Total RNA was extracted from C. higginsianum MAFF 305635, C. orbiculare MAFF 240422, and C. graminicola MAFF 244463 cultured in potato dextrose (PD) broth (BD Biosciences) at 24 • C in the dark for 2 days. Total RNA was extracted from strawberry (Sachinoka) leaves 3 days after inoculation with C. fructicola Nara gc5 (JCM 39093) as previously described (Gan et al, 2021). RNA was extracted using RNeasy Plant Mini Kit (Qiagen) with DNase I treatment according to the manufacturer's introductions, and reverse transcribed using ReverTraAce qPCR RT Kit (Toyobo, Co., Ltd.) or SuperScript III Reverse Transcriptase (Thermo Fisher Scientific).…”

“…To date, more than 100 genomes of Colletotrichum spp. have been sequenced due to their agricultural importance and scientific interest (O'Connell et al, 2012;Baroncelli et al, 2014Baroncelli et al, , 2016aGan et al, 2016Gan et al, , 2019Gan et al, , 2021Hacquard et al, 2016). Using these abundant genome resources, it is now feasible to conduct comparative genomic analysis and reverse genetics of Colletotrichum spp.…”

Identification and Comparison of Colletotrichum Secreted Effector Candidates Reveal Two Independent Lineages Pathogenic to Soybean

“…The identification of effector candidates is the first step into the functional characterization of these molecules. Until now, several studies on effectors of different species of Colletotrichum such as C. higginsianum [58,59] C. orbiculare [60,61] C. lentis [62-64], C. graminicola [65-67] C. simmondsii, C. fiorinae, C. nymphaeae, C. salicis [30], C. lindemunthianum [68], C. falcatum [69], C. fruticola, C. siamense, C. aenigma, C. tropicale, C. viniferum [44] have been published. On the other hand, comparative genomic studies of Colletotrichum spp.…”