Genetic map‐guided genome assembly reveals a virulence‐governing minichromosome in the lentil anthracnose pathogen Colletotrichum lentis

Abstract

Colletotrichum lentis causes anthracnose, which is a serious disease on lentil and can account for up to 70% crop loss. Two pathogenic races, 0 and 1, have been described in the C. lentis population from lentil. To unravel the genetic control of virulence, an isolate of the virulent race 0 was sequenced at 1481-fold genomic coverage. The 56.10-Mb genome assembly consists of 50 scaffolds with N scaffold length of 4.89 Mb. A total of 11 436 protein-coding gene models was predicted in the genome with 237 coding candidate effectors, 43 secondary metabolite biosynthetic enzymes and 229 carbohydrate-active enzymes (CAZymes), suggesting a contraction of the virulence gene repertoire in C. lentis. Scaffolds were assigned to 10 core and two minichromosomes using a population (race 0 × race 1, n = 94 progeny isolates) sequencing-based, high-density (14 312 single nucleotide polymorphisms) genetic map. Composite interval mapping revealed a single quantitative trait locus (QTL), qClVIR-11, located on minichromosome 11, explaining 85% of the variability in virulence of the C. lentis population. The QTL covers a physical distance of 0.84 Mb with 98 genes, including seven candidate effector and two secondary metabolite genes. Taken together, the study provides genetic and physical evidence for the existence of a minichromosome controlling the C. lentis virulence on lentil.

Colletotrichum shisoi sp. nov., an anthracnose pathogen of Perilla frutescens in Japan: molecular phylogenetic, morphological and genomic evidence

“…Further, BUSCO analysis of conserved genes reveals that only 0.1% of the conserved coding sequences present in the genome are duplicated, indicating that the genome is not heterozygous and that the gene coding regions at least are likely not to be duplicated. This is consistent with the predicted number of genes (11,848) in C. shisoi , which is within the range of other sequenced members of the C. destructivum species complex including the recently published genomes of C. lentis 21 (11,436), C. tanaceti 26 (12,172) and another isolate of C. higginsianum 25 (MAFF 305635-RFP), which has 12,915 protein coding genes. It is noted that the genome assembly of C. shisoi generated in this study was sequenced using only short reads and is highly fragmented, with more than half of the scaffolds (11,424 scaffolds totalling 5.73 Mb) being less or equal to 1 kb in length.…”

“…In order to characterise C. shisoi and to allow comparisons to other members of the Colletotrichum genus at the molecular level, the genome of C. shisoi was sequenced and assembled. The size of the C. shisoi assembly is 69.7 Mb, which is larger than those of other sequenced members in the C. destructivum species complex, including C. higginsianum 33 (50.72 Mb), C. lentis 21 (56.1 Mb) and, most recently, C. tanaceti 26 (57.9 Mb). These sizes are closer to the genome size of C. shisoi estimated by k-mer analysis (58.6 Mb).…”

“…For the genus-wide maximum likelihood tree of selected Colletotrichum species, BUSCO was run on the genome assemblies of C. trifolii (RYZW01000000) , C. sidae (QAPF01000000) , C. orbiculare (AMCV02000000) and C. spinosum (QAPG01000000) 24 , C. fructicola (ANPB00000000.1) 19 , C. gloeosporioides (QFRH00000000) 27 , C. chlorophyti (MPGH01000000) 53 , C. orchidophilum (MJBS00000000.1) 54 , C. salicis (JFFI00000000.1) , C. fioriniae (JARH00000000.1) , C. simondsii (JFBX00000000.1) , C. nymphaea (JEMN00000000.1) 28 , C. sublineola (JMSE00000000.1) 29 , C. graminicola (ACOD00000000.1) 18 , C. incanum (JTLR01000000) 17 , C. tofieldiae (LFIV01000000) 37 , C. lentis (NWBT01000000) 21 , C. tanaceti (PJEX00000000) 26 , C. higginsianum (LTAN01000000) 33 and Fusarium oxysporum (GCF_000149955.1) 55 to identify highly conserved, single copy eukaryote genes (eukaryote_odb9). Sequences of orthologs from 254 single copy genes that were identified as non-duplicated in all the tested genomes were aligned using MAFFT and trimmed using trimAl as described above.…”

Genomics of Plant Disease Resistance in Legumes

“…Anthracnose of lentils is caused by Colletotrichum lentis and accounts for 70% of the crop loss in lentils (Bhadauria et al, 2019). Recent genomic sequencing studies on one of the pathogenic races of C. lentis (virulent race 0) combined with QTL mapping led to the identification of a single QTL, qClVIR-11 , located on mini chromosome 11, thus explaining 85% of the variability in virulence of the C. lentis population (Bhadauria et al, 2019).…”

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

“…Despite the demonstration of 260 minichromosome transfer between vegetative incompatible isolates more than 20 years ago (He et 261 al. 1998), only recently has pathogenicity been linked to the presence of specific minichromosomes 262 in certain strains (Plaumann et al 2018;Bhadauria et al 2019). In these recent studies, the both types of chromosomes exist in the same nucleus, TE-dense accessory chromosomes may also 265 play an additional role, affecting "core" chromosomes through the exchange of genes and promoting 266…”