Genome sequencing and comparative genomics reveal a repertoire of putative pathogenicity genes in chilli anthracnose fungus Colletotrichum truncatum

Abstract

Colletotrichum truncatum, a major fungal phytopathogen, causes the anthracnose disease on an economically important spice crop chilli (Capsicum annuum), resulting in huge economic losses in tropical and sub-tropical countries. It follows a subcuticular intramural infection strategy on chilli with a short, asymptomatic, endophytic phase, which contrasts with the intracellular hemibiotrophic lifestyle adopted by most of the Colletotrichum species. However, little is known about the molecular determinants and the mechanism of pathogenicity in this fungus. A high quality whole genome sequence and gene annotation based on transcriptome data of an Indian isolate of C. truncatum from chilli has been obtained. Analysis of the genome sequence revealed a rich repertoire of pathogenicity genes in C. truncatum encoding secreted proteins, effectors, plant cell wall degrading enzymes, secondary metabolism associated proteins, with potential roles in the host-specific infection strategy, placing it next only to the Fusarium species. The size of genome assembly, number of predicted genes and some of the functional categories were similar to other sequenced Colletotrichum species. The comparative genomic analyses with other species and related fungi identified some unique genes and certain highly expanded gene families of CAZymes, proteases and secondary metabolism associated genes in the genome of C. truncatum. The draft genome assembly and functional annotation of potential pathogenicity genes of C. truncatum provide an important genomic resource for understanding the biology and lifestyle of this important phytopathogen and will pave the way for designing efficient disease control regimens.

Comparative genome analysis indicates rapid evolution of pathogenicity genes inColletotrichum tanaceti

“…Duplication of pathogenicity and virulence genes and a higher mutation rate may allow more rapid pathogen responses to evolution of resistance in existing hosts or adaptation to new host species. Genus Colletotrichum Phylogenetic relationship throughout the genus was consistent with previous observations, with gloeosporioides complex members and C. orbiculare forming a clade separately from the destructivum, graminicola and acutatum clades [9][10][11]. One notable difference was in the divergence time estimates for the divergence of Colletotrichum species complexes which were more ancient than reported by Liang et al [11], despite using the same calibration times.…”

“…Many Colletotrichum species are known to cause major economic losses globally, and have been extensively used in the study of the molecular and cellular bases of fungal pathogenicity [4]. The publication of 25 whole genome sequences of Colletotrichum species has significantly improved understanding of the biology, genetics and evolution of this genus [5][6][7][8][9][10][11]. However, a large research gap still exists with this ever-expanding genus consisting of more than 200 accepted species [12] and 14 major species complexes [13,14].…”

The Landscape of Repetitive Elements in the Refined Genome of Chilli Anthracnose Fungus Colletotrichum truncatum

“…The library was sequenced on three single-molecule real-time (SMRT) cells using the P6-C4 polymerase-chemistry at 50, 65, and 75 pM DNA concentrations. The hybrid scaffolding approach was used to map the filtered subreads, obtained with AHA module of SMRT portal of PacBio, on the Illumina assembly of C. truncatum ( Rao and Nandineni, 2017 ) and to fill the gaps within and between the scaffolds using PBJelly version 14.9.9 1 with default parameters. The refined assembly obtained with PBjelly was used for the subsequent analyses.…”

“…The genome sequences of many Colletotrichum species are available in public databases but most of these are fragmented into several contigs or scaffolds. Although a few species have relatively less fragmented genomes, like C. scovillei ( Han et al, 2016 ) and C. truncatum ( Rao and Nandineni, 2017 ) with 34 and 80 scaffolds, respectively. Only C. higginsianum is among a few phytopathogenic fungi for which nearly-complete genome sequence is publically available (11 complete chromosomes, 1 incomplete chromosome and 12 unitigs) ( Zampounis et al, 2016 ; Dallery et al, 2017 ).…”

“…A high quality genome sequence of C. truncatum is available which provides a glimpse of the genome composition and functionally important categories of genes ( Rao and Nandineni, 2017 ). However, there were several gaps in the existing draft assembly which was sequenced on an Illumina platform.…”