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

Abstract

The ascomycete fungus Colletotrichum truncatum is a major phytopathogen with a broad host range which causes anthracnose disease of chilli. The genome sequencing of this fungus led to the discovery of functional categories of genes that may play important roles in fungal pathogenicity. However, the presence of gaps in C. truncatum draft assembly prevented the accurate prediction of repetitive elements, which are the key players to determine the genome architecture and drive evolution and host adaptation. We re-sequenced its genome using single-molecule real-time (SMRT) sequencing technology to obtain a refined assembly with lesser and smaller gaps and ambiguities. This enabled us to study its genome architecture by characterising the repetitive sequences like transposable elements (TEs) and simple sequence repeats (SSRs), which constituted 4.9 and 0.38% of the assembled genome, respectively. The comparative analysis among different Colletotrichum species revealed the extensive repeat rich regions, dominated by Gypsy superfamily of long terminal repeats (LTRs), and the differential composition of SSRs in their genomes. Our study revealed a recent burst of LTR amplification in C. truncatum, C. higginsianum, and C. scovillei. TEs in C. truncatum were significantly associated with secretome, effectors and genes in secondary metabolism clusters. Some of the TE families in C. truncatum showed cytosine to thymine transitions indicative of repeat-induced point mutation (RIP). C. orbiculare and C. graminicola showed strong signatures of RIP across their genomes and “two-speed” genomes with extensive AT-rich and gene-sparse regions. Comparative genomic analyses of Colletotrichum species provided an insight into the species-specific SSR profiles. The SSRs in the coding and non-coding regions of the genome revealed the composition of trinucleotide repeat motifs in exons with potential to alter the translated protein structure through amino acid repeats. This is the first genome-wide study of TEs and SSRs in C. truncatum and their comparative analysis with six other Colletotrichum species, which would serve as a useful resource for future research to get insights into the potential role of TEs in genome expansion and evolution of Colletotrichum fungi and for development of SSR-based molecular markers for population genomic studies.

Comparative genome analysis indicates rapid evolution of pathogenicity genes inColletotrichum tanaceti

“…Transposons were in close proximity to gene categories of pathogenicity in C. tanaceti such as the SMB clusters, peptidases and effectors. The significant association of TE with pathogenicity genes were previously reported in C. truncatum [117] and C. higginsianum [15]. Colletotrichum tanaceti had the highest number of rapidly evolving CAZyme families among the 17 species studied which also was indicative of the rapid evolutionary rate in these pathogenicity genes.…”

“…The majority of TE were retro-transposons, similar to other Colletotrichum spp. [117]. Proliferation of repetitive elements especially transposons, is known to be a major mechanism driving expansion of eukaryote genomes [118,119] and therefore, could be the reason the C. tanaceti genome is larger than average for fungi in the phylum Ascomycota (36.91 Mb) [120].…”

“…Repeat-induced-point mutation (RIP) is a fungal-specific mechanism for limiting transposon proliferation below destructive levels [39]. RIP is known to generate A-T rich regions with lower gene densities and higher evolutionary rates than the core genome, thus generating "two-speed" genomes in several fungi [117,[121][122][123]. The presence of A-T rich, gene sparse regions in the C. tanaceti genome could therefore, be a byproduct of the RIP due to TE proliferation.…”

Genómica de hongos fitopatógenos como herramienta para el desarrollo de estrategias de manejo

“…Estudios de genómica comparativa de hongos de diferentes procedencias, como lo son oportunistas, patógenos animales y fitopatógenos han permitido establecer que estos últimos tienen secuencias más grandes, lo cual se ha asociado a la presencia de un alto número de fragmentos repetitivos y no necesariamente a que tengan un mayor número de genes (Aylward et al, 2017). Estas secuencias repetitivas corresponden a elementos transponibles (ET) y secuencias simples repetidas (SSRs) (Rao, Sharda, Oddi & Nandineni, 2018). Los ETs se han encontrado flanqueando genes que codifican proteínas efectoras y contribuyen a dos características principales de los hongos fitopatógenos: su variabilidad y adaptabilidad.…”

“…La presencia de ETs promueve la variabilidad genómica ya que estos pueden direccionar la generación de nuevas proteínas, las cuales confieren posibles ventajas a la supervivencia, que en el caso de los hongos fitopatógenos es superar el sistema de defensa de la planta para infectar y colonizar (Aylward et al, 2017;Mat, Cheah & Nadarajah, 2019). Por otro lado, los SSRs o microsatélites también juegan un rol importante en la organización génica y contribuyen a la evolución de una determinada especie, creando variantes genéticas (Rao et al, 2018).…”