Genome-Wide Transcriptomic Analysis of the Effects of Infection with the Hemibiotrophic Fungus Colletotrichum lindemuthianum on Common Bean

Abstract

Bean anthracnose caused by the hemibiotrophic fungus Colletotrichum lindemuthianum is one of the most important diseases of common bean (Phaseolus vulgaris) in the world. In the present study, the whole transcriptome of common bean infected with C. lindemuthianum during compatible and incompatible interactions was characterized at 48 and 72 hpi, corresponding to the biotrophy phase of the infection cycle. Our results highlight the prominent role of pathogenesis-related (PR) genes from the PR10/Bet vI family as well as a complex interplay of different plant hormone pathways including Ethylene, Salicylic acid (SA) and Jasmonic acid pathways. Gene Ontology enrichment analysis reveals that infected common bean seedlings responded by down-regulation of photosynthesis, ubiquitination-mediated proteolysis and cell wall modifications. In infected common bean, SA biosynthesis seems to be based on the PAL pathway instead of the ICS pathway, contrarily to what is described in Arabidopsis. Interestingly, ~30 NLR were up-regulated in both contexts. Overall, our results suggest that the difference between the compatible and incompatible reaction is more a question of timing and strength, than a massive difference in differentially expressed genes between these two contexts. Finally, we used RT-qPCR to validate the expression patterns of several genes, and the results showed an excellent agreement with deep sequencing.

Alterations in Gene Expression during Incompatible Interaction between Amendoim Cavalo Common Bean and Colletotrichum lindemuthianum

“…PR1a is postulated to encode a PR protein featuring the Bet v I domain [36]. A recent transcriptome study, delving into the incompatible interaction between strain C531 and the BAT93 cultivar, underscored the pivotal role of PR10/Bet v I in conferring disease resistance in common beans [37].…”

Global transcriptome analysis reveals resistance genes in the early response of common bean (Phaseolus vulgaris L.) to Colletotrichum lindemuthianum

“…To further identify resistance-related genes involved in the same common bean- C. lindemuthianum interaction, these genotypes were selected for transcriptome analysis. Previous common bean - C. lindemuthianum interaction studies focused on gene expression beyond 24 hpi [ 21 , 22 , 32 ]. However, the early response of common bean to C. lindemuthianum has not been fully characterized.…”

“…Phvul.001G241300 possibly interacted with Phvul.001G243600 and Phvul.001G243700 and may be involved in anthracnose resistance in common bean. Moreover, the candidate genes Phvul.002G293000 and Phvul.003G247200 were also shown to respond to C. lindemuthianum in BAT93 [ 32 ], indicating their putative roles in anthracnose resistance. Additionally, we explored DEGs at other anthracnose resistance-related loci.…”

Morphological and transcriptional analysis of Colletotrichum lindemuthianum race 7 during early stages of infection in common bean

“…The RNAseq methodology applied to eukaryotic pathosystems (e.g., Colletotrichum higginsianum - Arabidopsis thaliana , and Colletotrichum graminicola - Zea mays ) has allowed for the identification of putative effectors, secondary metabolites, and other genes whose expression are determinant in the infection processes ( O’Connell et al, 2012 ). The transcriptomic studies in the pathosystem C. lindemuthianum - P. vulgaris, have been focused on the host molecular response, particularly on the detection of differentially expressed genes encoding resistance proteins in the host ( Padder et al, 2016 ; Alvarez-Diaz et al, 2022 ). However, from the pathogen´s perspective, only one study has described a repertoire of effector candidate genes, and no study has performed a transcriptomic characterization of Clr7 at different times post-infection during an in vivo assay ( Padder et al , 2016 ; de Queiroz et al, 2019 ; Alvarez-Diaz et al , 2022 ).…”

“…The transcriptomic studies in the pathosystem C. lindemuthianum - P. vulgaris, have been focused on the host molecular response, particularly on the detection of differentially expressed genes encoding resistance proteins in the host ( Padder et al, 2016 ; Alvarez-Diaz et al, 2022 ). However, from the pathogen´s perspective, only one study has described a repertoire of effector candidate genes, and no study has performed a transcriptomic characterization of Clr7 at different times post-infection during an in vivo assay ( Padder et al , 2016 ; de Queiroz et al, 2019 ; Alvarez-Diaz et al , 2022 ). Therefore, we characterized for the first time the infection process of Clr7 at morphological and transcriptomic levels, establishing the correlation between the infection structures and gene repertoire from the pathogen in planta .…”