An updated phylogenetic classification of Corynespora cassiicola isolates and a practical approach to their identification based on the nucleotide polymorphisms at the ga4 and caa5 loci

Abstract

Corynespora cassiicola (Burk. & M.A. Curtis) C.T. Wei. is an anamorphic fungus that affects more than 530 plant species, including economically important crops. Several lineages of this pathogen have been recognized, but the classification of isolates into clades is time-consuming and still sometimes leads to unclear results. In this work, eight major phylogenetic clades (PhL1-PhL8) including 245 isolates of C. cassiicola from 44 plant species were established based on a Bayesian inference analysis of four combined C. cassiicola genomic loci retrieved from GenBank, i.e., rDNA internal transcribed spacer (ITS), actin-1,ga4, and caa5. The existence of PhL1-PhL5 and PhL7 as clonal lineages was further confirmed through the analysis of full-genome single-nucleotide polymorphisms of 39 isolates. Haplotypes of the caa5 locus were PhL specific and encode isoforms of the LDB19 domain of a putative α-arrestin N-terminal-like protein. Evolution of the Caa5 arrestin is in correspondence with the PhLs. ga4 and caa5 PhL consensus sequences and a cleaved amplified polymorphic sequence (CAPS) procedure were generated based on the conserved nucleotide sequences and enzyme restriction patterns observed among isolates from the same lineage, respectively. The CAPS method was validated in silico, and its practical use allowed us to differentiate between tomato and papaya isolates, as well as to reveal the prevalence of PhL1 among isolates infecting soybean in Brazil. This novel approach could be useful in the efforts to control the diseases associated with C. cassiicola.

Arrestin-Coding Genes Regulate Endocytosis, Sporulation, Pathogenicity, and Stress Resistance in Arthrobotrys oligospora

“…ARRDC1 (Arrestin domain containing 1) is considered as an autophagy-associated protein. The absence of ARRDC1 affects the expression profile of virulence-related transcription factor CCA1 and generates an acropetal array of conidia ( Banguela-Castillo et al., 2020 ). After the co-localization of ARRDC1 and Autophagy-related protein 8 (ATG8), other arrestin proteins enter the autophagic flux before autophagosome maturation ( Dong et al., 2016 ).…”

The fungal pathogen Corynespora cassiicola: A review and insights for target spot management on cotton and Soya bean

“…The wide host range of C. cassiicola and its cultivar preference were explained based on the pathogen diversity (Déon et al, 2014). Different genes of C. cassiicola have been amplified to construct phylogenetic trees to understand the evolution and variability of C. cassiicola isolates and to help build disease management strategies (Banguela-Castillo et al, 2020;Bentes et al, 2018;Déon et al, 2014;Dixon et al, 2009;Hieu et al, 2020;Nghia et al, 2008;Oktavia et al, 2017;Qi et al, ,2009Qi et al, , , 2011Shimomoto et al, 2011;Shrestha et al, 2017;Silva et al, 2003;Wu et al, 2019). Dixon et al, (2009) conducted the most prominent study on (Qi et al, 2009).…”

“…A wide genetic diversity was confirmed on C. cassiicola isolates from rubber tree (PhL1‐PhL5 and PhL7). Corynespora cassiicola isolates from Soya bean exhibited higher genetic diversity (PhL1, PhL3 and PhL5), than isolates from cotton (PhL1; Banguela‐Castillo et al., 2020).…”

“…The latest classification of C. cassiicola resulted in eight (PhL1‐PhL8) phylogenetic clades. In addition, the two‐locus CAPS (cleaved amplified polymorphic sequence) based on ga 4 and caa 5 loci was described as a novel approach to easily differentiate isolates (Banguela‐Castillo et al., 2020). A wide genetic diversity was confirmed on C. cassiicola isolates from rubber tree (PhL1‐PhL5 and PhL7).…”