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

P Gan,Y Narusaka,A Tsushima,M Kawaradani,M Narusaka,R Hiroyama,U Damm,Y Takano,K Shirasu

doi:10.1038/s41598-019-50076-5

Abstract

Species of the fungal genus Colletotrichum are among the most devastating pathogens of agricultural crops in the world. Based on DNA sequence data (ITS, GAPDH, CHS-1, ACT, TUB2) and morphology, we revealed Colletotrichum isolates infecting the oil crop Perilla frutescens, commonly known as shiso, to represent a previously unknown species of the C. destructivum species complex and described it as C. shisoi. We found that C. shisoi appears to be able to adopt a hemibiotrophic lifestyle, characterised by the formation of biotrophic hyphae followed by severe necrotic lesions on P. frutescens, but is less virulent on Arabidopsis, compared to its close relative C. higginsianum which also belongs to the C. destructivum species complex. The genome of C. shisoi was sequenced, annotated and its predicted proteome compared with four other Colletotrichum species. The predicted proteomes of C. shisoi and C. higginsianum, share many candidate effectors, which are small, secreted proteins that may contribute to infection. Interestingly, C. destructivum species complex-specific secreted proteins showed evidence of increased diversifying selection which may be related to their host specificities.

Highlights

Perilla frutescens, or shiso, is an herbaceous plant belonging to the Lamiaceae family and was originally cultivated throughout East and South-East Asia as a culinary herb, oil source and as a traditional medicine[1,2]
In order to identify these strains to the species level, a phylogenetic tree based on internal transcribed spacers (ITS), glyceraldehyde-3-phosphate dehydrogenase (GAPDH), chitin synthase 1 (CHS-1), actin (ACT) and beta-tubulin (TUB2) sequences was calculated and used for comparison of the strains from P. frutescens with all currently accepted species in the C. destructivum species complex (Supplementary Table S2)
DNA sequences obtained from the MAFF Genebank project of several strains isolated from L. amplexicaule, a host from the same family as P. frutescens, which had previously been identified as C. higginsianum based on ITS sequences[11], were included (Supplementary Table S2)

Summary

Introduction

Shiso, is an herbaceous plant belonging to the Lamiaceae family and was originally cultivated throughout East and South-East Asia as a culinary herb, oil source and as a traditional medicine[1,2]. The authors hypothesised the species described by Fukui to be a synonym of C. gloeosporioides, since C. gloeosporioides was more frequently isolated from infected plants[9]. None of these reports was confirmed by molecular data and the systematic position of C. yoshinaoi, which lacks a living type strain, is unknown. Sequenced genomes have included strains belonging to different species complexes, which comprise closely related species that are phylogenetically distinct from other members of the same genus. The aims of this study were to characterise one of the causal agents of anthracnose of P. frutescens in Japan based on multi-locus sequence data and morphology. We aimed to analyse the conservation patterns of genes encoding small, secreted proteins, since these may contribute to differences in infection outcomes

Objectives

Methods

Results

Conclusion