Recent Papers

Volume 7 - 2016 - Issue 8 (SI Colletotrichum)

1. Discovering and dealing with the unknown aspects of Colletotrichum

Authors: RS Jayawardena, JY Yan, L Cai, BD Shenoy, G Sharma

Recieved: 01 May 2016, Accepted: 31 May 2016, Published: 31 May 2016

Keywords:

2. Mycosphere Essay 6: Why is it important to correctly name Colletotrichum species?

Authors: Jayawardena RS, Hyde KD, Jeewon R, Li XH, Liu M, Yan JY

Recieved: 05 May 2016, Accepted: 18 June 2016, Published: 23 June 2016

Colletotrichum is one of the most important plant pathogenic genera worldwide. There have been many studies on this genus, as species are important in many disciplines, especially in plant disease diagnostics. In this paper we discuss the importance of accurately naming Colletotrichum species. In most cases we conclude that it is important to know the correct identity of species, as the name is the key to all data for that taxon. The entire knowledge and data on a species relies on it being correctly named. The naming of Colletotrichum species have become “mostly fit-for-purpose”, with the use of molecular data. The aim of this contribution is to illustrate the importance of naming Colletotrichum species using several essential examples.

Keywords: agriculture – evolutionary history – nomenclature – plant pathology – species complex – taxonomy

3. Colletotrichum systematics: Past, present and prospects

Authors: Sharma G, Shenoy BD

Recieved: 20 August 2016, Accepted: 01 November 2016, Published: 08 November 2016

Colletotrichum is one of the serious plant pathogens, with worldwide distribution, causing anthracnose in economically important crops. Every year many research papers and reports are published on Colletotrichum phylogeny and taxonomy. Many novel Colletotrichum species have been described based on morphological characters and multi-locus phylogenetic analysis. There is, however, a need to develop a consensus among researchers on the gene sets to be used in sequence-based identification and resolution of cryptic species of Colletotrichum. Though a polyphasic approach is recommended, it is not fully enforced in many publications. In this paper, the methods prevalent in Colletotrichum systematics are discussed, which is followed by our suggestions towards developing a stable and reliable classification system for Colletotrichum.

Keywords: anthracnose – barcoding – identification – morphology – new taxa – polyphasic taxonomy

4. Assessing the genetic diversity of grape ripe rot pathogen Colletotrichum using SRAP markers.

Authors: Huang YQ, Zang CQ, Li LX, Liang CH, Bai YJ, Xie JH

Recieved: 27 September 2016, Accepted: 06 November 2016, Published: 10 November 2016

Grape ripe rot caused by species of Colletotrichum is one of the most serious grape diseases worldwide. Information on the genetic variation and population structure of grape ripe rot pathogens would help to develop the theoretical framework of disease occurrence and prevention, epidemic dynamics, and control technologies. In this study, twenty five Colletotrichum gloeosporioides strains isolated from grape diseased samples that were collected from 17 different locations in China were analyzed using six sequence-related amplified polymorphism (SRAP) primer pairs. In total, 164 discernible bands were obtained. Of which 156 showed high polymorphism at a rate of 95.12%. Cluster analysis revealed that the 25 C. gloeosporioides strains had a close genetic relationship and rich genetic diversity with similarity coefficients that ranged from 0.61 to 0.95. The data also demonstrated that no correlation was identified between the isolates or SRAP groups and their geographical distribution.

Keywords: cluster analysis – Colletotrichum gloeosporioides – polymorphic richness – similarity coefficient

5. Colletotrichum aracearum and C. camelliae-japonicae, two holomorphic new species from China and Japan

Authors: Hou LW, Liu F, Duan WJ, Cai L

Recieved: 01 October 2016, Accepted: 27 November 2016, Published: 03 December 2016

Colletotrichum aracearum sp. nov. from Monstera delociosa and Philodenron selloum, and C. camelliae-japonicae sp. nov. from Camellia japonica, are described in this paper. Strains were isolated using single spore isolation technique from the spore masses formed on leaf lesions, and successfully induced for sexual states in cultivation. Morphological comparisons were made with related species. Phylogenetic relationships were inferred based on ITS, ACT, TUB2, and GAPDH sequences. C. camelliae-japonicae belongs to the C. boninense species complex, while C. aracearum does not nest within any currently known species complex but forms a sister clade to C. cliviae. This is the first report of Colletotrichum species from hosts Monstera delociosa and Philodenron selloum.

Keywords: Anthracnose – Camellia – Monstera – Morphology – Philodenron – Phylogeny – Taxonomy

6. Whole genome re-sequencing and transcriptome analysis of the Stylosanthes Anthracnose pathogen Colletotrichum gloeosporioides reveal its characteristics

Authors: Huang HP, Ma S, Huang JH, Zheng JL, Yi KX

Recieved: 01 October 2016, Accepted: 27 November 2016, Published: 03 December 2016

Stylosanthes anthracnose is an important disease caused by Colletotrichum gloeosporioides, which affects the production and utilization of Stylosanthes species in the world. Despite their importance, little progress has been made in understanding Stylosanthes anthracnose pathogens due to their insufficient genomic and transcriptomic data. In the current study, whole genome re-sequencing of seven C. gloeosporioides strains was carried out together with next generation RNA sequencing of C. gloeosporioides strain CH008. Whole genome re-sequencing was conducted with reference to the genome of highly virulent C. gloeosporioides strain CH008. It resulted in 10.06 G of effective data, with a mean proportion of 67.40% genes mapped to the reference strain and an average genome coverage of 79.71%. A total of 2,149,030 single nucleotide polymorphisms, 178,620 insertions and deletions, and 654 structural variations were discovered on the genomes of the seven tested strains. Transcriptomic analysis produced approximately 30.5 million high quality reads assembled into 33,529 contigs and further integrated into 25,376 unigenes. All assembled sequences were annotated against public databases. A total of 12,398 unigenes were assigned to 61 sub-categories of Gene Ontology terms. Among them, 3,717 unigenes were identified and mapped onto 264 pathways against Kyoto Encyclopaedia of Genes and Genomes pathway database. This study provides the first comprehensive transcriptomic resource available for C. gloeosporioides. The genome assembly and the unigenes identified in the study will benefit further studies on functional genes involved in pathogenicity. Simple sequence repeat markers developed in this study will facilitate studies on marker-assisted genomic and pathogenic diversities of Colletotrichum gloeosporioides.

Keywords: de novo transcriptome assembly – gene annotation – pathogenicity – pathway analysis– RNA sequencing – SSR

7. Mycosphere Essay 16: Colletotrichum: Biological control, bio-catalyst, secondary metabolites and toxins

Authors: Jayawardena RS, Li XH, Liu M, Zhang W, Yan JY

Recieved: 29 October 2016, Accepted: 29 November 2016, Published: 04 December 2016

The genus Colletotrichum has received considerable attention in the past decade because of its role as an important plant pathogen. The importance of Colletotrichum with regard to industrial application has however, received little attention from scientists over many years. The aim of the present paper is to explore the importance of Colletotrichum species as bio-control agents and as a bio-catalyst as well as secondary metabolites and toxin producers. Often the names assigned to the above four industrial applications have lacked an accurate taxonomic basis and this needs consideration. The current paper provides detailed background of the above topics.

Keywords: biotransformation – colletotrichin – mycoherbicide – mycoparasites – pathogenisis – phytopathogen

8. An account of Colletotrichum species associated with strawberry anthracnose in China based on morphology and molecular data

Authors: Jayawardena RS, Huang JK, Jin BC, Yan JY, Li XH, Hyde KD, Bahkali AH, Yin SL, Zhang GZ

Recieved: 31 October 2016, Accepted: 28 November 2016, Published: 06 December 2016

Strawberry anthracnose is an important disease in China that results in significant economic losses. A number of Colletotrichum species are known to be pathogens of strawberry. A survey of strawberry fields in eight provinces of China was carried out to identify the causal agents of strawberry anthracnose. The disease mainly causes crown rot, leading to plant wilt and death in the nursery stage, after transplanting in green house, which makes anthracnose a major threat to strawberry production and quality. Multi-locus sequence analysis coupled with morphological assessment revealed that the disease-associated taxa belong to two Colletotrichum species complexes: Colletotrichum nymphaeae (acutatum species complex), C. fructicola and C. changpingense sp. nov. (gloeosporioides species complex). The novel species is introduced in this paper and illustrated. The new species is closely related to C. theobromicola and pathogenicity tests proved that it is pathogenic to the strawberry crown, fruits and leaves.

Keywords: C. nymphaeae – crown rot – molecular phylogeny – morphology – pathogen

9. Identification and characterization of Colletotrichum species causing grape ripe rot in southern China

Authors: Lei Y, Tang XB, Jayawardena RS, Yan JY, Wang XD, Liu M, Chen T, Liu XM, Wang JC, Chen QX

Recieved: 08 November 2016, Accepted: 01 December 2016, Published: 15 December 2016

Grape ripe rot is known to be causing serious losses in grapes in many countries. In order to clarify the species of pathogen causing grape ripe rot in southern China, 62 samples with ripe rot symptoms were collected from Fujian and Guizhou Provinces. Single spore isolation techniques resulted in 50 isolates of Colletotrichum species. Based on multigene data and morphology, 48 isolates were identified as C. viniferum and one isolate was identified as C. citri. A Colletotrichum species, sister to C. cliviae, was identified to be causing grape ripe rot. However, until further collections are made, this species will be remain as Colletotrichum sp. This is the first time that C. citri and the undetermined Colletotrichum species sister to C. cliviae have been reported to be associated with grape ripe rot in the world.

Keywords: China – Colletotrichum citri – Grape ripe rot – Identification – Pathogenicity

10. Notes on currently accepted species of Colletotrichum

Authors: Jayawardena RS, Hyde KD, Damm U, Cai L, Liu M, Li XH, Zhang W, Zhao WS, Yan JY

Recieved: 01 December 2016, Accepted: 20 December 2016, Published: 26 December 2016

Colletotrichum is an economically important plant pathogenic genus worldwide, but can also have endophytic or saprobic lifestyles. The genus has undergone numerous revisions in the past decades with the addition, typification and synonymy of many species. In this study, we provide an account of the 190 currently accepted species, one doubtful species and one excluded species that have molecular data. Species are listed alphabetically and annotated with their habit, host and geographic distribution, phylogenetic position, their sexual morphs and uses (if there are any known). There are eleven species complexes in Colletotrichum and 23 singleton species. The main characters of each species complex are detailed with illustrations. Phylogenetic trees are provided for the whole genus and each species complex. Genes and combination of genes that can be used for identification of the species complexes are suggested. Specific genes that can be used in species identification are given when possible.

Keywords: Glomerellaceae – nomenclature – phylogeny – species complex – taxonomy