Single‐nucleotide polymorphism discovery in <i><scp>L</scp>eptographium longiclavatum</i>, a mountain pine beetle‐associated symbiotic fungus, using whole‐genome resequencing

Ojeda, Darío I.; Dhillon, Braham; Tsui, Clement K. M.; Hamelin, Richard

doi:10.1111/1755-0998.12191

Cited by 14 publications

(13 citation statements)

References 53 publications

(141 reference statements)

Supporting

Mentioning

Contrasting

Unclassified

Order By: Relevance

“…In barley powdery mildew ( Blumeria graminis ), the SNP rate observed between pairs of isolates was lower at 1 SNP/kbp [56]. Across isolates of the multinucleate endomycorrhizal Glomeromycete Rhizophagus irregularis [57] and the beetle-symbiont Leptographium longiclavatum [58], even lower SNP densities of 0.2 SNPs/kbp (28,872 SNPs in 140.9 Mb) and 0.6 SNPs/kbp (17,266 in 28.9 Mbp) respectively, were observed. In contrast, a population study of the multinucleate human pathogens Coccidioides immitis and C. posadasii reported a rate of 23.7 SNPs/kbp relative to the C. immitus RS reference genome assembly (687,250 SNPs in 28.95 Mb) [59], which though slightly higher is within a similar range to R. solani AG8 (Table 3).…”

Section: Resultsmentioning

confidence: 99%

Genome Sequencing and Comparative Genomics of the Broad Host-Range Pathogen Rhizoctonia solani AG8

et al. 2014

View full text Add to dashboard Cite

Rhizoctonia solani is a soil-borne basidiomycete fungus with a necrotrophic lifestyle which is classified into fourteen reproductively incompatible anastomosis groups (AGs). One of these, AG8, is a devastating pathogen causing bare patch of cereals, brassicas and legumes. R. solani is a multinucleate heterokaryon containing significant heterozygosity within a single cell. This complexity posed significant challenges for the assembly of its genome. We present a high quality genome assembly of R. solani AG8 and a manually curated set of 13,964 genes supported by RNA-seq. The AG8 genome assembly used novel methods to produce a haploid representation of its heterokaryotic state. The whole-genomes of AG8, the rice pathogen AG1-IA and the potato pathogen AG3 were observed to be syntenic and co-linear. Genes and functions putatively relevant to pathogenicity were highlighted by comparing AG8 to known pathogenicity genes, orthology databases spanning 197 phytopathogenic taxa and AG1-IA. We also observed SNP-level “hypermutation” of CpG dinucleotides to TpG between AG8 nuclei, with similarities to repeat-induced point mutation (RIP). Interestingly, gene-coding regions were widely affected along with repetitive DNA, which has not been previously observed for RIP in mononuclear fungi of the Pezizomycotina. The rate of heterozygous SNP mutations within this single isolate of AG8 was observed to be higher than SNP mutation rates observed across populations of most fungal species compared. Comparative analyses were combined to predict biological processes relevant to AG8 and 308 proteins with effector-like characteristics, forming a valuable resource for further study of this pathosystem. Predicted effector-like proteins had elevated levels of non-synonymous point mutations relative to synonymous mutations (dN/dS), suggesting that they may be under diversifying selection pressures. In addition, the distant relationship to sequenced necrotrophs of the Ascomycota suggests the R. solani genome sequence may prove to be a useful resource in future comparative analysis of plant pathogens.

show abstract

Section: Resultsmentioning

confidence: 99%

Genome Sequencing and Comparative Genomics of the Broad Host-Range Pathogen Rhizoctonia solani AG8

et al. 2014

View full text Add to dashboard Cite

show abstract

“…Three species-specific genotyping arrays have been developed using the Sequenom Iplex Gold technology (Ojeda et al 2014). These arrays consist of four panels, each containing up to 36 SNPs.…”

Section: Snp Panel Design and Genotypingmentioning

confidence: 99%

Fine-scale genetic diversity and relatedness in fungi associated with the mountain pine beetle

et al. 2019

Self Cite

View full text Add to dashboard Cite

The mountain pine beetle (MPB; Dendroctonus ponderosae Hopkins, 1902) forms beneficial symbiotic associations with fungi. Here we explored the fine-scale spatial genetic structure of three of those fungi using single nucleotide polymorphism. We found that single mated pairs of beetles carry not only multiple fungal species, but also multiple genotypes of each species into their galleries. We observed genetic diversity at a fine spatial scale. Most of the diversity was found within and among galleries with nonsignificant diversity among trees. We observed clonal propagation almost exclusively within galleries. Ophiostoma montium (Rumbold) Arx possessed a larger expected number of multilocus genotypes and lower linkage disequilibrium than Grosmannia clavigera (Rob.-Jeffr. & R.W. Davidson) Zipfel, Z.W. de Beer & M.J. Wingf. and Leptographium longiclavatum S.W. Lee, J.J. Kim & C. Breuil. More than 80% of fungal samples were genetically unrelated, a result that parallels what has been observed in the beetles. The proportion of genetically related samples within galleries was higher in O. montium (40%) than in G. clavigera (20%) or L. longiclavatum (6%), likely the consequence of within-gallery sexual recombination in O. montium. The underlying genetic diversity reported here and the differences among fungal species could enable the symbiont community to quickly respond to new environmental conditions or changes in the host, enhancing the maintenance of this multipartite relationship and allowing the MPB to colonize new habitats.

show abstract

“…SNP discovery has also been conducted in other fungal species such as Leptographium longiclavatum (Ojeda et al, 2014) and Venturia inaequalis (Celton et al, 2010). The former developed a SNP marker resource to analyse the population of L. longiclavatum in Canada and USA (Ojeda et al, 2014).…”

Section: Marker Assisted Studiesmentioning

confidence: 99%

Section: Marker Assisted Studiesmentioning

confidence: 99%

“…The former developed a SNP marker resource to analyse the population of L. longiclavatum in Canada and USA (Ojeda et al, 2014). They were also used to identify candidate adapter SNPs that play a role in pathogenicity and host defence detoxification (Ojeda et al, 2014). The latter used a bin mapping approach to identify SNPs via whole or partial genome resequencing of individuals in the progeny (Celton et al, 2010).…”

Section: Marker Assisted Studiesmentioning

confidence: 99%

See 1 more Smart Citation

Population diversity and genomics of the fungal pathogen of canola Leptosphaeria maculans

Patel¹

View full text Add to dashboard Cite

Canola (Brassica napus) is an important agricultural crop in Australia. Its value as an agricultural commodity has dramatically increased over the past few years to >$2000 million (AUD) in 2015.However, the production of this prosperous crop is threatened by up to 34 different pests, including fungal, bacterial and viral pathogens. Diseases caused by these pathogens lead to substantial crop losses that collectively amount to $130 million (AUD) each year. Leptosphaeria maculans (blackleg) is a ubiquitous ascomycete fungus that is the major causal agent of disease on canola plants. It is called blackleg due to its necrotrophic effects that cause stem canker at the base of the stem during the last stages of infection. When canola was first introduced to Australia as an agricultural crop in the 1970s, blackleg disease led to almost 90% crop losses, threatening to drive the nascent canola industry in Australia to the ground. In recent years, crop losses still amount to $76.6 million (AUD) per annum. Therefore, it is imperative to devise methods to control the devastating effects of this pathogen to protect this economically significant crop. In order to do so, we must decipher the genomic content that drives this pathogen to cause large-scale infections in the field.Blackleg disease is a major concern not only in Australia, but also in other parts of the world such as Europe and Canada. Over the past few years, scientists have made significant advances in decoding the genome of this pathogen. It has been established that L. maculans interacts in a genefor-gene manner with its host. It is composed of disease-causing avirulence (Avr) genes that are specifically recognised by the corresponding resistance (R) gene in the host plant. The specific location and characterisation of the Avr genes AvrLm1, AvrLm6, AvrLm4-7, AvrLm11, AvrLmJ1, AvrLm2 and AvrLm3 has been determined. Furthermore, the reference genome for this pathogen was sequenced in 2011. The reference genome based on the strain v23.1.3 is 45.12 Mb and is scaffolded onto 76 supercontigs. It was reported to be bipartite in nature, composed of AT and GCrich blocks and riddled with truncated copies of transposable elements (TEs) that were affected by Repeat-Induced Point (RIP) mutations. The availability of a reference genome has greatly assisted in designing bioinformatics tools to analyse the genomic content of this pathogen. Here we contribute to the growing pool of knowledge of blackleg genomics.This thesis begins by shedding light on the population diversity of this pathogen in Australia. We used Single Nucleotide Polymorphisms (SNPs) and sampled a large variety of isolates from different canola-growing regions across Australia. We were able to conclude that the Australian blackleg population is panmictic in nature, where members of the population interact randomly with one another, leading to high diversity via sexual reproduction. Increased genetic diversity amongst the population contributes significantly to increase the evolutionary potential of thi...

show abstract

Single‐nucleotide polymorphism discovery in Leptographium longiclavatum, a mountain pine beetle‐associated symbiotic fungus, using whole‐genome resequencing

Cited by 14 publications

References 53 publications

Genome Sequencing and Comparative Genomics of the Broad Host-Range Pathogen Rhizoctonia solani AG8

Genome Sequencing and Comparative Genomics of the Broad Host-Range Pathogen Rhizoctonia solani AG8

Fine-scale genetic diversity and relatedness in fungi associated with the mountain pine beetle

Population diversity and genomics of the fungal pathogen of canola Leptosphaeria maculans

Contact Info

Product

Resources

About