Population Diversity of Leptosphaeria maculans in Australia

Patel, Dhwani A.; Zander, Manuel; Wouw, Angela P. Van de; Mason, Annaliese S.; Edwards, David; Batley, Jacqueline

doi:10.5539/ijb.v7n3p18

Cited by 8 publications

(11 citation statements)

References 33 publications

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“…The overall method of genetic spread of L. maculans in the environment is yet to be elucidated, as the latest studies have shown contrasting population structures in different regions (Dilmaghani et al, 2012, Travadon et al, 2011. A recent diversity analysis by Patel et al (2015) indicates that the L. maculans population in Australia is panmictic, with high rate of sexual reproduction and evolutionary diversification within fungal populations.…”

Section: Maculans Genetics and Genomicsmentioning

confidence: 99%

Understanding the structure and variation within the genome of the pathogenic ascomycete fungus Leptosphaeria maculans

Zander¹

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The ascomycete fungus Leptosphaeria maculans is a major pathogen of Brassica species, particularly canola (Brassica napus; rapeseed; oil-seed rape), and the primary cause of crop losses of canola in Australia, causing blackleg disease. L. maculans, a filamentous ascomycete, is the causal agent of phoma stem canker, commonly referred to as blackleg.In late stages of infection, it spreads through the stem vasculature causing lesions, leading to poor growth, lodging and eventually plant death. This fungus is found in canola-growing regions worldwide such as Australia, Canada and Europe. Increased production of canola in these regions has led to a rise in the severity of the disease. In Australia alone, L. maculans infection is responsible for an estimated Australian $100 million in crop losses each year, with average losses ranging from 15-48 % and significant efforts are underway to improve resistance to this disease.Understanding the characteristics of L. maculans is vital for developing an effective and sustainable approach to the management of blackleg disease on Brassica species. The completion of the L. maculans genome sequence was a significant development in the study of this fungal pathogen and provides a reference genome to which molecular markers can be physically mapped. This has been highly useful in other plant pathogens with sequenced genomes, such as the wheat pathogen Parastagonospora nodorum and the cereal pathogen Fusarium graminearum. Importantly, a reference genome also allows mapping of whole genome re-sequencing data, which is becoming a high-throughput, costeffective method to study genome-wide diversity, particularly for the relatively small, lower complexity genomes of many fungal species. By re-sequencing the genome of different L. maculans isolates, variations in genome sequence and structure can be elucidated.Advances in genome sequencing technologies have revolutionised plant and fungal genomics. They have made genome sequencing, re-sequencing and Single Nucleotide Polymorphism (SNP) discovery highly accessible, high-throughput and cost-effective. The process of whole genome re-sequencing involves aligning millions of short sequence reads to a reference genome sequence. Once this has been achieved, it is possible to identify genetic variation between individuals, which can be linked to variation in phenotype to provide molecular genetic markers and insights into gene function.Sequence variation can have a major impact on how an organism develops and responds to the environment. III | P a g eThis thesis describes the implementation of several approaches to elucidating the genome structure and variation of a number of L. maculans isolates, including SNPs and presence/absence variations (PAVs).Initially, the re-sequencing of two L. maculans isolates for the identification of 21,814 SNPs was performed. I demonstrated the application of a novel SNP calling method, SGSautoSNP and its robustness and sensitivity in identifying polymorphisms in L.maculans. I described the use of these S...

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Section: Maculans Genetics and Genomicsmentioning

confidence: 99%

Understanding the structure and variation within the genome of the pathogenic ascomycete fungus Leptosphaeria maculans

Zander¹

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“…Previous work (Chapter 3; Rouxel et al, 2011;Zander et al, 2013;Grandaubert et al, 2014b;Patel et al, 2015) has led us to understand that the Australian blackleg population is highly diverse.…”

Section: Discussionmentioning

confidence: 99%

“…On the other hand, Dilmaghani et al (2012) proposed from minisatellite marker results that two genetically different populations of blackleg are present in Western Canada. Zander et al (2013) conducted a small scale population diversity study using SNPs, whose successful results were used as a foundation for the large-scale study described in Patel et al (2015) (Chapter 3).…”

Section: Population Diversitymentioning

confidence: 99%

“…This sort of adaptive divergence is consistent with the permanent arms race the pathogen is involved in with its host. Previous studies have established that L. maculans possesses a high evolutionary potential and rapidly evolves to overcome host resistance (Chapter 3; Barrins et al, 2004;Rouxel et al, 2011;Travadon et al, 2011;Dilmaghani et al, 2012;Zander et al, 2013;Grandaubert et al, 2014b;Patel et al, 2015). Gene loss via deletion is an effective method of adaptation employed by several fungal pathogens like Magnaporthe oryzae (Couch et al, 2005), Blumeria graminis (Wicker et al, 2013), including L. maculans (Gout et al, 2006b;Fudal et al, 2007).…”

Section: Overcoming Host Resistancementioning

confidence: 99%

“…SGSautoSNP predicts single nucleotide point mutations between the samples provided as input (Lorenc et al, 2012). Zander et al (2013) and Patel et al (2015) applied this tool to two different sample sets. The former highlighted the efficacy of this tool in identifying differences between two blackleg isolates without the need of a reference genome whereas the latter used the SNP resource generated from this tool for population genetic analyses of the pathogen.…”

Section: Three Approaches For L Maculans Avirulence Gene Identificationmentioning

confidence: 99%

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

Patel¹

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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...

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