CMap3D: a 3D visualization tool for comparative genetic maps

Duran, Chris; Boskovic, Zoran; Imelfort, Michael; Batley, Jacqueline; Hamilton, Nicholas A.; Edwards, David

doi:10.1093/bioinformatics/btp646

Cited by 17 publications

(7 citation statements)

References 13 publications

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“…The high heritability of SNPs makes them an excellent indicator of genetic diversity and phylogeny in pathogenic fungal species, such as L. maculans. This allows for the construction of high-density genetic maps which can provide a scaffold to map important genetic traits (Duran et al, 2010a;Edwards and Batley, 2004;Edwards et al, 2007a).…”

Section: Single Nucleotide Polymorphisms (Snps)mentioning

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: Single Nucleotide Polymorphisms (Snps)mentioning

confidence: 99%

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

Zander¹

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“…This includes the development of custom visualisation tools , Duran et al, 2010a, Duran et al, 2009b and bioinformatics systems to traverse the genome to phenome divide (Duran et al, 2010b, Edwards and. Many molecular marker databases provide various types of markers for a range of species while some databases provide information on a single type of marker (Lai et al, 2012c).…”

Section: Molecular Databasesmentioning

confidence: 99%

“…Wheatgenome.info provides a GBrowse2 based wheat genome viewer, CMap and CMap3D comparative genetic map viewers (Duran et al, 2010a, Youens-Clark et al, 2009. From the GBrowse2-based wheat genome viewer, wheat reference genomic sequences are currently only available for wheat group 7 chromosomes (Berkman et al, 2011a, Berkman et al, 2013.…”

Section: Molecular Databasesmentioning

confidence: 99%

Genome diversity in Triticum aestivum

Lai¹

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The aims of this PhD research are to identify and characterise genome diversity in Triticum aestivum (bread wheat).This research will establish a process for the identification of large numbers of single nucleotide polymorphisms (SNPs) and other genetic variations in Triticum aestivum.Single nucleotide polymorphisms (SNPs) are the most abundant type of molecular genetic marker and can be used for producing high-resolution genetic maps, marker-trait association studies and marker assisted breeding. Large polyploid genomes, such as wheat, present a challenge for SNP discovery due to the potential presence of multiple homoeologues for each gene.AutoSNPdb has been successfully applied to identify SNPs from Sanger sequence data for several species, including barley, rice and Brassica, but the volume of data required to accurately call SNPs in the complex genome of wheat has prevented its application to this important crop. DNA sequencing technology has been revolutionised by the introduction of next generation sequencing, and it is now possible to generate several million sequence reads in a timely and cost effective manner.Wheat transcriptome sequence data has been generated using Roche 454 Life Sciences technology. This data has been applied for SNP discovery using a modified autoSNPdb method, which integrates SNP and gene annotation information with a graphical viewer. A total of 4,694,141 sequence reads from three bread wheat varieties were assembled to identify a total of 38,928 candidate SNPs. Each SNP is within an assembly complete with annotation, enabling the selection of polymorphism within genes of interest.The discovery of large numbers of genomic SNPs across 16 Australian diverse bread wheat varieties has been completed using a novel algorithm SGSautoSNP. More than 10x whole genome shotgun Illumina paired read sequence data was generated through a bioplatforms collaboration and the data mapped to the draft assemblies of chromosomes ii 7A, 7B and 7D. Over 4 million inter-varietal SNPs were identified. SNP density varied along the lengths chromosome syntenic builds as well as between genomes.SNP density analysis and SNP transition/transversion ratio analysis provide insights into the evolution and breeding history of this important crop. Both the SNP density and SNP transition/transversion ratios across the D genome are significantly lower than across the A and B genomes. This difference reflects the evolutionary history of this crop. In addition, genes within low SNP density regions may have been selected during domestication and breeding. Furthermore, this SNP resource permits the application of high resolution skim based genotyping by sequencing (GBS), trait association and analysis of structural variation in populations.An integrated database and portal for wheat genome resource, WheatGenome.info, has been established and published online. This portal provides a variety of web-based systems hosting wheat genome and genomic data, including genomic SNPs, to support wheat research and crop improve...

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“…Studying the genetic diversity of fungal genomes using SNPs as genetic markers is becoming an increasingly popular approach due to several beneficial features (Appleby et al, 2009). SNPs are found in high densities in genomes, which assists in applications like map-based positional cloning, creating highdensity genetic maps and genome mapping (Edwards and Batley, 2004;Edwards et al, 2007;Duran et al, 2010). Furthermore, SNPs are also a very good indicator of genetic diversity within fungal pathogenic species such as L. maculans.…”

Section: Single Nucleotide Polymorphisms (Snps)mentioning

confidence: 99%

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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CMap3D: a 3D visualization tool for comparative genetic maps

Abstract: The software is a stand-alone application written in Processing and Java. Binaries are available for Windows, OSX and Linux, and require Sun Microsystems Java Runtime Environment 1.6 or later. The software is freely available for non-commercial use from http://flora.acpfg.com.au/.

Cited by 17 publications

References 13 publications

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

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

Genome diversity in Triticum aestivum

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

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