Gapless Genome Assembly of the Potato and Tomato Early Blight Pathogen <i>Alternaria solani</i>

Wolters, Pieter J.; Faino, Luigi; Bosch, Trudy B. M. van den; Evenhuis, B.; Visser, R.G.F.; Seidl, Michael; Vleeshouwers, Vivianne G. A. A.

doi:10.1094/mpmi-12-17-0309-a

Cited by 45 publications

(46 citation statements)

References 19 publications

Supporting

Mentioning

Contrasting

Unclassified

Order By: Relevance

“…Both genomes had a large number of Copia and Gypsy LTRs, which are known to be both abundant and diverse in fungal genomes [23]. In contrast, only the 11-12 genome containing endogenous retrovirus 4 (ERV4) LTRs, which were only found within the smaller contigs of the genome and have previously been identified in other fungal genomes [24].…”

Section: Resultsmentioning

confidence: 99%

Assembly, annotation, and comparison of Macrophomina phaseolina isolates from strawberry and other hosts

Burkhardt

Childs

Wang

et al. 2019

Preprint

View full text Add to dashboard Cite

Background Macrophomina phaseolina is traditionally considered a broad host range fungal pathogen, but one genotype was recently shown to exhibit a host preference/specificity on strawberry. This fungus lacked a high-quality genome assembly and annotation, and little is known about genomic differences between isolates from different hosts. Results This study used PacBio sequencing and Hi-C scaffolding to provide nearly complete genome assemblies from M. phaseolina isolates recovered from strawberry and alfalfa with 60 or fewer scaffolds and N50 metrics at 4.3 and 5.0 Mb, respectively. The genomes were annotated with MAKER using multiple RNA-Seq libraries generated in this study, and over 13,000 protein-coding genes were predicted. Unique groups of orthologous genes for each M. phaseolina isolate were identified when compared to several closely related fungal species. Comparative genomics between the isolates reveal large-scale structural rearrangements including chromosomal inversions and translocations. An additional 30 isolates of M. phaseolina from various hosts, including several from strawberry, were sequenced with Illumina and compared to the high-quality strawberry isolate assembly. No conserved structural rearrangements were identified among the isolates from strawberry compared to those from other hosts, but some candidate genes were identified that were largely present in isolates pathogenic on strawberry and absent in isolates not pathogenic on this host. Conclusions High-quality reference genomes of M. phaseolina generated in this study have allowed for comparative genomics to be used to investigate the genomic changes that might have led to a host preference toward strawberry and will enable future comparative genomics studies. Having more complete scaffolds allows for structural rearrangements to be more fully assessed and ensures a greater representation of all the genes that are truly present in the genome. Work with the additional isolates in this study suggests that some genes are predominately only present in isolates that are pathogenic on strawberry, but additional work is needed to confirm the role of these genes in pathogenesis. Additional work is also needed to complete the scaffolding of smaller contigs representing smaller chromosomes identified in the strawberry genotype assembly and to determine how gene expression plays a role in pathogenicity.

show abstract

Section: Resultsmentioning

confidence: 99%

Assembly, annotation, and comparison of Macrophomina phaseolina isolates from strawberry and other hosts

Burkhardt

Childs

Wang

et al. 2019

Preprint

View full text Add to dashboard Cite

show abstract

“…Six contigs in each of 153 the two assemblies contained telomeric repeats on both ends and therefore, are most likely to represent full 154 chromosomal molecules. Four other contigs in both the assemblies contained telomeric repeats on one end 155 but were of similar size of full chromosome molecules as described in A. solani 13 . Therefore, the genome 156 assemblies for A. alternata isolates represented ten nearly complete chromosomes each.…”

mentioning

confidence: 82%

“…In addition to the three genomes, we also predicted genes de novo in the genome assemblies of 169 three other Alternaria species which were sequenced using long-read technologies viz. A. brassicicola 170 (abra43) 11 , A. alternata (ATCC34957) 12 , and A. solani (altNL03003) 13 (Table 1). These six genomes and 171 their gene predictions were used for the comparative analyses of secondary metabolite encoding gene 172 clusters and effector-coding genes.…”

mentioning

confidence: 99%

Comparative genomics of Alternaria species provides insights into the pathogenic lifestyle of Alternaria brassicae – a pathogen of the Brassicaceae family

Rajarammohan

Paritosh

Pental

et al. 2019

Preprint

View full text Add to dashboard Cite

1 Alternaria brassicae, a necrotrophic pathogen, causes Alternaria Leaf Spot, one of the 2 economically important diseases of Brassica crops. Many other Alternaria spp. such as A. brassicicola and 3A. alternata are known to cause secondary infections in the A. brassicae-infected Brassicas. The genome 4 architecture, pathogenicity factors, and determinants of host-specificity of A. brassicae are unknown. In 5 this study, we annotated and characterised the recently announced genome assembly of A. brassicae and 6 compared it with other Alternaria spp. to gain insights into its pathogenic lifestyle. Additionally, we 7 sequenced the genomes of two A. alternata isolates that were co-infecting B. juncea. Genome alignments 8 within the Alternaria spp. revealed high levels of synteny between most chromosomes with some 9 intrachromosomal rearrangements. We show for the first time that the genome of A. brassicae, a large-10 spored Alternaria species, contains a dispensable chromosome. We identified 460 A. brassicae-specific 11 genes, which included many secreted proteins and effectors. Furthermore, we have identified the gene 12 clusters responsible for the production of Destruxin-B, a known pathogenicity factor of A. brassicae. The 13 study provides a perspective into the unique and shared repertoire of genes within the Alternaria genus and 14 identifies genes that could be contributing to the pathogenic lifestyle of A. brassicae. 15 16 crops. Some of the most damaging species include Alternaria brassicae, A. brassicicola, A. 43 alternata, A. raphani, A. japonicus, and A. tenuissima. A. brassicae preferentially infects the oleiferous 44 Brassicas while the others are more devastating on the vegetable Brassicas. A. brassicae is particularly 45 more damaging in the hilly regions of the Indian subcontinent, where conducive climatic conditions allow 46 it to profusely reproduce and cause infections on almost all parts of the plant. Extensive screening for 47 resistance to A. brassicae in the cultivated Brassica germplasms has not revealed any source of resistance 2 . 48The factors that contribute to the pathogenicity of A. brassicae are relatively unknown. 49Pathogenicity of many Alternaria spp. has been mainly attributed to the secretion of host-specific toxins 50 (HSTs). HSTs induce pathogenesis on a rather narrow species range and are mostly indispensable for 51 pathogenicity. At least 12 A. alternata pathotypes have been reported to produce HSTs and thereby cause 52 disease on different species 3 . Many of the HST producing genes/gene clusters have been found on 53 supernumerary chromosomes or dispensable chromosomes 4 . A. brassicae has been reported to produce low 54 molecular weight cyclic depsipeptides named destruxins. Destruxin B is known to be a major phytotoxin 55 and is reported to be a probable HST of A. brassicae 5 . Additionally, a proteinaceous HST (ABR-toxin), 56 was isolated from the spore germination fluid of A. brassicae but was only partially characterised 6,7 . 57Genome sequencing and comparative analysi...

show abstract

“…Five isolates belonging to three different species of Alternaria from different locations were used in this study (Table 2). We have previously described A. solani isolate CBS 143772 (Iftikhar et al 2017;Wolters et al 2018) and additional Alternaria isolates were ordered from the fungal culture collection (CBS) of the Westerdijk Institute (Utrecht, the Netherlands). The Alternaria isolates were maintained on potato dextrose agar (Beever and Bollard 1970) in Petri dishes.…”

mentioning

confidence: 99%

A rapid method to screen wild Solanum for resistance to early blight

et al. 2019

Self Cite

View full text Add to dashboard Cite

Early blight of potato and tomato is caused by Alternaria fungi and negatively impacts crop yields. Environmental factors and plant maturity influence disease development, which is usually kept under control by fungicide applications. Wild tuber-bearing Solanum section Petota species are a promising source of resistance to early blight that could be used to control the disease, for example by crossbreeding or modern breeding approaches. An efficient screening method is a first prerequisite for the identification of resistant genotypes in wild Solanum germplasm. Here, we describe a protocol that can be used to rapidly screen for resistance to early blight in wild Solanum collections. This protocol provides a good starting point for the identification of resistant genotypes and is a step towards breeding for resistance to early blight using wild Solanum species.

show abstract

Gapless Genome Assembly of the Potato and Tomato Early Blight Pathogen Alternaria solani

Cited by 45 publications

References 19 publications

Assembly, annotation, and comparison of Macrophomina phaseolina isolates from strawberry and other hosts

Assembly, annotation, and comparison of Macrophomina phaseolina isolates from strawberry and other hosts

Comparative genomics of Alternaria species provides insights into the pathogenic lifestyle of Alternaria brassicae – a pathogen of the Brassicaceae family

A rapid method to screen wild Solanum for resistance to early blight

Contact Info

Product

Resources

About