Reference genome assembly for Australian<i>Ascochyta lentis</i>isolate Al4

Lee, Robert C.; Farfan-Caceres, Lina M; Debler, Johannes Wolfram; Williams, Angela H.; Syme, Robert A.; Henares, Bernadette M.

doi:10.1093/g3journal/jkab006

Cited by 9 publications

(22 citation statements)

References 94 publications

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“…Genotyping of the P94‐24 × Al Kewell A . lentis population ( N = 95) using double‐digested restriction site‐associated DNA sequencing (ddRADseq) yielded 587 high‐quality markers after filtering (Table S1 ), and these were mapped to the published reference genome assembly for isolate Al4 (Lee et al, 2021 ). A genotype marker map is provided in Figure S1 .…”

Section: Resultsmentioning

confidence: 99%

“…Genotyping of the P94-24 × AlKewell A. lentis population (N = 95) using double-digested restriction site-associated DNA sequencing (ddRADseq) yielded 587 high-quality markers after filtering (Table S1), and these were mapped to the published reference genome assembly for isolate Al4 (Lee et al, 2021). A genotype marker map is provided in The region on A. lentis Al4 chromosome 3 from 2.14 Mb to the end of the chromosome at 2.317 Mb where the major QTL was identified contains 28 annotated genes (Figure 3a).…”

Section: Genetic Mapping Reveals a Hurricane Pathogenicity Quantitati...mentioning

confidence: 99%

“…4.4.1 | QTL analysis of the AlKewell × P94-24 mapping population QTL mapping of ILL6002 disease and normalized disease scores for Hurricane and Nipper was performed using the R-based program R/ qtl2 (Broman et al, 2019). ddRADseq marker positions were mapped to the 23-contig A. lentis Al4 genome assembly (GenBank accession GCA_004011695.1; Lee et al, 2021) using BLASTn (Altschul et al, 1990). Unmapped loci were binned to the "unmapped" group designated "chr24".…”

Section: Isolate Genotypingmentioning

confidence: 99%

“…A. lentis is from the family Didymellaceae, within the Pleosporales, and provides an additional plant disease model to research molecular mechanisms of pathogen-host interaction that contrasts with the pathogens from cereal and oilseed crops described above. A near-complete genome assembly for A. lentis has been recently published (Lee et al, 2021), and agroinfiltration, genetic transformation, and gene knockout protocols are available for research in the lentil-ascochyta pathosystem (Debler & Henares, 2020;Debler et al, 2021;Henares et al, 2019). However, so far very limited information is available about the pathogen-host interaction at the molecular level.…”

Section: Introductionmentioning

confidence: 99%

“…A near‐complete genome assembly for A . lentis has been recently published (Lee et al, 2021 ), and agroinfiltration, genetic transformation, and gene knockout protocols are available for research in the lentil–ascochyta pathosystem (Debler & Henares, 2020 ; Debler et al, 2021 ; Henares et al, 2019 ). However, so far very limited information is available about the pathogen–host interaction at the molecular level.…”

Section: Introductionmentioning

confidence: 99%

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The novel avirulence effector AlAvr1 from Ascochyta lentis mediates host cultivar specificity of ascochyta blight in lentil

Henares

Debler

Farfan-Caceres

et al. 2022

Molecular Plant Pathology

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Ascochyta lentis is a fungal pathogen that causes ascochyta blight in the important grain legume species lentil, but little is known about the molecular mechanism of disease or host specificity. We employed a map‐based cloning approach using a biparental A. lentis population to clone the gene AlAvr1‐1 that encodes avirulence towards the lentil cultivar PBA Hurricane XT. The mapping population was produced by mating A. lentis isolate P94‐24, which is pathogenic on the cultivar Nipper and avirulent towards Hurricane, and the isolate AlKewell, which is pathogenic towards Hurricane but not Nipper. Using agroinfiltration, we found that AlAvr1‐1 from the isolate P94‐24 causes necrosis in Hurricane but not in Nipper. The homologous corresponding gene in AlKewell, AlAvr1‐2, encodes a protein with amino acid variation at 23 sites and four of these sites have been positively selected in the P94‐24 branch of the phylogeny. Loss of AlAvr1‐1 in a gene knockout experiment produced a P94‐24 mutant strain that is virulent on Hurricane. Deletion of AlAvr1‐2 in AlKewell led to reduced pathogenicity on Hurricane, suggesting that the gene may contribute to disease in Hurricane. Deletion of AlAvr1‐2 did not affect virulence for Nipper and AlAvr1‐2 is therefore not an avirulence gene for Nipper. We conclude that the hemibiotrophic pathogen A. lentis has an avirulence effector, AlAvr1‐1, that triggers a hypersensitive resistance response in Hurricane. This is the first avirulence gene to be characterized in a legume pathogen from the Pleosporales and may help progress research on other damaging Ascochyta pathogens.

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Section: Resultsmentioning

confidence: 99%

Section: Genetic Mapping Reveals a Hurricane Pathogenicity Quantitati...mentioning

confidence: 99%

Section: Isolate Genotypingmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 3 more Smart Citations

The novel avirulence effector AlAvr1 from Ascochyta lentis mediates host cultivar specificity of ascochyta blight in lentil

Henares

Debler

Farfan-Caceres

et al. 2022

Molecular Plant Pathology

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Tackling Lentil Biotic Stresses in the Genomic Era

Vega

Garcı́a

Gutiérrez-González

et al. 2022

Genomic Designing for Biotic Stress Resistant Pulse Crops

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Lentils are already one of the main pulses of the world, as they are one of the main sources of protein for humans. As a crop, they are also gaining momentum because the rusticity and tolerance to water scarcity of some varieties are a good fit with the current global warming trend and climate change in general. However, while the harvested area and overall production have drastically increased over the last decades, yield has only experienced very modest increments. The reasons are two-fold. First, pathogens are affecting the crop as never before, likely due to not only the changing climate but also to the expansion of lentil cultivation to new geographic areas. Second, genomics-aided breeding is far behind many other crops. This is in partly due to the lack of genomic tools currently available to researchers. Progress is being made to adopt high-throughput genomic methods, and researchers will be able to tackle lentil gene discovery and breeding for pathogen resistance and other biotic stresses more efficiently in the coming years. We outline the current situation, novel findings, and prospects of lentil research for biotic stresses. IntroductionLentil (Lens culinaris Medik. subsp. culinaris) is one of the first domesticated species in the Fertile Crescent and along with barley, emmer wheat and einkorn wheat, pea, chickpea, and flax was part of the set of crops that defined the beginnings of the Neolithic transition to agriculture in this part of the World. The origin of the cultivated form is the wild L. culinaris subsp. orientalis (Boiss.) Ponert (syn. L. orientalis Boiss.). A recent publication by Liber et al. (2021) suggests that phylogenetics, population structure, and archeological data coincide in a lentil domestication prolonged in time in Southwest Asia, with two different domesticated gene pools. From the

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