ORCID Profile
0000-0002-6321-1206
Current Organisations
Indonesian Institute of Sciences
,
Research Center for Plant Conservation, Botanical Garden and Forestry - National Research and Innovation Agency, Indonesia
,
University of Minnesota
,
University of Minnesota Twin Cities
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Publications
De Novo Assembly and Phasing of Dikaryotic Genomes from Two Isolates of Puccinia coronata f. sp. avenae , the Causal Ag
Publisher: American Society for Microbiology
Date: 07-03-2018
Abstract: Oat crown rust, caused by the fungus Pucinnia coronata f. sp. avenae , is a devastating disease that impacts worldwide oat production. For much of its life cycle, P. coronata f. sp. avenae is dikaryotic, with two separate haploid nuclei that may vary in virulence genotype, highlighting the importance of understanding haplotype ersity in this species. We generated highly contiguous de novo genome assemblies of two P. coronata f. sp. avenae isolates, 12SD80 and 12NC29, from long-read sequences. In total, we assembled 603 primary contigs for 12SD80, for a total assembly length of 99.16 Mbp, and 777 primary contigs for 12NC29, for a total length of 105.25 Mbp approximately 52% of each genome was assembled into alternate haplotypes. This revealed structural variation between haplotypes in each isolate equivalent to more than 2% of the genome size, in addition to about 260,000 and 380,000 heterozygous single-nucleotide polymorphisms in 12SD80 and 12NC29, respectively. Transcript-based annotation identified 26,796 and 28,801 coding sequences for isolates 12SD80 and 12NC29, respectively, including about 7,000 allele pairs in haplotype-phased regions. Furthermore, expression profiling revealed clusters of coexpressed secreted effector candidates, and the majority of orthologous effectors between isolates showed conservation of expression patterns. However, a small subset of orthologs showed ergence in expression, which may contribute to differences in virulence between 12SD80 and 12NC29. This study provides the first haplotype-phased reference genome for a dikaryotic rust fungus as a foundation for future studies into virulence mechanisms in P. coronata f. sp. avenae . IMPORTANCE Disease management strategies for oat crown rust are challenged by the rapid evolution of Puccinia coronata f. sp. avenae , which renders resistance genes in oat varieties ineffective. Despite the economic importance of understanding P. coronata f. sp. avenae , resources to study the molecular mechanisms underpinning pathogenicity and the emergence of new virulence traits are lacking. Such limitations are partly due to the obligate biotrophic lifestyle of P. coronata f. sp. avenae as well as the dikaryotic nature of the genome, features that are also shared with other important rust pathogens. This study reports the first release of a haplotype-phased genome assembly for a dikaryotic fungal species and demonstrates the amenability of using emerging technologies to investigate genetic ersity in populations of P. coronata f. sp. avenae .
Emergence of the Ug99 lineage of the wheat stem rust pathogen through somatic hybridisation
Publisher: Springer Science and Business Media LLC
Date: 07-11-2019
DOI: 10.1038/S41467-019-12927-7
Abstract: Parasexuality contributes to ersity and adaptive evolution of haploid (monokaryotic) fungi. However, non-sexual genetic exchange mechanisms are not defined in dikaryotic fungi (containing two distinct haploid nuclei). Newly emerged strains of the wheat stem rust pathogen, Puccinia graminis f. sp. tritici ( Pgt ), such as Ug99, are a major threat to global food security. Here, we provide genomics-based evidence supporting that Ug99 arose by somatic hybridisation and nuclear exchange between dikaryons. Fully haplotype-resolved genome assembly and DNA proximity analysis reveal that Ug99 shares one haploid nucleus genotype with a much older African lineage of Pgt , with no recombination or chromosome reassortment. These findings indicate that nuclear exchange between dikaryotes can generate genetic ersity and facilitate the emergence of new lineages in asexual fungal populations.
KARAKTER HABITAT, POPULASI, PRODUKTIVITAS, MORFOLOGI BUAH SERTA BIJI, PERILAKU SIMPAN DAN PERILAKU PERKECAMBAHAN Casearia flavovirens Blume
Publisher: National Research and Innovation Agency
Date: 20-06-2022
Related Organisations
Research Center For Plant Conservation, Botanical Garden And Forestry - National Research And Innovation Agency, Indonesia
Location: Indonesia
University Of Minnesota Twin Cities
Location: United States of America
Related Funding Activities
No related grants have been discovered for Dewi Lestari.