The Genome Sequence of Five Highly Pathogenic Isolates of <i>Fusarium oxysporum</i> f. sp. <i>lini</i>

Kanapin, Alexander; Samsonova, Anastasia; Rozhmina, Tatiana A.; Bankin, Mikhail; Logachev, Anton; Samsonova, Maria

doi:10.1094/mpmi-05-20-0130-sc

Cited by 20 publications

(20 citation statements)

References 19 publications

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“…The development of the disease causes dieback of the seedlings and in the case of adult plants fusarium head blight. It is estimated that around 20% of flax cultivation loss is a result of fusariosis [2,3].…”

Section: Introductionmentioning

confidence: 99%

Transcriptomic profiling of susceptible and resistant flax seedlings after Fusarium oxysporum lini infection

et al. 2021

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In this study transcriptome was analyzed on two fibrous varieties of flax: the susceptible Regina and the resistant Nike. The experiment was carried out on 2-week-old seedlings, because in this phase of development flax is the most susceptible to infection. We analyzed the whole seedlings, which allowed us to recognize the systemic response of the plants to the infection. We decided to analyze two time points: 24h and 48h, because our goal was to learn the mechanisms activated in the initial stages of infection, these points were selected based on the previous analysis of chitinase gene expression, whose increase in time of Fusarium oxysporum lini infection has been repeatedly confirmed both in the case of flax and other plant species. The results show that although qualitatively the responses of the two varieties are similar, it is the degree of the response that plays the role in the differences of their resistance to F. oxysporum.

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Section: Introductionmentioning

confidence: 99%

Transcriptomic profiling of susceptible and resistant flax seedlings after Fusarium oxysporum lini infection

et al. 2021

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“…The so-called "variable", dynamic compartment is just the opposite of the core and includes chromosomes 12-15. This part of the genome is highly syntenic with LS chromosomes of Fol [20] and features low number of protein-coding genes, as well as both high rates of intra-strain variation and density of repeats. Genomic regions comprising rest of the genome (chromosomes 2, 5, 7, 8-11, 17, and 18) exhibit a mixed profile of features which complicate their attribution to either of the compartments.…”

Section: Discussionmentioning

confidence: 99%

“…Previously, MI39 whole genome assembly chromosomes were assigned to core and variable (auxiliary, lineage-specific) compartments of the size of 47.55 and 21.77 Mb, correspondingly [20]. Chromosomes were assigned to the core compartment based on high levels of homology and synteny with the core chromosomes of F. oxysporum f. sp.…”

Section: Organization Of Mi39 Reference Genomementioning

confidence: 99%

“…The nucleotide sequences assembly, de novo prediction, and annotation of coding regions of monoisolate 39 and 4 strains (282, 289, 324, 327) have been described in our previous publication [20]. De novo prediction of repetitive sequences was made using RepeatScout [25] version 1.0.6 MIMPs have been predicted using custom Perl scripts and regular expressions/CAGTGGG.GCAA[TA] AA/and/TT[TA]TTGC.CCCACTG/, described in [4].…”

Section: Data Sources and Sequence Analysismentioning

confidence: 99%

“…Recently, we reported genome assemblies of five highly pathogenic Fusarium oxysporum f. sp. lini (FOLINI) strains: the reference hybrid assembly of monoisolate 39 (MI39) sequenced with SMRT technology and Illumina-based assemblies of strains F329, F324, F282, F287 [20]. Syntenic analyses of MI39 assembly and the reference Fol genome facilitated provisional attribution of FOLINI chromosomes into two genomic compartments.…”

Section: Introductionmentioning

confidence: 99%

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A Genomic Blueprint of Flax Fungal Parasite Fusarium oxysporum f. sp. lini

Samsonova

Kanapin

Bankin

et al. 2021

IJMS

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Fusarium wilt of flax is an aggressive disease caused by the soil-borne fungal pathogen Fusarium oxysporum f. sp. lini. It is a challenging pathogen presenting a constant threat to flax production industry worldwide. Previously, we reported chromosome-level assemblies of 5 highly pathogenic F. oxysporum f. sp. lini strains. We sought to characterize the genomic architecture of the fungus and outline evolutionary mechanisms shaping the pathogen genome. Here, we reveal the complex multi-compartmentalized genome organization and uncover its diverse evolutionary dynamics, which boosts genetic diversity and facilitates host adaptation. In addition, our results suggest that host of functions implicated in the life cycle of mobile genetic elements are main contributors to dissimilarity between proteomes of different Fusaria. Finally, our experiments demonstrate that mobile genetics elements are expressed in planta upon infection, alluding to their role in pathogenicity. On the whole, these results pave the way for further in-depth studies of evolutionary forces shaping the host–pathogen interaction.

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Population genomics reveals historical and ongoing recombination in the Fusarium oxysporum species complex

McTaggart

James

Shivas

et al. 2021

Studies in Mycology

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The Fusarium oxysporum species complex (FOSC) is a group of closely related plant pathogens long-considered strictly clonal, as sexual stages have never been recorded. Several studies have questioned whether recombination occurs in FOSC, and if it occurs its nature and frequency are unknown. We analysed 410 assembled genomes to answer whether FOSC diversified by occasional sexual reproduction interspersed with numerous cycles of asexual reproduction akin to a model of predominant clonal evolution (PCE). We tested the hypothesis that sexual reproduction occurred in the evolutionary history of FOSC by examining the distribution of idiomorphs at the mating locus, phylogenetic conflict and independent measures of recombination from genome-wide SNPs and genes. A phylogenomic dataset of 40 single copy orthologs was used to define structure a priori within FOSC based on genealogical concordance. Recombination within FOSC was tested using the pairwise homoplasy index and divergence ages were estimated by molecular dating. We called SNPs from assembled genomes using a k-mer approach and tested for significant linkage disequilibrium as an indication of PCE. We clone-corrected and tested whether SNPs were randomly associated as an indication of recombination. Our analyses provide evidence for sexual or parasexual reproduction within, but not between, clades of FOSC that diversified from a most recent common ancestor about 500 000 years ago. There was no evidence of substructure based on geography or host that might indicate how clades diversified. Competing evolutionary hypotheses for FOSC are discussed in the context of our results.

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The Genome Sequence of Five Highly Pathogenic Isolates of Fusarium oxysporum f. sp. lini

Cited by 20 publications

References 19 publications

Transcriptomic profiling of susceptible and resistant flax seedlings after Fusarium oxysporum lini infection

Transcriptomic profiling of susceptible and resistant flax seedlings after Fusarium oxysporum lini infection

A Genomic Blueprint of Flax Fungal Parasite Fusarium oxysporum f. sp. lini

Population genomics reveals historical and ongoing recombination in the Fusarium oxysporum species complex

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