Assembling Quality Genomes of Flax Fungal Pathogens from Oxford Nanopore Technologies Data

Sigova, Elizaveta A.; Pushkova, Elena N.; Rozhmina, Tatiana A.; Kudryavtseva, L. P.; Жученко, А. А.; Novakovskiy, Roman O.; Zhernova, Daiana A.; Povkhova, Liubov V.; Turba, Anastasia A.; Borkhert, Elena V.; Melnikova, N. V.; Dmitriev, Alexey A.; Dvorianinova, Ekaterina M.

doi:10.3390/jof9030301

Cited by 6 publications

(17 citation statements)

References 78 publications

(81 reference statements)

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“…While the usage of medaka for diploid cells has been controversial because of the diploid nature of yeast, we found that the newer version of medaka provided more accurate assemblies. These results are in line with Sigova et al [ 32 ]. In their study, they reported that read correction with medaka is superior to read correction with racon in fungal pathogens.…”

Section: Resultssupporting

confidence: 94%

“…In their study, they reported that read correction with medaka is superior to read correction with racon in fungal pathogens. In addition, the percentage of genome completeness significantly decreases (by ~40%) when a reference is added, even after using six read correction tools [ 32 ]. Moreover, Zhang et al showed that medaka performance was superior against other read correction/polishing tools in which medaka improved the continuity and reduced mismatches in S. cerevisiae -assembled genomes [ 33 ].…”

Section: Resultsmentioning

confidence: 99%

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Three Rounds of Read Correction Significantly Improve Eukaryotic Protein Detection in ONT Reads

Safar,

Alatar,

Mustafa

2024

Microorganisms

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Background: Eukaryotes’ whole-genome sequencing is crucial for species identification, gene detection, and protein annotation. Oxford Nanopore Technology (ONT) is an affordable and rapid platform for sequencing eukaryotes; however, the relatively higher error rates require computational and bioinformatic efforts to produce more accurate genome assemblies. Here, we evaluated the effect of read correction tools on eukaryote genome completeness, gene detection and protein annotation. Methods: Reads generated by ONT of four eukaryotes, C. albicans, C. gattii, S. cerevisiae, and P. falciparum, were assembled using minimap2 and underwent three rounds of read correction using flye, medaka and racon. The generates consensus FASTA files were compared for total length (bp), genome completeness, gene detection, and protein-annotation by QUAST, BUSCO, BRAKER1 and InterProScan, respectively. Results: Genome completeness was dependent on the assembly method rather than on the read correction tool; however, medaka performed better than flye and racon. Racon significantly performed better than flye and medaka in gene detection, while both racon and medaka significantly performed better than flye in protein-annotation. Conclusion: We show that three rounds of read correction significantly affect gene detection and protein annotation, which are dependent on assembly quality in preference to assembly completeness.

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Section: Resultssupporting

confidence: 94%

Section: Resultsmentioning

confidence: 99%

Three Rounds of Read Correction Significantly Improve Eukaryotic Protein Detection in ONT Reads

Safar,

Alatar,

Mustafa

2024

Microorganisms

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“…When comparing the read correction tools, medaka was also more superior than flye and racon in genome completeness in all four species samples (Figure 1). These results are in line with Sigova et al [32]. In their study, they reported that read correction with medaka is superior to read correction with racon in fungal pathogens.…”

Section: Resultssupporting

confidence: 90%

“…In their study, they reported that read correction with medaka is superior to read correction with racon in fungal pathogens. In addition, the percentage of genome completeness significantly decreases (by ~40%) when a reference is added, even after using six read correction tools [32]. Genome completeness is majorly affected by sequencing methods and genome assembly tools rather than read correction tools [33].…”

Section: Resultsmentioning

confidence: 99%

Three Rounds of Read Correction Significantly Improves Eukaryotic Protein Detection in ONT Reads

Safar,

Mustafa,

Alatar

2023

Preprint

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Background: Eukaryotes whole-genome sequencing is crucial for species identification, gene detection and protein-annotation. Oxford Nanopore sequencing serves as an affordable and rapid platform for sequencing eukaryotes, however the relatively higher error rates require computational and bioinformatic efforts to produce more accurate genome assemblies. Here, we evaluated the effect of read correction tools on eukaryotes genome completeness, gene detection and protein-annotation. Methods: Reads generated by ONT of four eukaryotes, C. albicans, C. gattii, S. cerevisiae, and P. falciparum, were assembled using minimap2 and underwent three rounds of read correction using flye, medaka and racon. The generates consensus FASTA files were compared for total length (bp), genome completeness, gene detection, and protein-annotation by QUAST, BUSCO, BRAKER1 and InterProScan, respectively. Results: genome completeness was dependent on assembly method rather than read correction tool, however, medaka performed better than flye and racon. Racon significantly performed better than flye and medaka in gene detection, while both racon and medaka significantly performed better than flye in protein-annotation. Conclusion: We show that three rounds of read correction significantly affects gene detection and protein-annotation which are dependent on assembly quality in preference to assembly completeness.

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“…Recently, DNA sequences that are frequently used for phylogenetic studies have been obtained for 203 flax fungal pathogens including various Fusarium spp. [17,[96][97][98], Colletotrichum lini [99], Aureobasidium pullulans [99], Septoria linicola [23] and Melampsora lini [100,101]. These sequences can be used to develop PCR-based detection systems for flax pathogen identification [13] and are of great use for studying the virulence mechanisms of these pathogens and improving management strategies.…”

Section: Pathogen Characterizationmentioning

confidence: 99%

Overview and Management of the Most Common Eukaryotic Diseases of Flax (Linum usitatissimum)

Moyse,

Lecomte,

Marcou

et al. 2023

Plants

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Flax is an important crop cultivated for its seeds and fibers. It is widely grown in temperate regions, with an increase in cultivation areas for seed production (linseed) in the past 50 years and for fiber production (fiber flax) in the last decade. Among fiber-producing crops, fiber flax is the most valuable species. Linseed is the highest omega-3 oleaginous crop, and its consumption provides several benefits for animal and human health. However, flax production is impacted by various abiotic and biotic factors that affect yield and quality. Among biotic factors, eukaryotic diseases pose a significant threat to both seed production and fiber quality, which highlights the economic importance of controlling these diseases. This review focuses on the major eukaryotic diseases that affect flax in the field, describing the pathogens, their transmission modes and the associated plant symptoms. Moreover, this article aims to identify the challenges in disease management and provide future perspectives to overcome these biotic stresses in flax cultivation. By emphasizing the key diseases and their management, this review can aid in promoting sustainable and profitable flax production.

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Assembling Quality Genomes of Flax Fungal Pathogens from Oxford Nanopore Technologies Data

Cited by 6 publications

References 78 publications

Three Rounds of Read Correction Significantly Improve Eukaryotic Protein Detection in ONT Reads

Three Rounds of Read Correction Significantly Improve Eukaryotic Protein Detection in ONT Reads

Three Rounds of Read Correction Significantly Improves Eukaryotic Protein Detection in ONT Reads

Overview and Management of the Most Common Eukaryotic Diseases of Flax (Linum usitatissimum)

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