Data on genetic polymorphism of flax (Linum usitatissimum L.) pathogenic fungi of Fusarium, Colletotrichum, Aureobasidium, Septoria, and Melampsora genera

Novakovskiy, Roman O.; Dvorianinova, Ekaterina M.; Rozhmina, Tatiana A.; Kudryavtseva, L. P.; Gryzunov, A.A.; Pushkova, Elena N.; Povkhova, Liubov V.; Snezhkina, Anastasiya V.; Krasnov, George S.; Kudryavtseva, Anna V.; Melnikova, Nataliya V.; Dmitriev, Alexey A.

doi:10.1016/j.dib.2020.105710

Cited by 16 publications

(12 citation statements)

References 8 publications

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“…This knowledge is useful for phylogenetic studies and species resolution [ 14 , 15 ]. For initial identification, fungal barcodes can be used, e.g., the beta-tubulin ( TUB2 ) gene or the ITS region [ 16 , 17 , 18 , 19 ]. However, molecular markers sometimes provide limited information on species.…”

Section: Introductionmentioning

confidence: 99%

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

Sigova

Pushkova

Rozhmina

et al. 2023

JoF

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Flax (Linum usitatissimum L.) is attacked by numerous devastating fungal pathogens, including Colletotrichum lini, Aureobasidium pullulans, and Fusarium verticillioides (Fusarium moniliforme). The effective control of flax diseases follows the paradigm of extensive molecular research on pathogenicity. However, such studies require quality genome sequences of the studied organisms. This article reports on the approaches to assembling a high-quality fungal genome from the Oxford Nanopore Technologies data. We sequenced the genomes of C. lini, A. pullulans, and F. verticillioides (F. moniliforme) and received different volumes of sequencing data: 1.7 Gb, 3.9 Gb, and 11.1 Gb, respectively. To obtain the optimal genome sequences, we studied the effect of input data quality and genome coverage on assembly statistics and tested the performance of different assembling and polishing software. For C. lini, the most contiguous and complete assembly was obtained by the Flye assembler and the Homopolish polisher. The genome coverage had more effect than data quality on assembly statistics, likely due to the relatively low amount of sequencing data obtained for C. lini. The final assembly was 53.4 Mb long and 96.4% complete (according to the glomerellales_odb10 BUSCO dataset), consisted of 42 contigs, and had an N50 of 4.4 Mb. For A. pullulans and F. verticillioides (F. moniliforme), the best assemblies were produced by Canu–Medaka and Canu–Homopolish, respectively. The final assembly of A. pullulans had a length of 29.5 Mb, 99.4% completeness (dothideomycetes_odb10), an N50 of 2.4 Mb and consisted of 32 contigs. F. verticillioides (F. moniliforme) assembly was 44.1 Mb long, 97.8% complete (hypocreales_odb10), consisted of 54 contigs, and had an N50 of 4.4 Mb. The obtained results can serve as a guideline for assembling a de novo genome of a fungus. In addition, our data can be used in genomic studies of fungal pathogens or plant–pathogen interactions and assist in the management of flax diseases.

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Section: Introductionmentioning

confidence: 99%

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

Sigova

Pushkova

Rozhmina

et al. 2023

JoF

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“…This approach significantly reduces the cost of sequencing per genotype compared to the whole genome analysis and allows the sequencing of dozens and hundreds of genome regions in hundreds and thousands of samples. It also overcomes the difficulties of Sanger sequencing associated with polyploidy of plant genomes and a high degree of duplication of their genes [ 18 , 97 , 98 , 99 , 100 , 101 ]. Therefore, the third approach, developed by us, for the identification of the three low-LIN mutations in the FAD3A and FAD3B genes in flax genotypes was based on targeted deep sequencing.…”

Section: Discussionmentioning

confidence: 99%

Development and Complex Application of Methods for the Identification of Mutations in the FAD3A and FAD3B Genes Resulting in the Reduced Content of Linolenic Acid in Flax Oil

Povkhova

Pushkova

Rozhmina

et al. 2022

Plants

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Flax is grown worldwide for seed and fiber production. Linseed varieties differ in their oil composition and are used in pharmaceutical, food, feed, and industrial production. The field of application primarily depends on the content of linolenic (LIN) and linoleic (LIO) fatty acids. Inactivating mutations in the FAD3A and FAD3B genes lead to a decrease in the LIN content and an increase in the LIO content. For the identification of the three most common low-LIN mutations in flax varieties (G-to-A in exon 1 of FAD3A substituting tryptophan with a stop codon, C-to-T in exon 5 of FAD3A leading to arginine to a stop codon substitution, and C-to-T in exon 2 of FAD3B resulting in histidine to tyrosine substitution), three approaches were proposed: (1) targeted deep sequencing, (2) high resolution melting (HRM) analysis, (3) cleaved amplified polymorphic sequences (CAPS) markers. They were tested on more than a thousand flax samples of various types and showed promising results. The proposed approaches can be used in marker-assisted selection to choose parent pairs for crosses, separate heterogeneous varieties into biotypes, and select genotypes with desired homozygous alleles of the FAD3A and FAD3B genes at the early stages of breeding for the effective development of varieties with a particular LIN and LIO content, as well as in basic studies of the molecular mechanisms of fatty acid synthesis in flax seeds to select genotypes adequate to the tasks.

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“…One microgram of RNA for each sample was treated with DNase I (Thermo Fisher Scientific, Waltham, MA, United States) and used for reverse transcription with random hexamer primers (Evrogen, Moscow, Russia) and Mint reverse transcriptase (Evrogen) following the manufacturer's protocol. Primers were designed for amplification of parts of the TCP, CLC, and MET1 genes and further sequencing on the Illumina platform as described in our previous works (Melnikova et al, 2019;Dmitriev et al, 2020;Novakovskiy et al, 2020). In brief, two PCRs were used for the library preparation.…”

Section: Targeted Genome and Transcriptome Sequencingmentioning

confidence: 99%

Genome and Transcriptome Sequencing of Populus × sibirica Identified Sex-Associated Allele-Specific Expression of the CLC Gene

et al. 2021

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Transcriptome sequencing of leaves, catkin axes, and flowers from male and female trees of Populus × sibirica and genome sequencing of the same plants were performed for the first time. The availability of both genome and transcriptome sequencing data enabled the identification of allele-specific expression. Such an analysis was performed for genes from the sex-determining region (SDR). P. × sibirica is an intersectional hybrid between species from sections Aigeiros (Populus nigra) and Tacamahaca (Populus laurifolia, Populus suaveolens, or Populus × moskoviensis); therefore, a significant number of heterozygous polymorphisms were identified in the SDR that allowed us to distinguish between alleles. In the SDR, both allelic variants of the TCP (T-complex protein 1 subunit gamma), CLC (Chloride channel protein CLC-c), and MET1 (DNA-methyltransferase 1) genes were expressed in females, while in males, two allelic variants were expressed for TCP and MET1 but only one allelic variant prevailed for CLC. Targeted sequencing of TCP, CLC, and MET1 regions on a representative set of trees confirmed the sex-associated allele-specific expression of the CLC gene in generative and vegetative tissues of P. × sibirica. Our study brings new knowledge on sex-associated differences in Populus species.

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Data on genetic polymorphism of flax (Linum usitatissimum L.) pathogenic fungi of Fusarium, Colletotrichum, Aureobasidium, Septoria, and Melampsora genera

Cited by 16 publications

References 8 publications

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

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

Development and Complex Application of Methods for the Identification of Mutations in the FAD3A and FAD3B Genes Resulting in the Reduced Content of Linolenic Acid in Flax Oil

Genome and Transcriptome Sequencing of Populus × sibirica Identified Sex-Associated Allele-Specific Expression of the CLC Gene

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