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Pushkova EN, Povkhova LV, Dvorianinova EM, Novakovskiy RO, Rozhmina TA, Gryzunov AA, Sigova EA, Zhernova DA, Borkhert EV, Turba AA, Yablokov AG, Bolsheva NL, Dmitriev AA, Melnikova NV. Expression of FAD and SAD Genes in Developing Seeds of Flax Varieties under Different Growth Conditions. Plants (Basel) 2024; 13:956. [PMID: 38611485 PMCID: PMC11013676 DOI: 10.3390/plants13070956] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Revised: 03/10/2024] [Accepted: 03/12/2024] [Indexed: 04/14/2024]
Abstract
Flax seed is one of the richest plant sources of linolenic acid (LIN) and also contains unsaturated linoleic acid (LIO) and oleic acid (OLE). Stearoyl-ACP desaturases (SADs) and fatty acid desaturases (FADs) play key roles in the synthesis of flax fatty acids (FAs). However, there is no holistic view of which genes from the SAD and FAD families and at which developmental stages have the highest expression levels in flax seeds, as well as the influence of genotype and growth conditions on the expression profiles of these genes. We sequenced flax seed transcriptomes at 3, 7, 14, 21, and 28 days after flowering (DAF) for ten flax varieties with different oil FA compositions grown under three temperature/watering conditions. The expression levels of 25 genes of the SAD, FAD2, and FAD3 families were evaluated. FAD3b, FAD3a, FAD2b-2, SAD3-1, SAD2-1, SAD2-2, SAD3-2, FAD2a-1, and FAD2a-2 had the highest expression levels, which changed significantly during seed development. These genes probably play a key role in FA synthesis in flax seeds. High temperature and insufficient watering shifted the maximum expression levels of FAD and SAD genes to earlier developmental stages, while the opposite trend was observed for low temperature and excessive watering. Differences in the FAD and SAD expression profiles under different growth conditions may affect the FA composition of linseed oil. Stop codons in the FAD3a gene, resulting in a reduced LIN content, decreased the level of FAD3a transcript. The obtained results provide new insights into the synthesis of linseed oil.
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Affiliation(s)
- Elena N. Pushkova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia; (E.N.P.); (L.V.P.); (E.M.D.); (R.O.N.); (T.A.R.); (E.A.S.); (D.A.Z.); (E.V.B.); (A.A.T.); (A.G.Y.); (N.L.B.)
| | - Liubov V. Povkhova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia; (E.N.P.); (L.V.P.); (E.M.D.); (R.O.N.); (T.A.R.); (E.A.S.); (D.A.Z.); (E.V.B.); (A.A.T.); (A.G.Y.); (N.L.B.)
| | - Ekaterina M. Dvorianinova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia; (E.N.P.); (L.V.P.); (E.M.D.); (R.O.N.); (T.A.R.); (E.A.S.); (D.A.Z.); (E.V.B.); (A.A.T.); (A.G.Y.); (N.L.B.)
- Moscow Institute of Physics and Technology, 141701 Moscow, Russia
| | - Roman O. Novakovskiy
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia; (E.N.P.); (L.V.P.); (E.M.D.); (R.O.N.); (T.A.R.); (E.A.S.); (D.A.Z.); (E.V.B.); (A.A.T.); (A.G.Y.); (N.L.B.)
| | - Tatiana A. Rozhmina
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia; (E.N.P.); (L.V.P.); (E.M.D.); (R.O.N.); (T.A.R.); (E.A.S.); (D.A.Z.); (E.V.B.); (A.A.T.); (A.G.Y.); (N.L.B.)
- Federal Research Center for Bast Fiber Crops, 172002 Torzhok, Russia
| | - Aleksey A. Gryzunov
- All-Russian Scientific Research Institute of Refrigeration Industry—Branch of V.M. Gorbatov Federal Research Center for Food Systems of Russian Academy of Sciences, 127422 Moscow, Russia;
| | - Elizaveta A. Sigova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia; (E.N.P.); (L.V.P.); (E.M.D.); (R.O.N.); (T.A.R.); (E.A.S.); (D.A.Z.); (E.V.B.); (A.A.T.); (A.G.Y.); (N.L.B.)
- Moscow Institute of Physics and Technology, 141701 Moscow, Russia
| | - Daiana A. Zhernova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia; (E.N.P.); (L.V.P.); (E.M.D.); (R.O.N.); (T.A.R.); (E.A.S.); (D.A.Z.); (E.V.B.); (A.A.T.); (A.G.Y.); (N.L.B.)
- Faculty of Biology, Lomonosov Moscow State University, 119234 Moscow, Russia
| | - Elena V. Borkhert
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia; (E.N.P.); (L.V.P.); (E.M.D.); (R.O.N.); (T.A.R.); (E.A.S.); (D.A.Z.); (E.V.B.); (A.A.T.); (A.G.Y.); (N.L.B.)
| | - Anastasia A. Turba
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia; (E.N.P.); (L.V.P.); (E.M.D.); (R.O.N.); (T.A.R.); (E.A.S.); (D.A.Z.); (E.V.B.); (A.A.T.); (A.G.Y.); (N.L.B.)
| | - Arthur G. Yablokov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia; (E.N.P.); (L.V.P.); (E.M.D.); (R.O.N.); (T.A.R.); (E.A.S.); (D.A.Z.); (E.V.B.); (A.A.T.); (A.G.Y.); (N.L.B.)
| | - Nadezhda L. Bolsheva
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia; (E.N.P.); (L.V.P.); (E.M.D.); (R.O.N.); (T.A.R.); (E.A.S.); (D.A.Z.); (E.V.B.); (A.A.T.); (A.G.Y.); (N.L.B.)
| | - Alexey A. Dmitriev
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia; (E.N.P.); (L.V.P.); (E.M.D.); (R.O.N.); (T.A.R.); (E.A.S.); (D.A.Z.); (E.V.B.); (A.A.T.); (A.G.Y.); (N.L.B.)
| | - Nataliya V. Melnikova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia; (E.N.P.); (L.V.P.); (E.M.D.); (R.O.N.); (T.A.R.); (E.A.S.); (D.A.Z.); (E.V.B.); (A.A.T.); (A.G.Y.); (N.L.B.)
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Zhernova DA, Pushkova EN, Rozhmina TA, Povkhova LV, Novakovskiy RO, Turba AA, Borkhert EV, Sigova EA, Dvorianinova EM, Krasnov GS, Melnikova NV, Dmitriev AA. ITS and 16S rDNA metagenomic dataset of different soils from flax fields. Data Brief 2024; 52:109827. [PMID: 38059001 PMCID: PMC10696428 DOI: 10.1016/j.dib.2023.109827] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 10/28/2023] [Accepted: 11/14/2023] [Indexed: 12/08/2023] Open
Abstract
Flax (Linum usitatissimum L.), one of the important and versatile crops, is used for the production of oil and fiber. To obtain high and stable yields of flax products, L. usitatissimum varieties should be cultivated under optimal conditions, including the composition of the soil microbiome. We evaluated the diversity of microorganisms in soils under conditions unfavorable for flax cultivation (suboptimal acidity or herbicide treatment) or infected with causative agents of harmful flax diseases (Septoria linicola, Colletotrichum lini, Melampsora lini, or Fusarium oxysporum f. sp. lini). For this purpose, twenty-two sod-podzolic soil samples were collected from flax fields and their metagenomes were analyzed using the regions of 16S ribosomal RNA gene (16S rDNA) and internal transcribed spacers (ITS) of the ribosomal RNA genes, which are used in phylogenetic studies of bacteria and fungi. Amplicons were sequenced on the Illumina MiSeq platform (reads of 300 + 300 bp). On average, we obtained 8,400 reads for ITS and 43,300 reads for 16S rDNA per sample. For identification of microorganisms in the soil samples, the Illumina reads were processed using DADA2. The raw data are deposited in the Sequence Read Archive under the BioProject accession number PRJNA956957. Tables listing the microorganisms identified in the soil samples are available in this article. The obtained dataset can be used to analyze the fungal and bacterial composition of flax field soils and their relationship to environmental conditions, including suboptimal soil acidity and infection with fungal pathogens. In addition, it can help to understand the influence of herbicide treatment on the microbial diversity of flax fields. Another useful application of our data is the ability to assess the suitability of the soil microbiome for flax cultivation.
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Affiliation(s)
- Daiana A. Zhernova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 32 Vavilova, Moscow 119991, Russia
| | - Elena N. Pushkova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 32 Vavilova, Moscow 119991, Russia
| | - Tatiana A. Rozhmina
- Federal Research Center for Bast Fiber Crops, 35 Lunacharskogo, Torzhok 172002, Russia
| | - Liubov V. Povkhova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 32 Vavilova, Moscow 119991, Russia
| | - Roman O. Novakovskiy
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 32 Vavilova, Moscow 119991, Russia
| | - Anastasia A. Turba
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 32 Vavilova, Moscow 119991, Russia
| | - Elena V. Borkhert
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 32 Vavilova, Moscow 119991, Russia
| | - Elizaveta A. Sigova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 32 Vavilova, Moscow 119991, Russia
| | - Ekaterina M. Dvorianinova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 32 Vavilova, Moscow 119991, Russia
| | - George S. Krasnov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 32 Vavilova, Moscow 119991, Russia
| | - Nataliya V. Melnikova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 32 Vavilova, Moscow 119991, Russia
| | - Alexey A. Dmitriev
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 32 Vavilova, Moscow 119991, Russia
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Dvorianinova EM, Sigova EA, Mollaev TD, Rozhmina TA, Kudryavtseva LP, Novakovskiy RO, Turba AA, Zhernova DA, Borkhert EV, Pushkova EN, Melnikova NV, Dmitriev AA. Comparative Genomic Analysis of Colletotrichum lini Strains with Different Virulence on Flax. J Fungi (Basel) 2023; 10:32. [PMID: 38248942 PMCID: PMC10817032 DOI: 10.3390/jof10010032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2023] [Revised: 12/04/2023] [Accepted: 12/24/2023] [Indexed: 01/23/2024] Open
Abstract
Colletotrichum lini is a flax fungal pathogen. The genus comprises differently virulent strains, leading to significant yield losses. However, there were no attempts to investigate the molecular mechanisms of C. lini pathogenicity from high-quality genome assemblies until this study. In this work, we sequenced the genomes of three C. lini strains of high (#390-1), medium (#757), and low (#771) virulence. We obtained more than 100× genome coverage with Oxford Nanopore Technologies reads (N50 = 12.1, 6.1, 5.0 kb) and more than 50× genome coverage with Illumina data (150 + 150 bp). Several assembly strategies were tested. The final assemblies were obtained using the Canu-Racon ×2-Medaka-Polca scheme. The assembled genomes had a size of 54.0-55.3 Mb, 26-32 contigs, N50 values > 5 Mb, and BUSCO completeness > 96%. A comparative genomic analysis showed high similarity among mitochondrial and nuclear genomes. However, a rearrangement event and the loss of a 0.7 Mb contig were revealed. After genome annotation with Funannotate, secreting proteins were selected using SignalP, and candidate effectors were predicted among them using EffectorP. The analysis of the InterPro annotations of predicted effectors revealed unique protein categories in each strain. The assembled genomes and the conducted comparative analysis extend the knowledge of the genetic diversity of C. lini and form the basis for establishing the molecular mechanisms of its pathogenicity.
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Affiliation(s)
- Ekaterina M. Dvorianinova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia; (E.A.S.); (T.D.M.); (R.O.N.); (A.A.T.); (D.A.Z.); (E.V.B.); (E.N.P.); (N.V.M.)
| | - Elizaveta A. Sigova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia; (E.A.S.); (T.D.M.); (R.O.N.); (A.A.T.); (D.A.Z.); (E.V.B.); (E.N.P.); (N.V.M.)
- Moscow Institute of Physics and Technology, Moscow 141701, Russia
| | - Timur D. Mollaev
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia; (E.A.S.); (T.D.M.); (R.O.N.); (A.A.T.); (D.A.Z.); (E.V.B.); (E.N.P.); (N.V.M.)
- Agrarian and Technological Institute, Peoples Friendship University of Russia (RUDN University), Moscow 117198, Russia
| | - Tatiana A. Rozhmina
- Federal Research Center for Bast Fiber Crops, Torzhok 172002, Russia; (T.A.R.); (L.P.K.)
| | | | - Roman O. Novakovskiy
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia; (E.A.S.); (T.D.M.); (R.O.N.); (A.A.T.); (D.A.Z.); (E.V.B.); (E.N.P.); (N.V.M.)
| | - Anastasia A. Turba
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia; (E.A.S.); (T.D.M.); (R.O.N.); (A.A.T.); (D.A.Z.); (E.V.B.); (E.N.P.); (N.V.M.)
| | - Daiana A. Zhernova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia; (E.A.S.); (T.D.M.); (R.O.N.); (A.A.T.); (D.A.Z.); (E.V.B.); (E.N.P.); (N.V.M.)
- Faculty of Biology, Lomonosov Moscow State University, Moscow 119234, Russia
| | - Elena V. Borkhert
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia; (E.A.S.); (T.D.M.); (R.O.N.); (A.A.T.); (D.A.Z.); (E.V.B.); (E.N.P.); (N.V.M.)
| | - Elena N. Pushkova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia; (E.A.S.); (T.D.M.); (R.O.N.); (A.A.T.); (D.A.Z.); (E.V.B.); (E.N.P.); (N.V.M.)
| | - Nataliya V. Melnikova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia; (E.A.S.); (T.D.M.); (R.O.N.); (A.A.T.); (D.A.Z.); (E.V.B.); (E.N.P.); (N.V.M.)
| | - Alexey A. Dmitriev
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia; (E.A.S.); (T.D.M.); (R.O.N.); (A.A.T.); (D.A.Z.); (E.V.B.); (E.N.P.); (N.V.M.)
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Pushkova EN, Borkhert EV, Novakovskiy RO, Dvorianinova EM, Rozhmina TA, Zhuchenko AA, Zhernova DA, Turba AA, Yablokov AG, Sigova EA, Krasnov GS, Bolsheva NL, Melnikova NV, Dmitriev AA. Selection of Flax Genotypes for Pan-Genomic Studies by Sequencing Tagmentation-Based Transcriptome Libraries. Plants (Basel) 2023; 12:3725. [PMID: 37960081 PMCID: PMC10650069 DOI: 10.3390/plants12213725] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Revised: 10/25/2023] [Accepted: 10/27/2023] [Indexed: 11/15/2023]
Abstract
Flax (Linum usitatissimum L.) products are used in the food, pharmaceutical, textile, polymer, medical, and other industries. The creation of a pan-genome will be an important advance in flax research and breeding. The selection of flax genotypes that sufficiently cover the species diversity is a crucial step for the pan-genomic study. For this purpose, we have adapted a method based on Illumina sequencing of transcriptome libraries prepared using the Tn5 transposase (tagmentase). This approach reduces the cost of sample preparation compared to commercial kits and allows the generation of a large number of cDNA libraries in a short time. RNA-seq data were obtained for 192 flax plants (3-6 individual plants from 44 flax accessions of different morphology and geographical origin). Evaluation of the genetic relationship between flax plants based on the sequencing data revealed incorrect species identification for five accessions. Therefore, these accessions were excluded from the sample set for the pan-genomic study. For the remaining samples, typical genotypes were selected to provide the most comprehensive genetic diversity of flax for pan-genome construction. Thus, high-throughput sequencing of tagmentation-based transcriptome libraries showed high efficiency in assessing the genetic relationship of flax samples and allowed us to select genotypes for the flax pan-genomic analysis.
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Affiliation(s)
- Elena N. Pushkova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia; (E.N.P.); (E.V.B.); (R.O.N.); (E.M.D.); (D.A.Z.); (A.A.T.); (A.G.Y.); (E.A.S.); (G.S.K.); (N.L.B.)
| | - Elena V. Borkhert
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia; (E.N.P.); (E.V.B.); (R.O.N.); (E.M.D.); (D.A.Z.); (A.A.T.); (A.G.Y.); (E.A.S.); (G.S.K.); (N.L.B.)
| | - Roman O. Novakovskiy
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia; (E.N.P.); (E.V.B.); (R.O.N.); (E.M.D.); (D.A.Z.); (A.A.T.); (A.G.Y.); (E.A.S.); (G.S.K.); (N.L.B.)
| | - Ekaterina M. Dvorianinova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia; (E.N.P.); (E.V.B.); (R.O.N.); (E.M.D.); (D.A.Z.); (A.A.T.); (A.G.Y.); (E.A.S.); (G.S.K.); (N.L.B.)
- Moscow Institute of Physics and Technology, 141701 Moscow, Russia
| | - Tatiana A. Rozhmina
- Federal Research Center for Bast Fiber Crops, 172002 Torzhok, Russia; (T.A.R.); (A.A.Z.)
| | - Alexander A. Zhuchenko
- Federal Research Center for Bast Fiber Crops, 172002 Torzhok, Russia; (T.A.R.); (A.A.Z.)
- All-Russian Horticultural Institute for Breeding, Agrotechnology and Nursery, 115598 Moscow, Russia
| | - Daiana A. Zhernova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia; (E.N.P.); (E.V.B.); (R.O.N.); (E.M.D.); (D.A.Z.); (A.A.T.); (A.G.Y.); (E.A.S.); (G.S.K.); (N.L.B.)
- Faculty of Biology, Lomonosov Moscow State University, 119234 Moscow, Russia
| | - Anastasia A. Turba
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia; (E.N.P.); (E.V.B.); (R.O.N.); (E.M.D.); (D.A.Z.); (A.A.T.); (A.G.Y.); (E.A.S.); (G.S.K.); (N.L.B.)
| | - Arthur G. Yablokov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia; (E.N.P.); (E.V.B.); (R.O.N.); (E.M.D.); (D.A.Z.); (A.A.T.); (A.G.Y.); (E.A.S.); (G.S.K.); (N.L.B.)
| | - Elizaveta A. Sigova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia; (E.N.P.); (E.V.B.); (R.O.N.); (E.M.D.); (D.A.Z.); (A.A.T.); (A.G.Y.); (E.A.S.); (G.S.K.); (N.L.B.)
- Moscow Institute of Physics and Technology, 141701 Moscow, Russia
| | - George S. Krasnov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia; (E.N.P.); (E.V.B.); (R.O.N.); (E.M.D.); (D.A.Z.); (A.A.T.); (A.G.Y.); (E.A.S.); (G.S.K.); (N.L.B.)
| | - Nadezhda L. Bolsheva
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia; (E.N.P.); (E.V.B.); (R.O.N.); (E.M.D.); (D.A.Z.); (A.A.T.); (A.G.Y.); (E.A.S.); (G.S.K.); (N.L.B.)
| | - Nataliya V. Melnikova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia; (E.N.P.); (E.V.B.); (R.O.N.); (E.M.D.); (D.A.Z.); (A.A.T.); (A.G.Y.); (E.A.S.); (G.S.K.); (N.L.B.)
| | - Alexey A. Dmitriev
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia; (E.N.P.); (E.V.B.); (R.O.N.); (E.M.D.); (D.A.Z.); (A.A.T.); (A.G.Y.); (E.A.S.); (G.S.K.); (N.L.B.)
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Dvorianinova EM, Zinovieva OL, Pushkova EN, Zhernova DA, Rozhmina TA, Povkhova LV, Novakovskiy RO, Sigova EA, Turba AA, Borkhert EV, Krasnov GS, Ruan C, Dmitriev AA, Melnikova NV. Key FAD2, FAD3, and SAD Genes Involved in the Fatty Acid Synthesis in Flax Identified Based on Genomic and Transcriptomic Data. Int J Mol Sci 2023; 24:14885. [PMID: 37834335 PMCID: PMC10573214 DOI: 10.3390/ijms241914885] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2023] [Revised: 09/28/2023] [Accepted: 09/29/2023] [Indexed: 10/15/2023] Open
Abstract
FAD (fatty acid desaturase) and SAD (stearoyl-ACP desaturase) genes play key roles in the synthesis of fatty acids (FA) and determination of oil composition in flax (Linum usitatissimum L.). We searched for FAD and SAD genes in the most widely used flax genome of the variety CDC Bethune and three available long-read assembled flax genomes-YY5, 3896, and Atlant. We identified fifteen FAD2, six FAD3, and four SAD genes. Of all the identified genes, 24 were present in duplicated pairs. In most cases, two genes from a pair differed by a significant number of gene-specific SNPs (single nucleotide polymorphisms) or even InDels (insertions/deletions), except for FAD2a-1 and FAD2a-2, where only seven SNPs distinguished these genes. Errors were detected in the FAD2a-1, FAD2a-2, FAD3c-1, and FAD3d-2 sequences in the CDC Bethune genome assembly but not in the long-read genome assemblies. Expression analysis of the available transcriptomic data for different flax organs/tissues revealed that FAD2a-1, FAD2a-2, FAD3a, FAD3b, SAD3-1, and SAD3-2 were specifically expressed in embryos/seeds/capsules and could play a crucial role in the synthesis of FA in flax seeds. In contrast, FAD2b-1, FAD2b-2, SAD2-1, and SAD2-2 were highly expressed in all analyzed organs/tissues and could be involved in FA synthesis in whole flax plants. FAD2c-2, FAD2d-1, FAD3c-1, FAD3c-2, FAD3d-1, FAD3d-2, SAD3-1, and SAD3-2 showed differential expression under stress conditions-Fusarium oxysporum infection and drought. The obtained results are essential for research on molecular mechanisms of fatty acid synthesis, FAD and SAD editing, and marker-assisted and genomic selection for breeding flax varieties with a determined fatty acid composition of oil.
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Affiliation(s)
| | - Olga L. Zinovieva
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia
| | - Elena N. Pushkova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia
| | - Daiana A. Zhernova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia
- Faculty of Biology, Lomonosov Moscow State University, Moscow 119234, Russia
| | - Tatiana A. Rozhmina
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia
- Federal Research Center for Bast Fiber Crops, Torzhok 172002, Russia
| | - Liubov V. Povkhova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia
- Moscow Institute of Physics and Technology, Moscow 141701, Russia
| | - Roman O. Novakovskiy
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia
| | - Elizaveta A. Sigova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia
- Moscow Institute of Physics and Technology, Moscow 141701, Russia
| | - Anastasia A. Turba
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia
| | - Elena V. Borkhert
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia
| | - George S. Krasnov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia
| | - Chengjiang Ruan
- Key Laboratory of Biotechnology and Bioresources Utilization, Ministry of Education, Institute of Plant Resources, Dalian Minzu University, Dalian 116600, China
| | - Alexey A. Dmitriev
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia
- Moscow Institute of Physics and Technology, Moscow 141701, Russia
| | - Nataliya V. Melnikova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia
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6
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Borkhert EV, Pushkova EN, Nasimovich YA, Kostina MV, Vasilieva NV, Murataev RA, Novakovskiy RO, Dvorianinova EM, Povkhova LV, Zhernova DA, Turba AA, Sigova EA, Snezhkina AV, Kudryavtseva AV, Bolsheva NL, Krasnov GS, Dmitriev AA, Melnikova NV. Sex-determining region complements traditionally used in phylogenetic studies nuclear and chloroplast sequences in investigation of Aigeiros Duby and Tacamahaca Spach poplars (genus Populus L., Salicaceae). Front Plant Sci 2023; 14:1204899. [PMID: 37860260 PMCID: PMC10582643 DOI: 10.3389/fpls.2023.1204899] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Accepted: 08/07/2023] [Indexed: 10/21/2023]
Abstract
Members of the genus Populus L. play an important role in the formation of forests in the northern hemisphere and are used in urban landscaping and timber production. Populus species of closely related sections show extensive hybridization. Therefore, the systematics of the genus is rather complicated, especially for poplars of hybrid origin. We aimed to assess the efficiency of application of the sex-determining region (SDR) in addition to the nuclear and chloroplast genome loci traditionally used in phylogenetic studies of poplars to investigate relationships in sections Aigeiros Duby and Tacamahaca Spach. Targeted deep sequencing of NTS 5S rDNA, ITS, DSH 2, DSH 5, DSH 8, DSH 12, DSH 29, 6, 15, 16, X18, trnG-psbK-psbI, rps2-rpoC2, rpoC2-rpoC1, as well as SDR and ARR17 gene was performed for 379 poplars. The SDR and ARR17 gene together with traditionally used multicopy and single-copy loci of nuclear and chloroplast DNA allowed us to obtain a clustering that is most consistent with poplar systematics based on morphological data and to shed light on several controversial hypotheses about the origin of the studied taxa (for example, the inexpediency of separating P. koreana, P. maximowiczii, and P. suaveolens into different species). We present a scheme of relationships between species and hybrids of sections Aigeiros and Tacamahaca based on molecular genetic, morphological, and geographical data. The geographical proximity of species and, therefore, the possibility of hybridization between them appear to be more important than the affiliation of species to the same section. We speculate that sections Aigeiros and Tacamahaca are distinguished primarily on an ecological principle (plain and mountain poplars) rather than on a genetic basis. Joint analysis of sequencing data for the SDR and chloroplast genome loci allowed us to determine the ancestors of P. × petrovskoe - P. laurifolia (female tree) × P. × canadensis (male tree), and P. × rasumovskoe - P. nigra (female tree) × P. suaveolens (male tree). Thus, the efficiency of using the SDR for the study of poplars of sections Aigeiros and Tacamahaca and the prospects of its use for the investigation of species of the genus Populus were shown.
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Affiliation(s)
- Elena V. Borkhert
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Elena N. Pushkova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Yuri A. Nasimovich
- State Environmental Protection Budgetary Institution of Moscow “Mospriroda”, Moscow, Russia
| | - Marina V. Kostina
- Institute of Biology and Chemistry, Moscow Pedagogical State University, Moscow, Russia
| | | | - Ramil A. Murataev
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
- Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Roman O. Novakovskiy
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Ekaterina M. Dvorianinova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
- Moscow Institute of Physics and Technology, Moscow, Russia
| | - Liubov V. Povkhova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
- Moscow Institute of Physics and Technology, Moscow, Russia
| | - Daiana A. Zhernova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
- Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Anastasia A. Turba
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Elizaveta A. Sigova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
- Moscow Institute of Physics and Technology, Moscow, Russia
| | | | - Anna V. Kudryavtseva
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Nadezhda L. Bolsheva
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - George S. Krasnov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Alexey A. Dmitriev
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
- Moscow Institute of Physics and Technology, Moscow, Russia
| | - Nataliya V. Melnikova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
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7
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Gorshkova EA, Gubernatorova EO, Dvorianinova EM, Yurakova TR, Marey MV, Averina OA, Holtze S, Hildebrandt TB, Dmitriev AA, Drutskaya MS, Vyssokikh MY, Nedospasov SA. Macrophages from naked mole-rat possess distinct immunometabolic signatures upon polarization. Front Immunol 2023; 14:1172467. [PMID: 37153552 PMCID: PMC10154529 DOI: 10.3389/fimmu.2023.1172467] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Accepted: 04/04/2023] [Indexed: 05/09/2023] Open
Abstract
The naked mole-rat (NMR) is a unique long-lived rodent which is highly resistant to age-associated disorders and cancer. The immune system of NMR possesses a distinct cellular composition with the prevalence of myeloid cells. Thus, the detailed phenotypical and functional assessment of NMR myeloid cell compartment may uncover novel mechanisms of immunoregulation and healthy aging. In this study gene expression signatures, reactive nitrogen species and cytokine production, as well as metabolic activity of classically (M1) and alternatively (M2) activated NMR bone marrow-derived macrophages (BMDM) were examined. Polarization of NMR macrophages under pro-inflammatory conditions led to expected M1 phenotype characterized by increased pro-inflammatory gene expression, cytokine production and aerobic glycolysis, but paralleled by reduced production of nitric oxide (NO). Under systemic LPS-induced inflammatory conditions NO production also was not detected in NMR blood monocytes. Altogether, our results indicate that NMR macrophages are capable of transcriptional and metabolic reprogramming under polarizing stimuli, however, NMR M1 possesses species-specific signatures as compared to murine M1, implicating distinct adaptations in NMR immune system.
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Affiliation(s)
- Ekaterina A. Gorshkova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Ekaterina O. Gubernatorova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | | | - Taisiya R. Yurakova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Maria V. Marey
- Federal State Budget Institution “National Medical Research Center for Obstetrics, Gynecology and Perinatology Named after Academician V.I. Kulakov”, Ministry of Healthcare of the Russian Federation, Moscow, Russia
| | - Olga A. Averina
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Susanne Holtze
- Department of Reproduction Management, Leibnitz Institute for Wildlife Research, Berlin, Germany
| | - Thomas B. Hildebrandt
- Department of Reproduction Management, Leibnitz Institute for Wildlife Research, Berlin, Germany
| | - Alexey A. Dmitriev
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Marina S. Drutskaya
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Mikhail Yu. Vyssokikh
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
- Federal State Budget Institution “National Medical Research Center for Obstetrics, Gynecology and Perinatology Named after Academician V.I. Kulakov”, Ministry of Healthcare of the Russian Federation, Moscow, Russia
| | - Sergei A. Nedospasov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
- Division of Immunobiology and Biomedicine, Center of Genetics and Life Sciences, Sirius University of Science and Technology, Federal Territory Sirius, Krasnodar Krai, Russia
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8
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Ustiugova AS, Dvorianinova EM, Melnikova NV, Dmitriev AA, Kuprash DV, Afanasyeva MA. Corrigendum to "CRISPR/Cas9 genome editing demonstrates functionality of the autoimmunity-associated SNP rs12946510" [Biochim. Biophys. Acta (BBA) - Mol. Basis Dis. 1869 (2023) 166599]. Biochim Biophys Acta Mol Basis Dis 2023; 1869:166649. [PMID: 36706683 DOI: 10.1016/j.bbadis.2023.166649] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Affiliation(s)
- Alina S Ustiugova
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia; Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia.
| | - Ekaterina M Dvorianinova
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia; Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia
| | - Nataliya V Melnikova
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia; Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia
| | - Alexey A Dmitriev
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia; Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia
| | - Dmitry V Kuprash
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia; Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia
| | - Marina A Afanasyeva
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia; Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia
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9
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Povkhova LV, Pushkova EN, Rozhmina TA, Zhuchenko AA, Frykin RI, Novakovskiy RO, Dvorianinova EM, Gryzunov AA, Borkhert EV, Sigova EA, Vladimirov GN, Snezhkina AV, Kudryavtseva AV, Krasnov GS, Dmitriev AA, Melnikova NV. 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. Plants (Basel) 2022; 12:95. [PMID: 36616223 PMCID: PMC9824437 DOI: 10.3390/plants12010095] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Revised: 12/14/2022] [Accepted: 12/16/2022] [Indexed: 06/17/2023]
Abstract
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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Affiliation(s)
- Liubov V. Povkhova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia
| | - Elena N. Pushkova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia
| | - Tatiana A. Rozhmina
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia
- Federal Research Center for Bast Fiber Crops, 172002 Torzhok, Russia
| | - Alexander A. Zhuchenko
- Federal Research Center for Bast Fiber Crops, 172002 Torzhok, Russia
- All-Russian Horticultural Institute for Breeding, Agrotechnology and Nursery, 115598 Moscow, Russia
| | - Roman I. Frykin
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia
- Faculty of Biology, Lomonosov Moscow State University, 119234 Moscow, Russia
| | - Roman O. Novakovskiy
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia
| | - Ekaterina M. Dvorianinova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia
- Moscow Institute of Physics and Technology, 141701 Moscow, Russia
| | - Aleksey A. Gryzunov
- All-Russian Scientific Research Institute of Refrigeration Industry—Branch of V.M. Gorbatov Federal Research Center for Food Systems of Russian Academy of Sciences, 127422 Moscow, Russia
| | - Elena V. Borkhert
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia
| | - Elizaveta A. Sigova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia
- Moscow Institute of Physics and Technology, 141701 Moscow, Russia
| | | | - Anastasiya V. Snezhkina
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia
| | - Anna V. Kudryavtseva
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia
| | - George S. Krasnov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia
| | - Alexey A. Dmitriev
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia
| | - Nataliya V. Melnikova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia
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10
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Dvorianinova EM, Bolsheva NL, Pushkova EN, Rozhmina TA, Zhuchenko AA, Novakovskiy RO, Povkhova LV, Sigova EA, Zhernova DA, Borkhert EV, Kaluzhny DN, Melnikova NV, Dmitriev AA. Isolating Linum usitatissimum L. Nuclear DNA Enabled Assembling High-Quality Genome. Int J Mol Sci 2022; 23:ijms232113244. [PMID: 36362031 PMCID: PMC9656206 DOI: 10.3390/ijms232113244] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 10/25/2022] [Accepted: 10/28/2022] [Indexed: 11/06/2022] Open
Abstract
High-quality genome sequences help to elucidate the genetic basis of numerous biological processes and track species evolution. For flax (Linum usitatissimum L.)—a multifunctional crop, high-quality assemblies from Oxford Nanopore Technologies (ONT) data were unavailable, largely due to the difficulty of isolating pure high-molecular-weight DNA. This article proposes a scheme for gaining a contiguous L. usitatissimum assembly using Nanopore data. We developed a protocol for flax nuclei isolation with subsequent DNA extraction, which allows obtaining about 5 μg of pure high-molecular-weight DNA from 0.5 g of leaves. Such an amount of material can be collected even from a single plant and yields more than 30 Gb of ONT data in two MinION runs. We performed a comparative analysis of different genome assemblers and polishers on the gained data and obtained the final 447.1-Mb assembly of L. usitatissimum line 3896 genome using the Canu—Racon (two iterations)—Medaka combination. The genome comprised 1695 contigs and had an N50 of 6.2 Mb and a completeness of 93.8% of BUSCOs from eudicots_odb10. Our study highlights the impact of the chosen genome construction strategy on the resulting assembly parameters and its eligibility for future genomic studies.
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Affiliation(s)
- Ekaterina M. Dvorianinova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia
- Correspondence: (E.M.D.); (A.A.D.)
| | - Nadezhda L. Bolsheva
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia
| | - Elena N. Pushkova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia
| | | | - Alexander A. Zhuchenko
- Federal Research Center for Bast Fiber Crops, Torzhok 172002, Russia
- All-Russian Horticultural Institute for Breeding, Agrotechnology and Nursery, Moscow 115598, Russia
| | - Roman O. Novakovskiy
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia
| | - Liubov V. Povkhova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia
- Moscow Institute of Physics and Technology, Moscow 141701, Russia
| | - Elizaveta A. Sigova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia
- Moscow Institute of Physics and Technology, Moscow 141701, Russia
| | - Daiana A. Zhernova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia
- Faculty of Biology, Lomonosov Moscow State University, Moscow 119234, Russia
| | - Elena V. Borkhert
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia
| | - Dmitry N. Kaluzhny
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia
| | - Nataliya V. Melnikova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia
| | - Alexey A. Dmitriev
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia
- Correspondence: (E.M.D.); (A.A.D.)
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11
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Bolsheva NL, Melnikova NV, Dvorianinova EM, Mironova LN, Yurkevich OY, Amosova AV, Krasnov GS, Dmitriev AA, Muravenko OV. Clarification of the Position of Linum stelleroides Planch. within the Phylogeny of the Genus Linum L. Plants (Basel) 2022; 11:652. [PMID: 35270121 PMCID: PMC8912650 DOI: 10.3390/plants11050652] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Revised: 02/21/2022] [Accepted: 02/21/2022] [Indexed: 06/14/2023]
Abstract
The phylogeny of members of the family Linaceae DC. ex Perleb has not been adequately studied. In particular, data on the phylogenetic relationship between Linum stelleroides Planch. and other representatives of the blue-flowered flax are very controversial. In the present work, to clarify this issue, we obtained DNA sequences of three nuclear loci (IGS and ITS1 + 5.8S rDNA + ITS2 of the 35S rRNA gene and the 5S rRNA gene) and eight chloroplast loci (rbcL, the trnL-trnF intergenic spacer, matK, the 3' trnK intron, ndhF, trnG, the psbA-trnH intergenic spacer, and rpl16) of 10 Linum L. species (L. stelleroides, L. hirsutum, L. perenne, L. leonii, L. lewisii, L. narbonense, L. decumbens, L. grandiflorum, L. bienne (syn. L. angustifolium), and L. usitatissimum) using high-throughput sequencing data. The phylogenetic analysis showed that L. stelleroides forms a basal branch in the blue-flowered flax clade. Previously found inconsistencies in the position of L. stelleroides and some other species in the Linaceae phylogenetic tree resulted from the erroneous species identification of some of the studied plant samples.
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Affiliation(s)
- Nadezhda L. Bolsheva
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia; (N.V.M.); (E.M.D.); (O.Y.Y.); (A.V.A.); (G.S.K.); (O.V.M.)
| | - Nataliya V. Melnikova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia; (N.V.M.); (E.M.D.); (O.Y.Y.); (A.V.A.); (G.S.K.); (O.V.M.)
| | - Ekaterina M. Dvorianinova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia; (N.V.M.); (E.M.D.); (O.Y.Y.); (A.V.A.); (G.S.K.); (O.V.M.)
- Moscow Institute of Physics and Technology, 141701 Moscow, Russia
| | - Liudmila N. Mironova
- Botanical Garden-Institute of the Far Eastern Branch of the Russian Academy of Sciences, 690024 Vladivostok, Russia;
| | - Olga Y. Yurkevich
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia; (N.V.M.); (E.M.D.); (O.Y.Y.); (A.V.A.); (G.S.K.); (O.V.M.)
| | - Alexandra V. Amosova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia; (N.V.M.); (E.M.D.); (O.Y.Y.); (A.V.A.); (G.S.K.); (O.V.M.)
| | - George S. Krasnov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia; (N.V.M.); (E.M.D.); (O.Y.Y.); (A.V.A.); (G.S.K.); (O.V.M.)
| | - Alexey A. Dmitriev
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia; (N.V.M.); (E.M.D.); (O.Y.Y.); (A.V.A.); (G.S.K.); (O.V.M.)
| | - Olga V. Muravenko
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia; (N.V.M.); (E.M.D.); (O.Y.Y.); (A.V.A.); (G.S.K.); (O.V.M.)
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12
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Povkhova LV, Melnikova NV, Rozhmina TA, Novakovskiy RO, Pushkova EN, Dvorianinova EM, Zhuchenko AA, Kamionskaya AM, Krasnov GS, Dmitriev AA. Genes Associated with the Flax Plant Type (Oil or Fiber) Identified Based on Genome and Transcriptome Sequencing Data. Plants (Basel) 2021; 10:plants10122616. [PMID: 34961087 PMCID: PMC8707629 DOI: 10.3390/plants10122616] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Revised: 11/25/2021] [Accepted: 11/26/2021] [Indexed: 06/14/2023]
Abstract
As a result of the breeding process, there are two main types of flax (Linum usitatissimum L.) plants. Linseed is used for obtaining seeds, while fiber flax is used for fiber production. We aimed to identify the genes associated with the flax plant type, which could be important for the formation of agronomically valuable traits. A search for polymorphisms was performed in genes involved in the biosynthesis of cell wall components, lignans, fatty acids, and ion transport based on genome sequencing data for 191 flax varieties. For 143 of the 424 studied genes (4CL, C3'H, C4H, CAD, CCR, CCoAOMT, COMT, F5H, HCT, PAL, CTL, BGAL, ABC, HMA, DIR, PLR, UGT, TUB, CESA, RGL, FAD, SAD, and ACT families), one or more polymorphisms had a strong correlation with the flax type. Based on the transcriptome sequencing data, we evaluated the expression levels for each flax type-associated gene in a wide range of tissues and suggested genes that are important for the formation of linseed or fiber flax traits. Such genes were probably subjected to the selection press and can determine not only the traits of seeds and stems but also the characteristics of the root system or resistance to stresses at a particular stage of development, which indirectly affects the ability of flax plants to produce seeds or fiber.
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Affiliation(s)
- Liubov V. Povkhova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia; (L.V.P.); (N.V.M.); (R.O.N.); (E.N.P.); (E.M.D.); (G.S.K.)
- Moscow Institute of Physics and Technology, 141701 Moscow, Russia
| | - Nataliya V. Melnikova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia; (L.V.P.); (N.V.M.); (R.O.N.); (E.N.P.); (E.M.D.); (G.S.K.)
| | - Tatiana A. Rozhmina
- Federal Research Center for Bast Fiber Crops, 172002 Torzhok, Russia; (T.A.R.); (A.A.Z.)
| | - Roman O. Novakovskiy
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia; (L.V.P.); (N.V.M.); (R.O.N.); (E.N.P.); (E.M.D.); (G.S.K.)
| | - Elena N. Pushkova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia; (L.V.P.); (N.V.M.); (R.O.N.); (E.N.P.); (E.M.D.); (G.S.K.)
| | - Ekaterina M. Dvorianinova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia; (L.V.P.); (N.V.M.); (R.O.N.); (E.N.P.); (E.M.D.); (G.S.K.)
- Moscow Institute of Physics and Technology, 141701 Moscow, Russia
| | - Alexander A. Zhuchenko
- Federal Research Center for Bast Fiber Crops, 172002 Torzhok, Russia; (T.A.R.); (A.A.Z.)
- All-Russian Horticultural Institute for Breeding, Agrotechnology and Nursery, 115598 Moscow, Russia
| | - Anastasia M. Kamionskaya
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia;
| | - George S. Krasnov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia; (L.V.P.); (N.V.M.); (R.O.N.); (E.N.P.); (E.M.D.); (G.S.K.)
| | - Alexey A. Dmitriev
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia; (L.V.P.); (N.V.M.); (R.O.N.); (E.N.P.); (E.M.D.); (G.S.K.)
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13
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Melnikova NV, Pushkova EN, Dvorianinova EM, Beniaminov AD, Novakovskiy RO, Povkhova LV, Bolsheva NL, Snezhkina AV, Kudryavtseva AV, Krasnov GS, Dmitriev AA. Genome Assembly and Sex-Determining Region of Male and Female Populus × sibirica. Front Plant Sci 2021; 12:625416. [PMID: 34567016 PMCID: PMC8455832 DOI: 10.3389/fpls.2021.625416] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Accepted: 07/30/2021] [Indexed: 06/13/2023]
Abstract
The genus Populus is presented by dioecious species, and it became a promising object to study the genetics of sex in plants. In this work, genomes of male and female Populus × sibirica individuals were sequenced for the first time. To achieve high-quality genome assemblies, we used Oxford Nanopore Technologies and Illumina platforms. A protocol for the isolation of long and pure DNA from young poplar leaves was developed, which enabled us to obtain 31 Gb (N50 = 21 kb) for the male poplar and 23 Gb (N50 = 24 kb) for the female one using the MinION sequencer. Genome assembly was performed with different tools, and Canu provided the most complete and accurate assemblies with a length of 818 Mb (N50 = 1.5 Mb) for the male poplar and 816 Mb (N50 = 0.5 Mb) for the female one. After polishing with Racon and Medaka (Nanopore reads) and then with POLCA (Illumina reads), assembly completeness was 98.45% (87.48% duplicated) for the male and 98.20% (76.77% duplicated) for the female according to BUSCO (benchmarking universal single-copy orthologs). A high proportion of duplicated BUSCO and the increased genome size (about 300 Mb above the expected) pointed at the separation of haplotypes in a large part of male and female genomes of P. × sibirica. Due to this, we were able to identify two haplotypes of the sex-determining region (SDR) in both assemblies; and one of these four SDR haplotypes, in the male genome, contained partial repeats of the ARR17 gene (Y haplotype), while the rest three did not (X haplotypes). The analysis of the male P. × sibirica SDR suggested that the Y haplotype originated from P. nigra, while the X haplotype is close to P. trichocarpa and P. balsamifera species. Moreover, we revealed a Populus-specific repeat that could be involved in translocation of the ARR17 gene or its part to the SDR of P. × sibirica and other Populus species. The obtained results expand our knowledge on SDR features in the genus Populus and poplar phylogeny.
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Affiliation(s)
- Nataliya V. Melnikova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Elena N. Pushkova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Ekaterina M. Dvorianinova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
- Moscow Institute of Physics and Technology, Moscow, Russia
| | - Artemy D. Beniaminov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Roman O. Novakovskiy
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Liubov V. Povkhova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
- Moscow Institute of Physics and Technology, Moscow, Russia
| | - Nadezhda L. Bolsheva
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | | | - Anna V. Kudryavtseva
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - George S. Krasnov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Alexey A. Dmitriev
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
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14
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Pushkova EN, Krasnov GS, Lakunina VA, Novakovskiy RO, Povkhova LV, Dvorianinova EM, Beniaminov AD, Fedorova MS, Snezhkina AV, Kudryavtseva AV, Dmitriev AA, Melnikova NV. Genome and Transcriptome Sequencing of Populus × sibirica Identified Sex-Associated Allele-Specific Expression of the CLC Gene. Front Genet 2021; 12:676935. [PMID: 34456967 PMCID: PMC8385651 DOI: 10.3389/fgene.2021.676935] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2021] [Accepted: 05/28/2021] [Indexed: 12/04/2022] Open
Abstract
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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Affiliation(s)
- Elena N Pushkova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - George S Krasnov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Valentina A Lakunina
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Roman O Novakovskiy
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Liubov V Povkhova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia.,Moscow Institute of Physics and Technology, Moscow, Russia
| | - Ekaterina M Dvorianinova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia.,Moscow Institute of Physics and Technology, Moscow, Russia
| | - Artemy D Beniaminov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Maria S Fedorova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | | | - Anna V Kudryavtseva
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Alexey A Dmitriev
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Nataliya V Melnikova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
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15
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Dvorianinova EM, Pushkova EN, Novakovskiy RO, Povkhova LV, Bolsheva NL, Kudryavtseva LP, Rozhmina TA, Melnikova NV, Dmitriev AA. Nanopore and Illumina Genome Sequencing of Fusarium oxysporum f. sp. lini Strains of Different Virulence. Front Genet 2021; 12:662928. [PMID: 34220940 PMCID: PMC8248858 DOI: 10.3389/fgene.2021.662928] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Accepted: 05/06/2021] [Indexed: 11/15/2022] Open
Affiliation(s)
- Ekaterina M Dvorianinova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia.,Moscow Institute of Physics and Technology, Moscow, Russia
| | - Elena N Pushkova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Roman O Novakovskiy
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Liubov V Povkhova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia.,Moscow Institute of Physics and Technology, Moscow, Russia
| | - Nadezhda L Bolsheva
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | | | | | - Nataliya V Melnikova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Alexey A Dmitriev
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
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16
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Dmitriev AA, Pushkova EN, Novakovskiy RO, Beniaminov AD, Rozhmina TA, Zhuchenko AA, Bolsheva NL, Muravenko OV, Povkhova LV, Dvorianinova EM, Kezimana P, Snezhkina AV, Kudryavtseva AV, Krasnov GS, Melnikova NV. Genome Sequencing of Fiber Flax Cultivar Atlant Using Oxford Nanopore and Illumina Platforms. Front Genet 2021; 11:590282. [PMID: 33519894 PMCID: PMC7841463 DOI: 10.3389/fgene.2020.590282] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Accepted: 11/02/2020] [Indexed: 01/11/2023] Open
Affiliation(s)
- Alexey A Dmitriev
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Elena N Pushkova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Roman O Novakovskiy
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Artemy D Beniaminov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Tatiana A Rozhmina
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia.,Federal Research Center for Bast Fiber Crops, Torzhok, Russia
| | - Alexander A Zhuchenko
- Federal Research Center for Bast Fiber Crops, Torzhok, Russia.,All-Russian Horticultural Institute for Breeding, Agrotechnology and Nursery, Moscow, Russia
| | - Nadezhda L Bolsheva
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Olga V Muravenko
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Liubov V Povkhova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia.,Moscow Institute of Physics and Technology, Moscow, Russia
| | - Ekaterina M Dvorianinova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia.,Moscow Institute of Physics and Technology, Moscow, Russia
| | - Parfait Kezimana
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia.,Peoples' Friendship University of Russia (RUDN University), Moscow, Russia
| | | | - Anna V Kudryavtseva
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - George S Krasnov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Nataliya V Melnikova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
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17
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Dmitriev AA, Novakovskiy RO, Pushkova EN, Rozhmina TA, Zhuchenko AA, Bolsheva NL, Beniaminov AD, Mitkevich VA, Povkhova LV, Dvorianinova EM, Snezhkina AV, Kudryavtseva AV, Krasnov GS, Melnikova NV. Transcriptomes of Different Tissues of Flax ( Linum usitatissimum L.) Cultivars With Diverse Characteristics. Front Genet 2020; 11:565146. [PMID: 33363567 PMCID: PMC7755106 DOI: 10.3389/fgene.2020.565146] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2020] [Accepted: 10/20/2020] [Indexed: 12/18/2022] Open
Affiliation(s)
- Alexey A Dmitriev
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Roman O Novakovskiy
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Elena N Pushkova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Tatiana A Rozhmina
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia.,Federal Research Center for Bast Fiber Crops, Torzhok, Russia
| | - Alexander A Zhuchenko
- Federal Research Center for Bast Fiber Crops, Torzhok, Russia.,All-Russian Horticultural Institute for Breeding, Agrotechnology and Nursery, Moscow, Russia
| | - Nadezhda L Bolsheva
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Artemy D Beniaminov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Vladimir A Mitkevich
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Liubov V Povkhova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia.,Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Ekaterina M Dvorianinova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia.,Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | | | - Anna V Kudryavtseva
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - George S Krasnov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Nataliya V Melnikova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
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18
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Krasnov GS, Pushkova EN, Novakovskiy RO, Kudryavtseva LP, Rozhmina TA, Dvorianinova EM, Povkhova LV, Kudryavtseva AV, Dmitriev AA, Melnikova NV. High-Quality Genome Assembly of Fusarium oxysporum f. sp. lini. Front Genet 2020; 11:959. [PMID: 33193577 PMCID: PMC7481384 DOI: 10.3389/fgene.2020.00959] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2019] [Accepted: 07/30/2020] [Indexed: 12/31/2022] Open
Abstract
In the present work, a highly pathogenic isolate of Fusarium oxysporum f. sp. lini, which is the most harmful pathogen affecting flax (Linum usitatissimum L.), was sequenced for the first time. To achieve a high-quality genome assembly, we used the combination of two sequencing platforms - Oxford Nanopore Technologies (MinION system) with long noisy reads and Illumina (HiSeq 2500 instrument) with short accurate reads. Given the quality of DNA is crucial for Nanopore sequencing, we developed the protocol for extraction of pure high-molecular-weight DNA from fungi. Sequencing of DNA extracted using this protocol allowed us to obtain about 85x genome coverage with long (N50 = 29 kb) MinION reads and 30x coverage with 2 × 250 bp HiSeq reads. Several tools were developed for genome assembly; however, they provide different results depending on genome complexity, sequencing data volume, read length and quality. We benchmarked the most requested assemblers (Canu, Flye, Shasta, wtdbg2, and MaSuRCA), Nanopore polishers (Medaka and Racon), and Illumina polishers (Pilon and POLCA) on our sequencing data. The assembly performed with Canu and polished with Medaka and POLCA was considered the most full and accurate. After further elimination of redundant contigs using Purge Haplotigs, we achieved a high-quality genome of F. oxysporum f. sp. lini with a total length of 59 Mb, N50 of 3.3 Mb, and 99.5% completeness according to BUSCO. We also obtained a complete circular mitochondrial genome with a length of 38.7 kb. The achieved assembly expands studies on F. oxysporum and plant-pathogen interaction in flax.
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Affiliation(s)
- George S. Krasnov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Elena N. Pushkova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Roman O. Novakovskiy
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | | | - Tatiana A. Rozhmina
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
- Federal Research Center for Bast Fiber Crops, Torzhok, Russia
| | - Ekaterina M. Dvorianinova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
- Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Liubov V. Povkhova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
- Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Anna V. Kudryavtseva
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Alexey A. Dmitriev
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Nataliya V. Melnikova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
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19
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Novakovskiy RO, Dvorianinova EM, Rozhmina TA, Kudryavtseva LP, Gryzunov AA, Pushkova EN, Povkhova LV, Snezhkina AV, Krasnov GS, Kudryavtseva AV, Melnikova NV, Dmitriev AA. Data on genetic polymorphism of flax ( Linum usitatissimum L.) pathogenic fungi of Fusarium, Colletotrichum, Aureobasidium, Septoria, and Melampsora genera. Data Brief 2020; 31:105710. [PMID: 32490079 PMCID: PMC7256288 DOI: 10.1016/j.dib.2020.105710] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Revised: 04/28/2020] [Accepted: 05/08/2020] [Indexed: 11/02/2022] Open
Abstract
Being a valuable agricultural plant, flax (Linum usitatissimum L.) is used for oil and fiber production. However, the cultivation of this agriculture faces an urgent problem of flax susceptibility to fungal diseases. The most destructive ones are caused by the representatives of Fusarium, Colletotrichum, Aureobasidium, Septoria, and Melampsora genera, reducing flax yields significantly. To combat such pathogens effectively, it is of high importance to assess their genetic diversity that can be used to develop molecular markers to distinguish fungal genera and species. Morphological analysis traditionally carried out for fungal identification requires a given amount of time and tends to be difficult. In the present work, we determined the DNA sequences that are frequently used for phylogenetic studies in fungi - internal transcribed spacer (ITS) and beta-tubulin (tub2), translation elongation factor 1-alpha (tef1), RNA polymerase II largest subunit (RPB1), RNA polymerase II second largest subunit (RPB2), and minichromosome maintenance protein (MCM7) genes - for 203 flax fungal pathogens of Fusarium oxysporum, F. avenaceum, F. solani, F. sporotrichiella, F. moniliforme, F. culmorum, F. semitectum, F. gibbosum, Colletotrichum lini, Aureobasidium pullulans, Septoria linicola, and Melampsora lini species. The sequencing was performed using the Illumina MiSeq platform with a 300+300 bp kit, and on average, about 2350 reads per sample were obtained that allows accurate identification of the genetic polymorphism. Raw data are stored at the Sequence Read Archive under the accession number PRJNA596387. The obtained data can be used for fungal phylogenetic studies and the development of a PCR-based test system for flax pathogen identification.
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Affiliation(s)
- Roman O Novakovskiy
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia
| | - Ekaterina M Dvorianinova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia.,Moscow Institute of Physics and Technology, Dolgoprudny 141701, Russia
| | - Tatiana A Rozhmina
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia.,Federal Research Center for Bast Fiber Crops, Torzhok 172002, Russia
| | | | - Aleksey A Gryzunov
- All-Russian Scientific Research Institute of Refrigeration Industry - branch of V.M. Gorbatov Federal Research Center for Food Systems of Russian Academy of Sciences, Moscow 127422, Russia
| | - Elena N Pushkova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia
| | - Liubov V Povkhova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia.,Moscow Institute of Physics and Technology, Dolgoprudny 141701, Russia
| | - Anastasiya V Snezhkina
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia
| | - George S Krasnov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia
| | - Anna V Kudryavtseva
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia
| | - Nataliya V Melnikova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia
| | - Alexey A Dmitriev
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia
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