1
|
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, SWITZERLAND) 2024; 13:956. [PMID: 38611485 PMCID: PMC11013676 DOI: 10.3390/plants13070956] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [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.
Collapse
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.)
| |
Collapse
|
2
|
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] [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.
Collapse
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
| |
Collapse
|
3
|
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). FRONTIERS IN PLANT SCIENCE 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] [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.
Collapse
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
| |
Collapse
|
4
|
Yan B, Haiyang Zhang, Li H, Gao Y, Wei Y, Chang C, Zhang L, Li Z, Zhu L, Xu J. Molecular regulation of lipid metabolism in Suaeda salsa. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2023; 201:107894. [PMID: 37482030 DOI: 10.1016/j.plaphy.2023.107894] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Revised: 06/27/2023] [Accepted: 07/11/2023] [Indexed: 07/25/2023]
Abstract
Suaeda salsa is remarkable for its high oil content and abundant unsaturated fatty acids. In this study, the regulatory networks on fatty acid and lipid metabolism were constructed by combining the de novo transcriptome and lipidome data. Differentially expressed genes (DEGs) associated with lipids biosynthesis pathways were identified in the S. salsa transcriptome. DEGs involved in fatty acid and glycerolipids were generally up-regulated in leaf tissues. DEGs for TAG assembly were enriched in developing seeds, while DEGs in phospholipid metabolic pathways were enriched in root tissues. Polar lipids were extracted from S. salsa tissues and analyzed by lipidomics. The proportion of galactolipid MGDG was the highest in S. salsa leaves. The molar percentage of PG was high in the developing seeds, and the other main phospholipids had higher molar percentage in roots of S. salsa. The predominant C36:6 molecular species indicates that S. salsa is a typical 18:3 plant. The combined transcriptomic and lipidomic data revealed that different tissues of S. salsa were featured with DEGs associated with specific lipid metabolic pathways, therefore, represented unique lipid profiles. This study will be helpful on understanding lipid metabolism pathway and exploring the key genes involved in lipid synthesis in S. salsa.
Collapse
Affiliation(s)
- Bowei Yan
- College of Agriculture, Heilongjiang Bayi Agricultural University, Daqing, 163319, China; Heilongjiang Academy of Agricultural Sciences Postdoctoral Programme, Institute of Industrial Crops, Heilongjiang Academy of Agricultural Sciences, Harbin, China
| | - Haiyang Zhang
- College of Agriculture, Heilongjiang Bayi Agricultural University, Daqing, 163319, China
| | - Huixin Li
- College of Agriculture, Heilongjiang Bayi Agricultural University, Daqing, 163319, China
| | - Yuqiao Gao
- College of Agriculture, Heilongjiang Bayi Agricultural University, Daqing, 163319, China
| | - Yulei Wei
- College of Agriculture, Heilongjiang Bayi Agricultural University, Daqing, 163319, China
| | - Chuanyi Chang
- Harbin Academy of Agricultural Science, Harbin, 150028, China
| | - Liguo Zhang
- Heilongjiang Academy of Agricultural Sciences Postdoctoral Programme, Institute of Industrial Crops, Heilongjiang Academy of Agricultural Sciences, Harbin, China
| | - Zuotong Li
- College of Agriculture, Heilongjiang Bayi Agricultural University, Daqing, 163319, China
| | - Lei Zhu
- College of Food Science and Technology, Heilongjiang Bayi Agricultural University, Daqing, 163319, China.
| | - Jingyu Xu
- College of Agriculture, Heilongjiang Bayi Agricultural University, Daqing, 163319, China.
| |
Collapse
|