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Brainard SH, Sanders DM, Bruna T, Shu S, Dawson JC. The first two chromosome-scale genome assemblies of American hazelnut enable comparative genomic analysis of the genus Corylus. PLANT BIOTECHNOLOGY JOURNAL 2024; 22:472-483. [PMID: 37870930 PMCID: PMC10826982 DOI: 10.1111/pbi.14199] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Revised: 09/11/2023] [Accepted: 09/29/2023] [Indexed: 10/25/2023]
Abstract
The native, perennial shrub American hazelnut (Corylus americana) is cultivated in the Midwestern United States for its significant ecological benefits, as well as its high-value nut crop. Implementation of modern breeding methods and quantitative genetic analyses of C. americana requires high-quality reference genomes, a resource that is currently lacking. We therefore developed the first chromosome-scale assemblies for this species using the accessions 'Rush' and 'Winkler'. Genomes were assembled using HiFi PacBio reads and Arima Hi-C data, and Oxford Nanopore reads and a high-density genetic map were used to perform error correction. N50 scores are 31.9 Mb and 35.3 Mb, with 90.2% and 97.1% of the total genome assembled into the 11 pseudomolecules, for 'Rush' and 'Winkler', respectively. Gene prediction was performed using custom RNAseq libraries and protein homology data. 'Rush' has a BUSCO score of 99.0 for its assembly and 99.0 for its annotation, while 'Winkler' had corresponding scores of 96.9 and 96.5, indicating high-quality assemblies. These two independent assemblies enable unbiased assessment of structural variation within C. americana, as well as patterns of syntenic relationships across the Corylus genus. Furthermore, we identified high-density SNP marker sets from genotyping-by-sequencing data using 1343 C. americana, C. avellana and C. americana × C. avellana hybrids, in order to assess population structure in natural and breeding populations. Finally, the transcriptomes of these assemblies, as well as several other recently published Corylus genomes, were utilized to perform phylogenetic analysis of sporophytic self-incompatibility (SSI) in hazelnut, providing evidence of unique molecular pathways governing self-incompatibility in Corylus.
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Affiliation(s)
- Scott H. Brainard
- Department of Plant and Agroecosystem SciencesUniversity of Wisconsin‐MadisonMadisonWisconsinUSA
| | - Dean M. Sanders
- University of Wisconsin Biotechnology CenterUniversity of Wisconsin‐MadisonMadisonWisconsinUSA
| | - Tomas Bruna
- U.S. Department of Energy Joint Genome InstituteLawrence Berkeley National LaboratoryBerkeleyCaliforniaUSA
| | - Shengqiang Shu
- U.S. Department of Energy Joint Genome InstituteLawrence Berkeley National LaboratoryBerkeleyCaliforniaUSA
| | - Julie C. Dawson
- Department of Plant and Agroecosystem SciencesUniversity of Wisconsin‐MadisonMadisonWisconsinUSA
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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, SWITZERLAND) 2023; 12:3725. [PMID: 37960081 PMCID: PMC10650069 DOI: 10.3390/plants12213725] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [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] [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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Glick L, Mayrose I. The Effect of Methodological Considerations on the Construction of Gene-Based Plant Pan-genomes. Genome Biol Evol 2023; 15:evad121. [PMID: 37401440 PMCID: PMC10340445 DOI: 10.1093/gbe/evad121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2023] [Revised: 06/21/2023] [Accepted: 06/28/2023] [Indexed: 07/05/2023] Open
Abstract
Pan-genomics is an emerging approach for studying the genetic diversity within plant populations. In contrast to common resequencing studies that compare whole genome sequencing data with a single reference genome, the construction of a pan-genome (PG) involves the direct comparison of multiple genomes to one another, thereby enabling the detection of genomic sequences and genes not present in the reference, as well as the analysis of gene content diversity. Although multiple studies describing PGs of various plant species have been published in recent years, a better understanding regarding the effect of the computational procedures used for PG construction could guide researchers in making more informed methodological decisions. Here, we examine the effect of several key methodological factors on the obtained gene pool and on gene presence-absence detections by constructing and comparing multiple PGs of Arabidopsis thaliana and cultivated soybean, as well as conducting a meta-analysis on published PGs. These factors include the construction method, the sequencing depth, and the extent of input data used for gene annotation. We observe substantial differences between PGs constructed using three common procedures (de novo assembly and annotation, map-to-pan, and iterative assembly) and that results are dependent on the extent of the input data. Specifically, we report low agreement between the gene content inferred using different procedures and input data. Our results should increase the awareness of the community to the consequences of methodological decisions made during the process of PG construction and emphasize the need for further investigation of commonly applied methodologies.
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Affiliation(s)
- Lior Glick
- Department of Life Sciences, School of Plant Sciences and Food Security, Tel-Aviv University, Tel Aviv, Israel
| | - Itay Mayrose
- Department of Life Sciences, School of Plant Sciences and Food Security, Tel-Aviv University, Tel Aviv, Israel
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Assembling Quality Genomes of Flax Fungal Pathogens from Oxford Nanopore Technologies Data. J Fungi (Basel) 2023; 9:jof9030301. [PMID: 36983469 PMCID: PMC10055923 DOI: 10.3390/jof9030301] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 02/22/2023] [Accepted: 02/23/2023] [Indexed: 03/03/2023] Open
Abstract
Flax (Linum usitatissimum L.) is attacked by numerous devastating fungal pathogens, including Colletotrichum lini, Aureobasidium pullulans, and Fusarium verticillioides (Fusarium moniliforme). The effective control of flax diseases follows the paradigm of extensive molecular research on pathogenicity. However, such studies require quality genome sequences of the studied organisms. This article reports on the approaches to assembling a high-quality fungal genome from the Oxford Nanopore Technologies data. We sequenced the genomes of C. lini, A. pullulans, and F. verticillioides (F. moniliforme) and received different volumes of sequencing data: 1.7 Gb, 3.9 Gb, and 11.1 Gb, respectively. To obtain the optimal genome sequences, we studied the effect of input data quality and genome coverage on assembly statistics and tested the performance of different assembling and polishing software. For C. lini, the most contiguous and complete assembly was obtained by the Flye assembler and the Homopolish polisher. The genome coverage had more effect than data quality on assembly statistics, likely due to the relatively low amount of sequencing data obtained for C. lini. The final assembly was 53.4 Mb long and 96.4% complete (according to the glomerellales_odb10 BUSCO dataset), consisted of 42 contigs, and had an N50 of 4.4 Mb. For A. pullulans and F. verticillioides (F. moniliforme), the best assemblies were produced by Canu–Medaka and Canu–Homopolish, respectively. The final assembly of A. pullulans had a length of 29.5 Mb, 99.4% completeness (dothideomycetes_odb10), an N50 of 2.4 Mb and consisted of 32 contigs. F. verticillioides (F. moniliforme) assembly was 44.1 Mb long, 97.8% complete (hypocreales_odb10), consisted of 54 contigs, and had an N50 of 4.4 Mb. The obtained results can serve as a guideline for assembling a de novo genome of a fungus. In addition, our data can be used in genomic studies of fungal pathogens or plant–pathogen interactions and assist in the management of flax diseases.
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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, SWITZERLAND) 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] [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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7
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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] [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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