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Karyotypes of blue-flowered flaxes with relatively small chromosomes. a, b-members of sect. Adenolinum: diploid L. perenne (a) and tetraploid L. perenne subsp. extraaxillare (b); c, d-members of sect. Linum with 2n = 16: L. grandiflorum (c) and L. decumbens (d); e, f-members of sect. Linum with 2n = 30: L. usitatissimum (e) and L. angustifolium (f). Chromosomes arranged according to their sizes. Inverted DAPI-staining of chromosomes are shown in shades of gray. The positions of rDNA loci revealed by FISH are shown in colored insertions below the karyotypes: 35S rDNA-green signals and 5S rDNA-red signals. Scale bar-5 μM
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Background:
The species relationships within the genus Linum have already been studied several times by means of different molecular and phylogenetic approaches. Nevertheless, a number of ambiguities in phylogeny of Linum still remain unresolved. In particular, the species relationships within the sections Stellerolinum and Dasylinum need further...
Contexts in source publication
Context 1
... studied samples were diploid with 2n = 18. The specimens L. perene K5500, L. perene ssp. anglicum and L. perene ssp. extraaxilare were tetraploid with 2n = 36. The 35S rDNA locus was revealed in the pericentromeric region of the short arm of chromosome 1, and 5S rDNA locus was localized in the median region of the long arm of the same chromosome (Fig. 2a, ...
Context 2
... and L. decumbens (2n = 16) had the similar structure of karyo- types, but their chromosomes were smaller (2-3.5 μm) than chromosomes of L. narbonense. The site of 35S rDNA was localized in the pericentromeric region of the long arm of chromosome 1, and the site of 5S rDNA was revealed in the distal region of the long arm of chromosome 3 ( Fig. 2c, d). The cultivated species L. usitatissimum as well as its wild ancestor L. angustifolium were mesotetraploids with 2n = 30 and had significantly smaller sizes of chromo- somes (1.2-3 μm) compared to the species mentioned above. The only site of 35S rDNA was observed in the proximal region of the short arm of metacentric chromosome 1. ...
Context 3
... smaller sizes of chromo- somes (1.2-3 μm) compared to the species mentioned above. The only site of 35S rDNA was observed in the proximal region of the short arm of metacentric chromosome 1. Sites of 5S rDNA were found in the proximal region of the long arm of chromosome 3 and also in the distal regions of long arms of chromosomes 8 and 13 (Fig. 2e, f ...
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... The genus Linum contains ~180-200 species distributed throughout temperate and subtropical regions of the world [21,28,29]. The genus can generally be divided into two major clades-a blue-flowered and a yellow-flowered clade [21]. ...
... In Y2-Y3, however, flax plants flower and set seed much earlier, and in many cases yield a second harvest which matures very late in the fall. Harvest 1 occurred in midsummer (~weeks [28][29], followed by harvest 2 in late fall (~weeks [44][45][46]. Plants were clipped at the base using pruners, then placed into labeled harvest bags for transport to St. Paul, MN facilities, where they were dried for 5 d at 32.2 °C and moved into dry, room temperature (~21 °C, day/night) storage. ...
Flaxseed has gained popularity as a health food. Wild, perennial Linum relatives of annual flax (L. usitatissimum) possess similar oil compositions, making them perennial oilseed (OS) alternatives. The objective of this study was to phenotype 25 OS and 17 cut flower (CF) breeding populations with 137 wild Linum species’ accessions in a common garden over three years (Y1–3) to quantify the impact of selection and identify top candidates. This study was intercepted by COVID-19, which prevented the same detailed phenotyping of Y1 from occurring in Y2–3. Traits measured from the perennial flax OS, in comparison with the CF ideotypes: weekly seed germination (Y1), yield per plant (Y1–3), seed weight (Y1–2), shattering (Y1–2), and seed capsule diameter (Y1). In Y1, OS selections had the highest yield per plant, followed by L. austriacum and then CF selections. The 1000 seed weights in Y1 were highest in annual flax, followed by L. grandiflorum and L. baicalense. Seed numbers/capsule were low in Y1–2, possibly due to shattering. Average yield per plant increased across Y1–3 indicating that, once plant establishment had occurred along with the potential for two harvests/year in Y2 onwards, significant OS yield can be realized. Harvest 1 yields were significantly higher than in harvest 2. In Y1–3, OS selections had the highest average seed yield. In Y1, OS and CF populations had smaller seeds, higher shattering, smaller capsule diameters, and lower germination than wild species. Significant breeding efforts are needed to increase perennial flax yield, using the multiple crop ideotypes.
... Then, the genome of the progeny probably underwent diploidization. Thus, the resulting ploidy of most genomic features is four (Bolsheva et al., 2017). ...
Sequencing whole plant genomes provides a solid foundation for applied and basic studies. Genome sequences of agricultural plants attract special attention, as they reveal information on the regulation of beneficial plant traits. Flax is a valuable crop cultivated for oil and fiber. Genome sequences of its representatives are rich sources of genetic information for the improvement of cultivated forms of the plant. In our work, we sequenced the first genome of flax with the dehiscence of capsules—Linum usitatissimum convar. сrepitans (Boenn.) Dumort—on the Oxford Nanopore Technologies (ONT) and Illumina platforms. We obtained 23 Gb of raw ONT data and 89 M of 150 + 150 paired-end Illumina reads and tested different tools for genome assembly and polishing. The genome assembly produced according to the Canu—Racon ×2—medaka—POLCA scheme had optimal contiguity and completeness: assembly length—412.6 Mb, N50—5.2 Mb, L50—28, and complete BUSCO—94.6% (64.0% duplicated, eudicots_odb10). The obtained high-quality genome assembly of L. usitatissimum convar. crepitans provides opportunities for further studies of evolution, domestication, and genome regulation in the section Linum.
... For most samples, on average, about 78% of the reads were uniquely mapped to the CDC Bethune genome assembly (GCA_000224295.2) ( Figure 2). About 18% of the reads were mapped to many loci; they may represent multicopy genes, which are expected since the whole-genome duplication occurred during the origin of L. usitatissimum [10,27,41]. Exceptions were 32 samples (plants of accessions p_10, p_11, p_12, p_13, ...
... For most samples, on average, about 78% of the reads were uniquely mapped to the CDC Bethune genome assembly (GCA_000224295.2) ( Figure 2). About 18% of the reads were mapped to many loci; they may represent multicopy genes, which are expected since the whole-genome duplication occurred during the origin of L. usitatissimum [10,27,41]. Exceptions were 32 samples (plants of accessions p_10, p_11, p_12, p_13, and p_14), for which on average only about 40% of the reads were uniquely mapped. ...
... Sequencing of organelle DNA, as well as ribosomal DNA, is commonly used to assess the genetic relationship of samples. However, such sequences are often insufficiently polymorphic to study groups of closely related plants, including flax [27,53]. This approach would allow us to detect an error in species identification for the accessions of cluster IV (L. ...
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.
... It is composed of tandem repeats of alternative arrays of sequences coding 5S-rRNA and non-transcribed spacers (NTSs) located separately from the 18S-26S rRNA gene clusters [45]. Over the years, relevant results have been obtained using RFLP analysis in the 5S-rRNA-NTS region [33,45,[85][86][87]. Consequently, to obtain a DNA molecular fingerprinting of the different coffee accessions, the PCR-RFLP method was applied combining MseI and Xhol as restriction enzymes to selectively cleave the resulting amplicons. ...
The genus Coffea is known for the two species C. arabica (CA) and C. canephora (CC), which are used to prepare the beverage coffee. Proper identification of green beans of coffee varieties is based on phenotypic and phytochemical/molecular characteristics. In this work, a combination of chemical (UV/Vis, HPLC-DAD-MS/MS, GC-MS, and GC-FID) and molecular (PCR-RFLP) fingerprinting was used to discriminate commercial green coffee accessions from different geographical origin. The highest content of polyphenols and flavonoids was always found in CC accessions, whereas CA showed lower values. ABTS and FRAP assays showed a significant correlation between phenolic content and antioxidant activity in most CC accessions. We identified 32 different compounds, including 28 flavonoids and four N-containing compounds. The highest contents of caffeine and melatonin were detected in CC accessions, whereas the highest levels of quercetin and kaempferol derivatives were found in CA accessions. Fatty acids of CC accessions were characterized by low levels of linoleic and cis octadecenoic acid and high amounts of elaidic acid and myristic acid. Discrimination of species according to their geographical origin was achieved using high-throughput data analysis, combining all measured parameters. Lastly, PCR-RFLP analysis was instrumental for the identification of recognition markers for the majority of accessions. Using the restriction enzyme AluI on the trnL-trnF region, we clearly discriminated C. canephora from C. arabica, whereas the cleavage performed by the restriction enzymes MseI and XholI on the 5S-rRNA-NTS region produced specific discrimination patterns useful for the correct identification of the different coffee accessions. This work extends our previous studies and provides new information on the complete flavonoid profile, combining high-throughput data with DNA fingerprinting to assess the geographical discrimination of green coffee.
... The genus Linum is distributed throughout temperate and subtropical regions of the world (Bolsheva et al., 2017;McDill et al., 2009) and taxonomically classified, based on morphological [4][5][6][7][8][9][10][11][12][13] and molecular traits [4]. The Adenolinum or L. perenne group within sect. ...
... The genus Linum is distributed throughout temperate and subtropical regions of the world (Bolsheva et al., 2017;McDill et al., 2009) and taxonomically classified, based on morphological [4][5][6][7][8][9][10][11][12][13] and molecular traits [4]. The Adenolinum or L. perenne group within sect. ...
... The genus Linum is distributed throughout temperate and subtropical regions of the world (Bolsheva et al., 2017;McDill et al., 2009) and taxonomically classified, based on morphological [4][5][6][7][8][9][10][11][12][13] and molecular traits [4]. The Adenolinum or L. perenne group within sect. ...
(1) Background: Annual flax (Linum usitatissimum) and many wild relatives possess showy blue flowers and finely textured foliage. To promote the use of blue-flowered flax as ornamentals, an herbaceous perennial flax breeding program was initiated to develop ideotypes and test their effectiveness. The objectives of this study were to (a) compare traits of interest for herbaceous perennials in breeding populations (CF, oilseed) and accessions of annual/perennial species in a common garden; (b) quantify the impact of selection (direct, indirect) for traits of interest; (c) identify top candidate species for continued breeding using the herbaceous perennial flax crop ideotype; (2) Methods: Recorded traits, based on the perennial flax ideotype, included: flower diameter, flowering period, stem length and diameter, plant width and height, summer and winter survival; (3) Results: OS and CF populations had smaller stem diameters, longer flowering periods, larger plant size, more uniform growth, and improved winter survival compared to wild species. Linum austriacum was the top wild species for the CF breeding ideotype but comparable in performance with L. perenne for the herbaceous perennial flax ideotype; (4) Conclusions: The effect of 1–5 yrs. on selection for target/non-target traits in wild species for future R&D is exemplified with selection and release of an herbaceous/garden ornamental perennial flax for the market.
... In this work, genome assemblies by Canu, Flye, and Shasta had proximate numbers of duplicated orthologs (57.9-61.8%). The resulting values agree with a probable history of L. usitatissimum genome origin-the species probably originated from the hybridisation of two Linum species with diploidisation of the hybrid genome [76]. Therefore, the differences in genome lengths of the CDC Bethune, YY5, and line 3896 are attributed to other structures than duplicated coding sequences, e.g., the repetitive DNA content as we observed in this study. ...
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.
... Components of the plant cytoskeleton (microtubules and actin filaments, F-actin) play central roles in cellular organization and intracellular transport 13,14 , and form distinct architectures to support IT ( Fig. 1d). Accordingly, there are two copies of KCBP in the allotetraploid Gossypium hirsutum 29 and Linum usitatissimum 30 , as well as in the ancient tetraploid Populus trichocarpa 31 , whereas there are four copies in Glycine max, another ancient tetraploid 32 . Furthermore, transcriptional data showed that the corresponding duplicated KCBP copies in G. max, L. japonicus and Phaseolus vulgaris also show predominant expression in nodules ( Supplementary Fig. 1b-d). ...
Symbioses between legumes and rhizobia require establishment of the plant-derived symbiosome membrane, which surrounds the rhizobia and accommodates the symbionts by providing an interface for nutrient and signal exchange. The host cytoskeleton and endomembrane trafficking systems play central roles in the formation of a functional symbiotic interface for rhizobia endosymbiosis; however, the underlying mechanisms remain largely unknown. Here we demonstrate that the nodulation-specific kinesin-like calmodulin-binding protein (nKCBP), a plant-specific microtubule-based kinesin motor, controls central vacuole morphogenesis in symbiotic cells in Medicago truncatula. Phylogenetic analysis further indicated that nKCBP duplication occurs solely in legumes of the clade that form symbiosomes. Knockout of nKCBP results in central vacuole deficiency, defective symbiosomes and abolished nitrogen fixation. nKCBP decorates linear particles along microtubules, and crosslinks microtubules with the actin cytoskeleton, to control central vacuole formation by modulating vacuolar vesicle fusion in symbiotic cells. Together, our findings reveal that rhizobia co-opted nKCBP to achieve symbiotic interface formation by regulating cytoskeletal assembly and central vacuole morphogenesis during nodule development.
... ex Prob. The same has already been considered in recent works [4,33,51]. This is based not only on the fact that the species has a geographical distribution range that is different from the rest (Eastern Asia) but also on the presence of stipulate glands provided with a small stipe, a character that does not appear in any other section. ...
The taxonomy of the subfamily Linoideae at the intergeneric and section levels has been questioned throughout the years, and the evolution of floral characters remains poorly understood. In particular, the evolution of flower color is still uncertain, despite its ecological importance and being one of the most variable and striking traits in Angiospermae. We evaluated the phylogenetic relationships of the genera and sections and used the phylogeny to reconstruct the ancestral state of flower color. The results suggest reevaluating the taxonomic status of segregated genera and re-incorporating them into Linum. Four of the five sections currently accepted were recovered as monophyletic (Cathartolinum, Dasylinum, Linum, and Syllinum). We propose accepting the section Stellerolinon and reevaluating Linopsis, whose representatives were recovered in three separate clades. The ancestral flower color for Linoideae was yellow-white. The flower colors purple and yellow-white were recovered at the deepest nodes of the two main clades. Pink, blue, and red colors were the most recent to evolve. These results appear to be related to diversification events, biogeographical history, and ecological aspects of the subfamily. Our reconstruction constitutes the first plausible scenario that explores the evolution of flower color, leading to new testable hypotheses for future research on the flax group.
... Dasylinum [5]. According to a sequence-specific amplified polymorphism (SSAP) analysis and data on nuclear internal transcribed spacers (ITS), three chloroplast DNA sequences (ndhF + trnK intron + trnL-trnF spacer), and the nuclear 5S ribosomal RNA (rRNA) gene, L. stelleroides formed an independent basal clade of the blueflowered flax [5,10,11]. Finally, combined data on ITS and seven plastid sequences (rbcL, the trnL-trnF spacer, the 3 trnK intron, ndhF, trnG, the psbA-trnH spacer, the rpl16 intron) showed that L. stelleroides takes an intermediate position between the clusters formed by representatives of the sect. Dasylinum on the one hand, and representatives of the sect. ...
... In this work, as well as in our previous studies [10,11], we used a sample of L. stelleroides collected in the natural habitat in the Far East of Russia and grown in the Botanical Garden-Institute of the Far-Eastern Branch of the Russian Academy of Sciences (BGI FEB RAS) in Vladivostok, Russia. It has all the specific morphological characteristics inherent in the L. stelleroides species. ...
... It has all the specific morphological characteristics inherent in the L. stelleroides species. Previously, we studied this sample using molecular karyological methods and found that its chromosome number is 2n = 20 [10], which completely agrees with the results of Sokolovskaya and Probatova [14]. In addition, the sequences of rbcL, the trnL-trnF spacer, ndhF, and ITS assembled from WGS reads of this specimen turned out to be highly homologous to the sequences of the same loci in the genomic DNA of herbarium samples [5]. ...
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.
... The genus Linum contains %180 to 200 species (Bolsheva et al., 2017;McDill et al., 2009). The most well-known of these is domesticated annual flax, L. usitatissimum L., common flax or linseed. ...
... Linum also contains a large number of wild perennial species that are distributed throughout the temperate and subtropical regions of Europe, Asia, and North America (Bolsheva et al., 2017;McDill et al., 2009). Several species of Linum have a history of cultivation as ornamentals, including L. perenne L., L. austriacum L., L. narbonense L., L. grandiflorum Desf., and L. flavum L., although few reports are available on the variation available for ornamental breeding, including for cut flower uses (Cullis, 2011;Diederichsen and Richards, 2003;Fu, 2019). ...
The genus Linum L. contains ≈200 primarily blue-flowered species, including several ornamentals, yet no reports exist regarding the cut flower potential of this genus. The objective of this study was to evaluate the cut flower potential of perennial flax cultivars ( L. perenne L. ‘Blue Flax’ and ‘Sapphire’; Expt. 1, 2018) and accessions ( L. austriacum L., L. lewisii Pursh., and L. perenne ; Expt. 2, 2019), and record traits that will enable breeding and selection for improved cut flower performance. The mean vase life across both cultivars in Expt. 1 was 9.2 days. In Expt. 2, L. perenne had the longest average vase life (9.3 days), followed by L. austriacum (9.1 days) and L. lewisii (8.3 days). The floral preservative (Floralife 300) significantly increased vase life by an average of 1.7 days in Expt. 1, and 1.6 days in Expt. 2, and resulted in a significantly greater number of flowers (≈2x) in both experiments. Significant variation was observed among genotypes for most traits, including vase life (6.2 to 11.3 days) and number of flowers (1.3 to 10.5), highlighting the opportunities for improving the potential of cut flower perennial flax through breeding.
