Cultivated flax (Linum usitatissimum L.) is widely used for production of textile, food, chemical and pharmaceutical products. However, various stresses decrease flax production. Search for genes, which are involved in stress response, is necessary for breeding of adaptive cultivars. Imbalanced concentration of nutrient elements in soil decrease flax yields and also results in heritable changes in some flax lines. The appearance of Linum Insertion Sequence 1 (LIS-1) is the most studied modification. However, LIS-1 function is still unclear. High-throughput sequencing of transcriptome of flax plants grown under normal (N), phosphate deficient (P), and nutrient excess (NPK) conditions was carried out using Illumina platform. The assembly of transcriptome was performed, and a total of 34924, 33797, and 33698 unique transcripts for N, P, and NPK sequencing libraries were identified, respectively. We have not revealed any LIS-1 derived mRNA in our sequencing data. The analysis of high-throughput sequencing data allowed us to identify genes with potentially differential expression under imbalanced nutrition. For further investigation with qPCR, 15 genes were chosen and their expression levels were evaluated in the extended sampling of 31 flax plants. Significant expression alterations were revealed for genes encoding WRKY and JAZ protein families under P and NPK conditions. Moreover, the alterations of WRKY family genes differed depending on LIS-1 presence in flax plant genome. Besides, we revealed slight and LIS-1 independent mRNA level changes of KRP2 and ING1 genes, which are adjacent to LIS-1, under nutrition stress. Differentially expressed genes were identified in flax plants, which were grown under phosphate deficiency and excess nutrition, on the basis of high-throughput sequencing and qPCR data. We showed that WRKY and JAS gene families participate in flax response to imbalanced nutrient content in soil. Besides, we have not identified any mRNA, which could be derived from LIS-1, in our transcriptome sequencing data. Expression of LIS-1 flanking genes, ING1 and KRP2, was suggested not to be nutrient stress-induced. Obtained results provide new insights into edaphic stress response in flax and the role of LIS-1 in these process.

The core Caryophyllales consist of approximately 30 families (12 000 species) distributed worldwide. Many members evolved one-seeded or conjoined fruits, but their origin and structural diversity have not been investigated. A comparative anatomical investigation of the one-seeded fruits within the core Caryophyllales was conducted. The origin of the one-seeded fruits and the evolutionary reconstructions of some carpological characters were traced using a tree based on rbcl and matK data in order to understand the ancestral characters and their changes. The one-seeded fruit type is inferred to be an ancestral character state in core Caryophyllales, with a subsequent increase in the seed number seen in all major clades. Most representatives of the ‘Earlier Diverging’ clade are distinguished in various carpological traits. The organization of the pericarp is diverse in many groups, although fruits with a dry, many-layered pericarp, consisting of sclerenchyma as outer layers and a thin-walled parenchyma below, with seeds occupying a vertical embryo position, are likely ancestral character states in the core Caryophyllales clade. Several carpological peculiarities in fruit and seed structure were discovered in obligate one-seeded Achatocarpaceae, Chenopodiaceae, Nyctaginaceae, Seguieriaceae and Sarcobataceae. The horizontal embryo evolved in only certain groups of Chenopodiaceae. The bar-thickening of endotegmen cells appears to be an additional character typical of core Caryophyllales. The syncarpy-to-lysicarpy paradigm in Caryophyllaceae needs to be reinterpreted.

Cultivated flax (Linum usitatissimum L.) is an important plant valuable for industry. Some flax lines can undergo heritable phenotypic and genotypic changes (LIS-1 insertion being the most common) in response to nutrient stress and are called plastic lines. Offspring of plastic lines, which stably inherit the changes, are called genotrophs. MicroRNAs (miRNAs) are involved in a crucial regulatory mechanism of gene expression. They have previously been assumed to take part in nutrient stress response and can, therefore, participate in genotroph formation. In the present study, we performed high-throughput sequencing of small RNAs extracted from flax plants grown under normal, phosphate deficient and nutrient excess conditions to identify miRNAs and evaluate their expression. Our analysis revealed expression of 96 conserved miRNAs from 21 families in flax. Moreover, 475 novel potential miRNAs were identified for the first time, and their targets were predicted. However, none of the identified miRNAs were transcribed from LIS-1. Expression of 7 miRNAs (miR168, miR169, miR395, miR398, miR399, miR408, and lus-miR-N1) with up- or down-regulation under nutrient stress (on the basis of high-throughput sequencing data) was evaluated on extended sampling using qPCR. Reference gene search identified ETIF3H and ETIF3E genes as most suitable for this purpose. Down-regulation of novel potential lus-miR-N1 and up-regulation of conserved miR399 were revealed under the phosphate deficient conditions. In addition, the negative correlation of expression of lus-miR-N1 and its predicted target, ubiquitin-activating enzyme E1 gene, as well as, miR399 and its predicted target, ubiquitin-conjugating enzyme E2 gene, was observed. Thus, in our study, miRNAs expressed in flax plastic lines and genotrophs were identified and their expression and expression of their targets was evaluated using high-throughput sequencing and qPCR for the first time. These data provide new insights into nutrient stress response regulation in plastic flax cultivars.

Scorzonera comprises 180–190 species and belongs to the subtribe Scorzonerinae. Its circumscription has long been the subject of debate and available molecular phylogenetic analyses affirmed the polyphyly of Scorzonera in its wide sense. We provide a re-evaluation of Scorzonera and other related genera, based on carpological (including anatomical) and extended molecular phylogenetic analyses. We present, for the first time, a comprehensive sampling, including Scorzonera in its widest sense and all other genera recognised in the Scorzonerinae. We conducted phylogenetic analyses using Maximum Parsimony, Maximum Likelihood and Bayesian analyses, based on sequences of the nuclear ribosomal ITS and of two plastid markers (partial rbcL and matK) and Maximum Parsimony for reconstructing the carpological character states at ancestral nodes. Achene characters, especially related to pericarp anatomy, such as general topography of the tissue types, disposition of the mechanical tissue and direction of its fibres, presence or absence of air cavities, provide, in certain cases, support for the phylogenetic lineages revealed. Confirming the polyphyly of Scorzonera, we propose a revised classification of the subtribe, accepting the genera Scorzonera (including four major clades: Scorzonera s. str., S. purpurea, S. albicaulis and Podospermum), Gelasia, Lipschitzia gen. nov. (for the Scorzonera divaricata clade), Pseudopodospermum, Pterachaenia (also including Scorzonera codringtonii), Ramaliella gen. nov. (for the S. polyclada clade) and Takhtajaniantha. A key to the revised genera and a characterisation of the genera and major clades are provided.