Common buckwheat (Fagopyrum esculentum) is an important non-cereal grain crop and a prospective component of functional food. Despite this, the genomic resources for this species and for the whole family Polygonaceae, to which it belongs, are scarce. Here, we report the assembly of the buckwheat genome using long-read technology and a high-resolution expression atlas including 46 organs and developmental stages. We found that the buckwheat genome has an extremely high content of transposable elements, including several classes of recently (0.5–1 Mya) multiplied TEs (“transposon burst”) and gradually accumulated TEs. The difference in TE content is a major factor contributing to the three-fold increase in the genome size of F. esculentum compared with its sister species F. tataricum. Moreover, we detected the differences in TE content between the wild ancestral subspecies F. esculentum ssp. ancestrale and buckwheat cultivars, suggesting that TE activity accompanied buckwheat domestication. Expression profiling allowed us to test a hypothesis about the genetic control of petaloidy of tepals in buckwheat. We showed that it is not mediated by B-class gene activity, in contrast to the prediction from the ABC model. Based on a survey of expression profiles and phylogenetic analysis, we identified the MYB family transcription factor gene tr_18111 as a potential candidate for the determination of conical cells in buckwheat petaloid tepals. The information on expression patterns has been integrated into the publicly available database TraVA: http://travadb.org/browse/Species=Fesc/. The improved genome assembly and transcriptomic resources will enable research on buckwheat, including practical applications.

Fagopyrum esculentum (common buckwheat) is an important agricultural non-cereal grain plant. Despite extensive genetic studies, the information on its mitochondrial genome is still lacking. Using long reads generated by single-molecule real-time technology coupled with circular consensus sequencing (CCS) protocol, we assembled the buckwheat mitochondrial genome and detected that its prevalent form consists of 10 circular chromosomes with a total length of 404 Kb. In order to confirm the presence of a multipartite structure, we developed a new targeted assembly tool capable of processing long reads. The mitogenome contains all genes typical for plant mitochondrial genomes and long inserts of plastid origin (~6.4% of the total mitogenome length). Using this new information, we characterized the genetic diversity of mitochondrial and plastid genomes in 11 buckwheat cultivars compared with the ancestral subspecies, F. esculentum ssp. ancestrale. We found it to be surprisingly low within cultivars: Only three to six variations in the mitogenome and one to two in the plastid genome. In contrast, the divergence with F. esculentum ssp. ancestrale is much higher: 220 positions differ in the mitochondrial genome and 159 in the plastid genome. The SNPs in the plastid genome are enriched in non-synonymous substitutions, in particular in the genes involved in photosynthesis: psbA, psbC, and psbH. This presumably reflects the selection for the increased photosynthesis efficiency as a part of the buckwheat breeding program.

From an analysis of 481 Rhizobium leguminosarum bv. viceae strains with 7 pea cultivars in pot and field experiments, we demonstrated that effective strains could be isolated from a rich medium-acid grey forest soil of the Or61 area (Central region of the European part of Russia) but not from a poor acid podzolic soil of the St. Petersburg area (North-West Russia). The proportion of the isolates significantly increasing N accumulation in pea plants (10.2%) is higher than that of strains increasing the shoot dry mass (4.6%) in the pot experiments. The mean values of the increase for N accumulation (33.8%) upon inoculation are also higher than for shoot mass (27.0%) in these experiments. N accumulation in the inoculated pea plants in the pot experiments was significantly correlated with seed yield and seed N accumulation in field experiments, while for shoot dry mass these correlations were either weak or not significant. Two-factor analysis of variance demonstrated that the contribution of plant cultivars to the variation of the major symbiotic efficiency parameters is higher (30.8-31.6%) and contributions of cultivar-strain specificity is lower (5.4-8.8%) than the contributions of strain genotypes (13.4-14.9%). We identified an ineffective R. leguminosarum bv. viceae strain 50 which can be used as a tester for assessing the nodulation competitiveness of the effective strains by an indirect method (analysis of dry mass and N accumulation in pea plants inoculated with the mixture of the tested effective strains and the tester strain). The relative competitive ability (RCA) determined by this method was 75.7-82.8% for strain 52 but only 10.5-13.8% for strain 250a; this difference was confirmed by a direct method (use of the streptomycin-resistant mutants). Results of screening of the diverse collection of 53 effective R. leguminosarum bv. viceae strains by the indirect method permits us to divide them into 3 groups (32 high-competitive, 10 medium-competitive and 11 low-competitive strains) but reveals no correlation between the competitiveness and symbiotic efficiency. N accumulation in the pea shoots is demonstrated to be a much more suitable criterion than the shoot mass for selection either of the highly-effective or of highly-competitive (by the indirect estimation) R. leguminosarum by. viceae strains in the pot experiments.

The studies on floral homeotic mutants of the model plant species Arabidopsis thaliana (L.) Heynh. and Antirrhinum majus L. have clarified many important aspects of the genetic control of flower development. However, the details of this process can vary in species representing different lineages of flowering plants. The studies on floral homeotic mutants of nonmodel plant species may significantly improve the understanding of the mechanisms of morphological evolution of flowers. We report here the results of the genetic and morphological analysis of two floral homeotic mutants of common buckwheat (Fagopyrum esculentum Moench.). The mutant, tepal-like bract (tlb), is characterized by the transformation of bracts into petaloid organs, whereas fagopyrum apetala (fap), has a carpelloid perianth. Both mutant phenotypes are caused by a single recessive nuclear mutation. The double mutant fap tlb combines the features of tlb and fap. Our results show that single gene mutations are sufficient to convert the buckwheat bract into a tepal and to confer carpel identity on first whorl organs. These results are consistent with the premise that variations on the ABC model can be used to explain a wide range of floral architectures.Résumé : L'étude de mutants floraux homéotiques des plantes modèles Arabidopsis thaliana (L.) Heynh. et Anthirrhinium majus L. ont clarifié plusieurs aspects du contrôle génétique du développement floral. Cependant, les détails de ce processus peuvent varier selon les espèces représentant différentes lignées de plantes à fleurs. Les études sur les mutants floraux homéotiques portant sur des espèces de plantes non-modèles peuvent améliorer significativement la compréhension des mécanismes de l'évolution morphologique des fleurs. Les auteurs rapportent les résultats de l'analyse morphologique et gé-nétique de deux mutants floraux homéotiques du sarrasin (Fagopyrum esculentum Moench.). Le mutant, bractées tépaloï-des (tlb), se caractérise par la transformation des bractées en organes pétaloïdes, alors que le fagopyrum apetala (fap) possède un périanthe carpelloïde. Ces deux phénotypes mutants sont causés par une mutation nucléique récessive unique. Le double mutant fap tlb combine les caractéristiques des tlb et des fap. Les résultats montrent que des mutations à gène unique suffisent pour convertir la bractée du sarrasin en tépale et à conférer une identité de carpelle au premier verticille d'organes. Ces résultats concordent avec la prémisse que les variations sur le modèle ABC peuvent être utilisées pour expliquer un ensemble d'architectures florales.

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