Abstract
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.
Highlights
Common buckwheat (Fagopyrum esculentum) is an important non-cereal grain crop of particular importance in Russia, China and Ukraine, with production of ∼ 2 million tons
The 250-bp Illumina reads and mate-pair reads provided a backbone for the assembly; further improvement of the assembly, including gap closing, was performed using long reads generated by SMRT CCS technology on the Pacific Bioscience platform (Supplementary Table 1)
The number of genes was close to that found in sugar beet (Dohm et al, 2014), which belongs to Caryophyllales along with buckwheat, and in A. thaliana and was generally within the range typical for the genomes of plants that have not undergone a recent whole-genome duplication
Summary
Common buckwheat (Fagopyrum esculentum) is an important non-cereal grain crop of particular importance in Russia, China and Ukraine, with production of ∼ 2 million tons. Sequencing technologies have been responsible for tremendous progress; one of the key innovations of these technologies in recent years was the development of NGS platforms capable of generating long reads This is of special importance for plant scientists because plant genomes are large and complex and are shaped by multiple segmental and wholegenome duplications and transposable element (TE) activity. Longread technologies have encouraged scientists to conduct studies that were impossible even with the gold-standard quality genome of Arabidopsis thaliana due to the complex rearrangements caused by transposition On this basis, we performed the sequencing, de novo assembly and annotation of the buckwheat genome using third-generation technologies – SMRT and nanopore sequencing – and generated a transcriptome map of F. esculentum from 46 organs and developmental stages. The development of a high-resolution transcriptome map will provide a resource for comparative transcriptomic analyses in the phylogenetic context
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