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Open Access Highly Accessed Research article

De novo sequencing and characterization of floral transcriptome in two species of buckwheat (Fagopyrum)

Maria D Logacheva124*, Artem S Kasianov3, Dmitriy V Vinogradov4, Tagir H Samigullin1, Mikhail S Gelfand45, Vsevolod J Makeev367 and Aleksey A Penin248

Author Affiliations

1 Department of Evolutionary Biochemistry, A.N. Belozersky Institute of Physico-Chemical Biology, M.V. Lomonosov Moscow State University, Moscow, Russia

2 Evolutionary Genomics Laboratory, Faculty of Bioengineering and Bioinformatics, M.V. Lomonosov Moscow State University, Moscow, Russia

3 V.A. Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia

4 A.A. Kharkevich Institute for Information Transmission Problems, Russian Academy of Science, Moscow, Russia

5 Faculty of Bioengineering and Bioinformatics, M.V. Lomonosov Moscow State University, Moscow, Russia

6 N.I Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, Russia

7 State Scientific Institute of Genetics and Selection of Industrial Microorganisms, GosNIIgenetika, Moscow, Russia

8 Department of Genetics, Biological faculty, M.V. Lomonosov Moscow State University, Moscow, Russia

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BMC Genomics 2011, 12:30  doi:10.1186/1471-2164-12-30

Published: 13 January 2011

Abstract

Background

Transcriptome sequencing data has become an integral component of modern genetics, genomics and evolutionary biology. However, despite advances in the technologies of DNA sequencing, such data are lacking for many groups of living organisms, in particular, many plant taxa. We present here the results of transcriptome sequencing for two closely related plant species. These species, Fagopyrum esculentum and F. tataricum, belong to the order Caryophyllales - a large group of flowering plants with uncertain evolutionary relationships. F. esculentum (common buckwheat) is also an important food crop. Despite these practical and evolutionary considerations Fagopyrum species have not been the subject of large-scale sequencing projects.

Results

Normalized cDNA corresponding to genes expressed in flowers and inflorescences of F. esculentum and F. tataricum was sequenced using the 454 pyrosequencing technology. This resulted in 267 (for F. esculentum) and 229 (F. tataricum) thousands of reads with average length of 341-349 nucleotides. De novo assembly of the reads produced about 25 thousands of contigs for each species, with 7.5-8.2× coverage. Comparative analysis of two transcriptomes demonstrated their overall similarity but also revealed genes that are presumably differentially expressed. Among them are retrotransposon genes and genes involved in sugar biosynthesis and metabolism. Thirteen single-copy genes were used for phylogenetic analysis; the resulting trees are largely consistent with those inferred from multigenic plastid datasets. The sister relationships of the Caryophyllales and asterids now gained high support from nuclear gene sequences.

Conclusions

454 transcriptome sequencing and de novo assembly was performed for two congeneric flowering plant species, F. esculentum and F. tataricum. As a result, a large set of cDNA sequences that represent orthologs of known plant genes as well as potential new genes was generated.