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

BMC Genomics

Research Article

Dmitriy V Vinogradov¹  Mikhail S Gelfand²  Tagir H Samigullin³  Maria D Logacheva⁴  Aleksey A Penin⁵  Artem S Kasianov⁶  Vsevolod J Makeev⁷ 

[1] A.A. Kharkevich Institute for Information Transmission Problems, Russian Academy of Science, Moscow, Russia;A.A. Kharkevich Institute for Information Transmission Problems, Russian Academy of Science, Moscow, Russia;Faculty of Bioengineering and Bioinformatics, M.V. Lomonosov Moscow State University, Moscow, Russia;Department of Evolutionary Biochemistry, A.N. Belozersky Institute of Physico-Chemical Biology, M.V. Lomonosov Moscow State University, Moscow, Russia;Department of Evolutionary Biochemistry, A.N. Belozersky Institute of Physico-Chemical Biology, M.V. Lomonosov Moscow State University, Moscow, Russia;Evolutionary Genomics Laboratory, Faculty of Bioengineering and Bioinformatics, M.V. Lomonosov Moscow State University, Moscow, Russia;A.A. Kharkevich Institute for Information Transmission Problems, Russian Academy of Science, Moscow, Russia;Evolutionary Genomics Laboratory, Faculty of Bioengineering and Bioinformatics, M.V. Lomonosov Moscow State University, Moscow, Russia;A.A. Kharkevich Institute for Information Transmission Problems, Russian Academy of Science, Moscow, Russia;Department of Genetics, Biological faculty, M.V. Lomonosov Moscow State University, Moscow, Russia;V.A. Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia;V.A. Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia;N.I Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, Russia;State Scientific Institute of Genetics and Selection of Industrial Microorganisms, GosNIIgenetika, Moscow, Russia;

关键词: Transcriptome Assembly;    Sister Relationship;    Artemisia Annua;    Basal Angiosperm;    Common Buckwheat;   

DOI  :  10.1186/1471-2164-12-30

 received in 2010-10-18, accepted in 2011-01-13,  发布年份 2011

来源: Springer

【 摘 要 】

BackgroundTranscriptome 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.ResultsNormalized 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.Conclusions454 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.

【 授权许可】

CC BY   
© Logacheva et al; licensee BioMed Central Ltd. 2011