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

Abstract

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.

Nutritional and Proteomic Profiles in Developing Olive Inflorescence

“…The size and the shape of petals as well as of the rest whorls is genetically determined (Laitinen et al, 2007). However little data are available until now concerning flower proteomic (Dafny-Yelin et al, 2005;Moccia et al, 2009;Sun et al, 2009;Logacheva et al 2011;Zhu et al, 2011).…”

Identification of a New IgE-Binding Epitope of Peanut Oleosin That Cross-Reacts with Buckwheat

“…The results of searches for buckwheat floral transcriptome provided nucleotide sequences of 25,435 and 25,401 contigs and 56,874 and 42,913 singletons for Fagopyrum esculentum and Fagopyrum tataricum that has been published by Logacheva et al 26) Each dataset was searched with the TBLASTN algorithm and BioEdit software (http:// www.mbio.ncsu.edu/bioedit/bioedit.html), using the PAM40 matrix, no filter for low-complexity regions and an E-value threshold of 100.…”

“…Under these circumstances, it is notable that Logacheva et al 26) have recently reported a buckwheat transcriptome analyzed by de novo sequencing for two close species. Using their data, we searched for novel buckwheat proteins with sequences homologous to SDQTRTGY by TBLASTN (Table 1).…”

Physiological Roles of Rutin in the Buckwheat Plant

“…Furthermore, the relationship between 3GT expression and RT activity, and its role in controlling rutin biosynthesis should be clarified, despite the lack of reports on RT characterization. However, in flowers of common and Tartary buckwheat, cDNAs with high homology to plant rhamnosyltransferases have been identified in de-novo sequencing analyses using next-generation sequencers (Logacheva et al 2011). Our research group also obtained cDNAs from Tartary buckwheat root with high homology to RT.…”