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.
Highlights
Transcriptome sequencing data has become an integral component of modern genetics, genomics and evolutionary biology
The raw data were deposited in the NCBI Sequence Read Archive (SRA) under the accession number SRA023408
25435 and 25401 contigs were obtained for F. esculentum and F. tataricum, respectively, while 56874 and 42913 reads were retained as singletons
Summary
Transcriptome sequencing data has become an integral component of modern genetics, genomics and evolutionary biology. 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 an important food crop Despite these practical and evolutionary considerations Fagopyrum species have not been the subject of large-scale sequencing projects. Many important taxonomic groups of living organisms remain underrepresented This is especially pressing problem for plants since few of them have been a priority for large-scale sequencing projects. Two more distant relatives of the cultivated buckwheat are F. homotropicum and F. tataricum [3] Both of them have an important favorable trait absent in the common buckwheat, the ability to self-pollination (self-compatibility). They have a potential for use in breeding for the development of self-compatible cultivars
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