De Novo Sequencing and Characterization of Floral Transcriptome in Two Species of Buckwheat (Fagopyrum)

Overview

Journal BMC Genomics

Publisher Biomed Central

Specialty Genetics

Date 2011 Jan 15

PMID 21232141

Citations 79

Authors

Maria D Logacheva

Artem S Kasianov

Dmitriy V Vinogradov

Tagir H Samigullin

Mikhail S Gelfand

Vsevolod J Makeev

Aleksey A Penin

Affiliations

Soon will be listed here.

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.

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References

Jaillon O, Aury J, Noel B, Policriti A, Clepet C, Casagrande A . The grapevine genome sequence suggests ancestral hexaploidization in major angiosperm phyla. Nature. 2007; 449(7161):463-7. DOI: 10.1038/nature06148. View

Keane T, Creevey C, Pentony M, Naughton T, Mclnerney J . Assessment of methods for amino acid matrix selection and their use on empirical data shows that ad hoc assumptions for choice of matrix are not justified. BMC Evol Biol. 2006; 6:29. PMC: 1435933. DOI: 10.1186/1471-2148-6-29. View

Ashburner M, Ball C, Blake J, Botstein D, Butler H, Cherry J . Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet. 2000; 25(1):25-9. PMC: 3037419. DOI: 10.1038/75556. View

Sharbel T, Voigt M, Corral J, Galla G, Kumlehn J, Klukas C . Apomictic and sexual ovules of Boechera display heterochronic global gene expression patterns. Plant Cell. 2010; 22(3):655-71. PMC: 2861462. DOI: 10.1105/tpc.109.072223. View

Logacheva M, Samigullin T, Dhingra A, Penin A . Comparative chloroplast genomics and phylogenetics of Fagopyrum esculentum ssp. ancestrale -a wild ancestor of cultivated buckwheat. BMC Plant Biol. 2008; 8:59. PMC: 2430205. DOI: 10.1186/1471-2229-8-59. View

Bailey C, Carr T, Harris S, Hughes C . Characterization of angiosperm nrDNA polymorphism, paralogy, and pseudogenes. Mol Phylogenet Evol. 2003; 29(3):435-55. DOI: 10.1016/j.ympev.2003.08.021. View

Roeding F, Borner J, Kube M, Klages S, Reinhardt R, Burmester T . A 454 sequencing approach for large scale phylogenomic analysis of the common emperor scorpion (Pandinus imperator). Mol Phylogenet Evol. 2009; 53(3):826-34. DOI: 10.1016/j.ympev.2009.08.014. View

Duarte J, Wall P, Edger P, Landherr L, Ma H, Pires J . Identification of shared single copy nuclear genes in Arabidopsis, Populus, Vitis and Oryza and their phylogenetic utility across various taxonomic levels. BMC Evol Biol. 2010; 10:61. PMC: 2848037. DOI: 10.1186/1471-2148-10-61. View

Edgar R . MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 2004; 32(5):1792-7. PMC: 390337. DOI: 10.1093/nar/gkh340. View

10.

Nishimoto Y, Ohnishi O, Hasegawa M . Topological incongruence between nuclear and chloroplast DNA trees suggesting hybridization in the urophyllum group of the genus Fagopyrum (Polygonaceae). Genes Genet Syst. 2003; 78(2):139-53. DOI: 10.1266/ggs.78.139. View

11.

Graham I, Besser K, Blumer S, Branigan C, Czechowski T, Elias L . The genetic map of Artemisia annua L. identifies loci affecting yield of the antimalarial drug artemisinin. Science. 2010; 327(5963):328-31. DOI: 10.1126/science.1182612. View

12.

Shagin D, Rebrikov D, Kozhemyako V, Altshuler I, Shcheglov A, Zhulidov P . A novel method for SNP detection using a new duplex-specific nuclease from crab hepatopancreas. Genome Res. 2002; 12(12):1935-42. PMC: 187582. DOI: 10.1101/gr.547002. View

13.

Lohne C, Borsch T . Molecular evolution and phylogenetic utility of the petD group II intron: a case study in basal angiosperms. Mol Biol Evol. 2004; 22(2):317-32. DOI: 10.1093/molbev/msi019. View

14.

Alagna F, DAgostino N, Torchia L, Servili M, Rao R, Pietrella M . Comparative 454 pyrosequencing of transcripts from two olive genotypes during fruit development. BMC Genomics. 2009; 10:399. PMC: 2748093. DOI: 10.1186/1471-2164-10-399. View

15.

Fesenko A, Fesenko I, Logacheva M, Penin A . [The role of gene tepal-like bract (TLB) in the separation between the bracts and perianth in Fagopyrum esculentum moench]. Genetika. 2006; 41(12):1644-9. View

16.

Yasui Y, Ohnishi O . Phylogenetic relationships among Fagopyrum species revealed by the nucleotide sequences of the ITS region of the nuclear rRNA gene. Genes Genet Syst. 1999; 73(4):201-10. DOI: 10.1266/ggs.73.201. View

17.

Min X, Butler G, Storms R, Tsang A . OrfPredictor: predicting protein-coding regions in EST-derived sequences. Nucleic Acids Res. 2005; 33(Web Server issue):W677-80. PMC: 1160155. DOI: 10.1093/nar/gki394. View

18.

Feng H, Taylor J, Benos P, Newton R, Waddell K, Lucas S . Human transcriptome subtraction by using short sequence tags to search for tumor viruses in conjunctival carcinoma. J Virol. 2007; 81(20):11332-40. PMC: 2045575. DOI: 10.1128/JVI.00875-07. View

19.

Sun C, Li Y, Wu Q, Luo H, Sun Y, Song J . De novo sequencing and analysis of the American ginseng root transcriptome using a GS FLX Titanium platform to discover putative genes involved in ginsenoside biosynthesis. BMC Genomics. 2010; 11:262. PMC: 2873478. DOI: 10.1186/1471-2164-11-262. View

20.

Zeng S, Xiao G, Guo J, Fei Z, Xu Y, Roe B . Development of a EST dataset and characterization of EST-SSRs in a traditional Chinese medicinal plant, Epimedium sagittatum (Sieb. Et Zucc.) Maxim. BMC Genomics. 2010; 11:94. PMC: 2829513. DOI: 10.1186/1471-2164-11-94. View