POSSIBILITIES OF DE NOVO TRANSCRIPTOME SEQUENCING IN PYLOGENETIC RESEARCH ON AN EXAMPLE OF TARAXACUM OFFICINALE (ASTERACEAE)

M. G. Kutsev, M. V. Skaptsov, S. V. Smirnov, T. A. Sinitsyna, A. A. Kechaykin, M. S. Ivanova, A. I. Shmakov

Abstract


 

As a result of the research we obtained a cDNA library, sequences and carried out de novo assembly and functional annotation of the transcriptome of systematically complex, almost cosmopolitan Taraxacum officinale. Systematics of the species is complicated because of separation of many microspecies and intraspecific taxa, which may be explained by the presence of ploidy races, the phenomenon of apomixis and significant polymorphism. Attempts of separation of microspecies and closely related species based on sequencing of chloroplast and nuclear DNA fragments, did not give acceptable results. We have made the first attempt to analyze the transcriptome for understanding the genome evolution of agamospermous-sexual complex of the species. A total of 84440 reads were obtained with a total 31,540,710 bp. As a result of the de novo assembly, we obtained 13902 contigs, with an average GC content equal to 38.1% and a maximum length of 5255 bp. In total, we received 3798 annotated genes. According to the functional annotation based on sequence homology, 2687 contigs were attributed to biological processes (19.32%), 3299 – to molecular functions (23.7%), 2157 – to the cellular component (15.51%) and 7497 contigs – with unknown functions. In the first category “single-organism cellular process”, “response to stimulus”, “photosynthesis-light reaction”, “oxidation-reduction” and “translation” have dominated. In the category of molecular function “nucleic acid binding”, “hydrolase activity”, “transferase” and “oxidoreductase” activities have dominated. In the cellular component category “integral component of membrane”, “chloroplast thylakoid membrane”, “photosystems” and “nucleus” have dominated.


Keywords


T. officinale; transcriptome; RNA; cDNA; pyrosequencing.

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DOI: http://dx.doi.org/10.15421/2016101

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