Sequencing and GO annotation of transcriptome of the cell and tissue in vitro culture of Rumex acetosa

Abstract

The paper presents sequencing data, de novo assemblies and a functional annotation of transcriptome of the callus culture of Rumex acetosa L. The callus culture was maintained for twelve months in the presence of benzyladenine and naphthylacetic acid. The cDNA library was prepared using the adapter ligation method according to the standard protocol of the sequencer manufacturer. In the work, the “shotgun” technique was not used, since only the spectrum of the expression genes was required. In total it was obtained 74067 reads with a total 25,110,194 bp nucleotides. 10169 contigs were obtained in the resulting assembly with a medium length of 339 bp. Based on the sequence homology of total contigs in the category of biological processes for transcriptome callus, “cell metabolism”, “nitrogen metabolism”, “biosynthetic processes” and “metabolic processes of organic substances” dominated. In the category of molecular function, “transferase activity”, “heterocyclic compounds binding activity” and “binding the ions” dominated. In the category of the cellular component, the “macromolecular complex”, “organelles”, “cell”, “membrane” dominated. In comparison with the control transcriptome, the result obtained by us was distinguished by a reduced variety of GO subcategories. Variations in the expression of gene groups may proof epigenetic variation, which we have identified by GO annotations and transcriptome analysis. The mRNA pool is less diverse in callus lines, which, apparently, is associated with reduced specialization and dedifferentiation of cells. For the mRNA pool of R. acetosa cell culture, a high content of transcripts of retroelements, such as Copia and Gypsy, was noted. Similar results indicate a possible stress response of in vitro culture of cells and tissues of R. acetosa and high genome variability.