Symmetry of Siberian Larch Transcriptome

Abstract

The paper presents a novel approach to infer a structuredness in a set of symbol sequences such as transcriptome nucleotide sequences. A distribution pattern of triplet frequencies in the Siberian larch (Larix sibirica Ledeb.) transcriptome sequences was investigated in the presented study. It was found that the larch transcriptome demonstrates a number of unexpected symmetries in the statistical and combinatorial properties.Keywords: nucleotide sequence complexity, frequency dictionary, order, Larix sibirica, Siberian larch, symmetry, transcriptome, triplet. DOI: 10.17516/1997-1389-2015 . For our further analysis we also assumed that neither other symbols, nor blan spaces are supposed to be found in a sequence; a sequence under consideration is also suppose to be coherent (i. e. consisting of a single piece).. For our further analysis we also assumed that neither other symbols, nor blank spaces are supposed to be found in a sequence; a sequence under consideration is also supposed to be coherent (i. e. consisting of a single piece).We studied an order and structuredness over a set of sequences from finite alphabet Key idea in our search for a structure and order in a set of symbol sequences (transcriptome nucleotide sequences) is to translate sequences into their frequency dictionary (Bugaenko et al., 1996(Bugaenko et al., , 1997(Bugaenko et al., , 1998Hu and Wang, 2001). There could be a number of various definitions of a frequency dictionary, but we will use the basic one that is a list of all the strings of a given length accompanied with a frequency of each string (a detailed description is given below). It is crucial that the transformation of a symbol sequence into a frequency dictionary allows us to map a set of sequences into a metric space. The latter provided us with powerful and extended tools for analysis.We will briefly outline the concept of our study and then demonstrate the main results obtained. First, we changed each symbol sequence (that is a nucleotide sequence in the Siberian larch transcriptome set) into a frequency dictionary. Then, we studied distribution of those dictionaries in a multidimensional space trying to infer any regularities and clusters.Second, for each clustering we checked for stability of clustering. This clustering was carried out using the K-means technique.Third, we compared the statistical properties of the clusters identified by K-means and found that these clusters demonstrated a very strong symmetry in terms of the statistical properties.In brief, the clusters showed extremely low level of discrepancy in the Chargaff's second parity rule. This low discrepancy is the most intriguing fact concerning the properties of the studied transcriptome sequence set. Materials and Methods Transcriptome nucleotide sequence dataThe transcriptome Surely, this part of the transcriptome requires special studies. Frequency DictionaryPreviously (Bugaenko et al., 1996(Bugaenko et al., , 1997(Bugaenko et al., , 1998Hu and Wang, 2001), a frequency dictionary was proposed to be a fun...

Eight-cluster structure of chloroplast genomes differs from similar one observed for bacteria

“…These facts may reveal the "independent" evolution of chloro- plast genomes (see also [34,39]), on the contrary to the synchronized evolution of these latter with the host nuclear genome [19]. Also, such symmetry may answer the question towards the attribution of contigs for de novo assembling genomes [30][31][32] (see also another sight on the problem in [36]).…”

“…It is extremely doubtful that junk has no matter in a genome, neither it plays no role in various and complicated biological processes involved into an inherited information processing and functioning. For some cases (see [30][31][32], the removal of junk enforces the clustering of coding regions and makes easier the comprehension of the peculiarities standing behind. Yet, special efforts must be addressed to reveal the role and impact of junk regions of a genome on the processes mentioned above.…”

Some preliminary results on relation between triplet composition and tissue source in larch total transcriptome

“…Similar approach has been used when studied the larch transcriptome [22,23], and the figures effectively identified bacterial contamination, and strand allocation of the contigs comprising various classes. Here we explore similar approach, and determined the discrepancy ξ for those four clusters shown in Figs.…”