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Amazing symmetrical clustering in chloroplast genomes

Authors
  • Sadovsky, Michael G.1, 2, 3
  • Senashova, Maria Yu1
  • Malyshev, Andrew V.1
  • 1 Institute of computational modelling SB RAS, Akademgorodok, Krasnoyarsk, 660036, Russia , Krasnoyarsk (Russia)
  • 2 Siberian federal university, Svobodny prosp. 79, Krasnoyarsk, 660041, Russia , Krasnoyarsk (Russia)
  • 3 V.F.Voino-Yasenetsky Krasnoyarsk State Medical University, P. Zheleznjaka str. 1, Krasnoyarsk, 660022, Russia , Krasnoyarsk (Russia)
Type
Published Article
Journal
BMC Bioinformatics
Publisher
Springer (Biomed Central Ltd.)
Publication Date
Mar 11, 2020
Volume
21
Issue
Suppl 2
Identifiers
DOI: 10.1186/s12859-020-3350-z
Source
Springer Nature
Keywords
License
Green

Abstract

BackgroundPreviously, a seven-cluster pattern claiming to be a universal one in bacterial genomes has been reported. Keeping in mind the most popular theory of chloroplast origin, we checked whether a similar pattern is observed in chloroplast genomes.ResultsSurprisingly, eight cluster structure has been found, for chloroplasts. The pattern observed for chloroplasts differs rather significantly, from bacterial one, and from that latter observed for cyanobacteria. The structure is provided by clustering of the fragments of equal length isolated within a genome so that each fragment is converted in triplet frequency dictionary with non-overlapping triplets with no gaps in frame tiling. The points in 63-dimensional space were clustered due to elastic map technique. The eight cluster found in chloroplasts comprises the fragments of a genome bearing tRNA genes and exhibiting excessively high GC-content, in comparison to the entire genome.ConclusionChloroplasts exhibit very specific symmetry type in distribution of coding and non-coding fragments of a genome in the space of triplet frequencies: this is mirror symmetry. Cyanobacteria may have both mirror symmetry, and the rotational symmetry typical for other bacteria.

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