Analysis of correlation structures in the Synechocystis PCC6803 genome

TL;DR

This paper investigates the correlation structures in the Synechocystis PCC6803 genome using recurrence plots and phase space reconstruction, revealing intrinsic dynamics and links to mobile genetic elements.

Contribution

It introduces a novel analysis of genome correlation structures, connecting them to mobile elements and intrinsic nucleotide transfer dynamics.

Findings

Periodic and non-periodic correlation structures identified

Mobile elements are associated with non-periodic correlation regions

Intrinsic transfer dynamics partly revealed by phase space analysis

Abstract

Transfer of nucleotide strings in the Synechocystis sp. PCC6803 genome is investigated to exhibit periodic and non-periodic correlation structures by using the recurrence plot method and the phase space reconstruction technique. The periodic correlation structures are generated by periodic transfer of several substrings in long periodic or non-periodic nucleotide strings embedded in the coding regions of genes. The non-periodic correlation structures are generated by non-periodic transfer of several substrings covering or overlapping with the coding regions of genes. In the periodic and non-periodic transfer, some gaps divide the long nucleotide strings into the substrings and prevent their global transfer. Most of the gaps are either the replacement of one base or the insertion/reduction of one base. In the reconstructed phase space, the points generated from two or three steps for the continuous iterative transfer via the second maximal distance can be fitted by two lines. It partly reveals an intrinsic dynamics in the transfer of nucleotide strings. Due to the comparison of the relative positions and lengths, the substrings concerned with the non-periodic correlation structures are almost identical to the mobile elements annotated in the genome. The mobile elements are thus endowed with the basic results on the correlation structures.