Journal of King Saud University: Computer and Information Sciences (Nov 2022)
Impact of Insertion Sequences and RNAs on Genomic Inversions in Pseudomonas aeruginosa
Abstract
In this article, a bioinformatics pipeline is proposed that focuses on two types of elements, namely the mobile genetic elements (MGE) and Ribonucleic acids (RNAs). The MGEs are called insertion sequences (ISs) in the prokaryotic domain. The objective of this research work is to study the behaviour of RNAs and MGEs genes, and the effects of their presence around inversions in genome sequences. The proposed pipeline finds the relation between the transposase gene types (e.g., DDE and DEDD) located within insertion sequences according to their IS family and sub-family, and RNAs (tRNA and rRNA) on the one hand, and genomic inversion on the other hand. More precisely, we wonder whether the insertion sequences and RNAs have any effects on the occurrence of inversions. To investigate this, we start by extracting all inversions between every two close isolates of P. aeruginosa from a high supported phylogenetic tree, and we investigate inversion boundaries, to determine the impact of IS elements and RNAs around these inversions. For RNAs genes, we noticed that a high occurrence of these elements are found in what we called InBoundary, while few to zero occurrences have been recorded in OutBoundary. We remark that the NCGM2.S1 genome has the largest amount of tRNAs and inversions comparing to other genomes. For RNA genes, the tRNAs genes (Arg, Ala, Leu) recorded the highest occurrences around the inversions, while there was few occurrences of rRNA genes, within all genomes. For IS elements, we noticed that the family of IS3 has the highest impact on inversions, but sometimes other type of IS elements can also be found with IS3 around the inversions. In this case, these types of ISs shared the same type of transposase gene (DDE). We finally conclude that the distribution of RNA and IS genes has a big impact on the inversions in bacterial genomes.
