Contribution of Mobile Group II Introns to Sinorhizobium meliloti Genome Evolution

Toro, Nicolás; Martı́nez-Abarca, Francisco; Molina-Sánchez, María Dolores; García-Rodríguez, Fernando M.; Nisa-Martínez, Rafael

doi:10.3389/fmicb.2018.00627

Cited by 14 publications

(8 citation statements)

References 74 publications

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“…Concerning the results of ncRNA families in plasmids, we observed a large number of Group II introns on the plasmids of all three species, especially in B. thuringiensis. This class of ncRNAs consists of elements characterized as ribozymes that act as mobile genetic elements (Harris and Breaker 2018;Toro et al 2018;Fayad et al 2019). Therefore, the abundance of these elements in B. cereus group strains reinforces the role of horizontal genetic transfer (HGT) in genome plasticity, evolution, and the acquisition of novel ncRNAs, as already observed for Streptococcus agalactiae (Wolf et al 2018).…”

Section: Discussionmentioning

confidence: 66%

Genomic Insights into the Diversity of Non-Coding RNAs in Bacillus Cereus Sensu Lato.

Gonçalves

Appel

Boas

et al. 2021

Preprint

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Bacillus cereus sensu lato is a group of bacteria of medical and agricultural importance in different ecological niches and with controversial taxonomic relationships. Studying the composition of non-coding RNAs (ncRNAs) in several bacterial groups has been an important tool for identifying genetic information. However, to date, no comparative genomics study of ncRNA has been performed in this group. Thus, this study aimed to identify and characterize the set of ncRNAs from 132 strains of Bacillus cereus, Bacillus thuringiensis and Bacillus anthracis to obtain an overview of the diversity and distribution of these genetic elements in these species. We observed that the number of ncRNAs differs in the chromosomes of the three species, but not in the plasmids, when species or phylogenetic clusters were compared. The prevailing functional/structural category was Cis-reg and the most frequent class was Riboswitch. However, in plasmids, the class Group II intron was the most frequent. Also, nine ncRNAs were selected for validation in the strain B. thuringiensis 407 by RT-PCR, which allowed to identify the expression of the ncRNAs. The wide distribution and diversity of ncRNAs in the B. cereus group, and more intensely in B. thuringiensis, may help improve the abilities of these species to adapt to various environmental changes.

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Section: Discussionmentioning

confidence: 66%

Genomic Insights into the Diversity of Non-Coding RNAs in Bacillus Cereus Sensu Lato.

Gonçalves

Appel

Boas

et al. 2021

Preprint

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“…Another source of false positives was related to mobile group II introns. Mobile group II introns are ribozymes and retroelements present in most E. meliloti strains and which natural target site lies within ISs (IS Rm2011-2 in the case of RmInt1 and on the left and right IRs of IS Rm17 in the case of RmInt2; Toro et al 2018 ). To avoid the errors in the detection generated by group II introns, comparisons between E. meliloti 1021 and GR4 strains were run using the -S (Shift) option with values in the range of 100 to 5000.…”

Section: Resultsmentioning

confidence: 99%

Easy identification of insertion sequence mobilization events in related bacterial strains with ISCompare

Mogro

Ambrosis

Lozano

2021

G3 Genes|Genomes|Genetics

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Bacterial genomes are composed of core and accessory genomes. The first is composed of housekeeping and essential genes, while the second is highly enriched in mobile genetic elements, including transposable elements (TEs). Insertion sequences (ISs), the smallest TEs, have an important role in genome evolution, and contribute to bacterial genome plasticity and adaptability. ISs can spread in a genome, presenting different locations in nearly related strains, and producing phenotypic variations. Few tools are available which can identify differentially located ISs (DLISs) on assembled genomes. Here, we introduce ISCompare, a new program to profile IS mobilization events in related bacterial strains using complete or draft genome assemblies. ISCompare was validated using artificial genomes with simulated random IS insertions and real sequences, achieving the same or better results than other available tools, with the advantage that ISCompare can analyze multiple ISs at the same time and outputs a list of candidate DLISs. ISCompare provides an easy and straightforward approach to look for differentially located ISs on bacterial genomes.

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“…Another source of false positives was related to mobile group II introns. Mobile group II introns are ribozymes and retroelements present in most E. meliloti strains and which natural target site lies within insertion sequences (ISRm2011-2 in the case of RmInt1 and on the left and right inverted repeats of ISRm17 in the case of RmInt2; Toro et al, 2018). To avoid the errors in the detection generated by group II introns, comparisons between E. meliloti 1021 and GR4 were run using the -S (Shift) option using values from 100 to 5000.…”

Section: Comparison Of E Meliloti 1021 and Pseudomonas Aeruginosa Pamentioning

confidence: 99%

Easy identification of insertion sequence mobilization events in related bacterial strains with ISCompare

Mogro

Ambrosis

Lozano

2020

Preprint

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Motivation: Bacterial genomes are composed by a core and an accessory genome. The first composed of housekeeping and essential genes, while the second is composed, in its majority, of mobile genetic elements, including transposable elements (TEs). Insertion sequences (ISs), the smallest TEs, have an important role in genome evolution, and contribute to bacterial genome plasticity and adaptability. ISs can spread in a genome, presenting different locations in nearly related strains, and producing phenotypic variations. Few tools are available which can identify differentially located ISs (DLIS) on assembled genomes. Results: We developed ISCompare to profile IS mobilization events in related bacterial strains using complete or draft genome assemblies. ISCompare was validated using artificial genomes with simulated random IS insertions and real sequences, achieving the same or better results than other available tools, with the advantage that ISCompare can analyse multiple ISs at the same time and outputs a list of candidate DLIS. We think that ISCompare provides an easy and straightforward approach to look for differentially located ISs on bacterial genomes. Availability and implementation: ISCompare was implemented in python3 and its source code is freely available for download at https://github.com/maurijlozano/ISCompare. Supplementary information: Supplementary data are available at Bioinformatics online.

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Contribution of Mobile Group II Introns to Sinorhizobium meliloti Genome Evolution

Cited by 14 publications

References 74 publications

Genomic Insights into the Diversity of Non-Coding RNAs in Bacillus Cereus Sensu Lato.

Genomic Insights into the Diversity of Non-Coding RNAs in Bacillus Cereus Sensu Lato.

Easy identification of insertion sequence mobilization events in related bacterial strains with ISCompare

Easy identification of insertion sequence mobilization events in related bacterial strains with ISCompare

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