Transposable elements and small RNAs: Genomic fuel for species diversity

Hoffmann, Federico G.; McGuire, L.; Counterman, Brian A.; Ray, David A.

doi:10.1080/2159256x.2015.1066919

Cited by 7 publications

(7 citation statements)

References 65 publications

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“…Whereas most Bifidobacterium strains and Lactobacillus strains of the VSL#3 product were predicted to have a relative low number of transposons, Streptococcus thermophilus strain BT01 and Lactobacillus helveticus strain BD08, in contrast, were estimated to harbor the most, respectively 27 and 24 IS transposons ( S1 Fig ). IS elements are known to be involved in chromosomal deletions and/or rearrangements, thus playing a role in ecological adaptation and species diversification [ 22 , 63 – 65 ]. Prophage-associated genes were also observed in some of the strains, including Lactobacillus paracasei BP07, Lactobacillus helveticus BBP06 and Bifidobacterium breve BB02.…”

Section: Resultsmentioning

confidence: 99%

Comparative genomic analysis of the multispecies probiotic-marketed product VSL#3

et al. 2018

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Several probiotic-marketed formulations available for the consumers contain live lactic acid bacteria and/or bifidobacteria. The multispecies product commercialized as VSL#3 has been used for treating various gastro-intestinal disorders. However, like many other products, the bacterial strains present in VSL#3 have only been characterized to a limited extent and their efficacy as well as their predicted mode of action remain unclear, preventing further applications or comparative studies. In this work, the genomes of all eight bacterial strains present in VSL#3 were sequenced and characterized, to advance insights into the possible mode of action of this product and also to serve as a basis for future work and trials. Phylogenetic and genomic data analysis allowed us to identify the 7 species present in the VSL#3 product as specified by the manufacturer. The 8 strains present belong to the species Streptococcus thermophilus, Lactobacillus acidophilus, Lactobacillus paracasei, Lactobacillus plantarum, Lactobacillus helveticus, Bifidobacterium breve and B. animalis subsp. lactis (two distinct strains). Comparative genomics revealed that the draft genomes of the S. thermophilus and L. helveticus strains were predicted to encode most of the defence systems such as restriction modification and CRISPR-Cas systems. Genes associated with a variety of potential probiotic functions were also identified. Thus, in the three Bifidobacterium spp., gene clusters were predicted to encode tight adherence pili, known to promote bacteria-host interaction and intestinal barrier integrity, and to impact host cell development. Various repertoires of putative signalling proteins were predicted to be encoded by the genomes of the Lactobacillus spp., i.e. surface layer proteins, LPXTG-containing proteins, or sortase-dependent pili that may interact with the intestinal mucosa and dendritic cells. Taken altogether, the individual genomic characterization of the strains present in the VSL#3 product confirmed the product specifications, determined its coding capacity as well as identified potential probiotic functions.

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Section: Resultsmentioning

confidence: 99%

Comparative genomic analysis of the multispecies probiotic-marketed product VSL#3

et al. 2018

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“…Because large expansions of TEs, and associated genomic changes, may promote evolutionary diversification ( Jurka et al. 2007 ; Belyayev 2014 ; Hoffmann et al. 2015 ) we looked for bursts of speciation that may coincide with major TE expansions in Piciformes.…”

Section: Resultsmentioning

confidence: 99%

“…Whereas TE insertions may occasionally impact some aspect of an organism’s phenotype, periods of intense TE amplification can potentially instigate profound genomic changes and may promote evolutionary diversification ( Jurka et al. 2007 ; Belyayev 2014 ; Hoffmann et al. 2015 ).…”

Section: Introductionmentioning

confidence: 99%

Multiple and Independent Phases of Transposable Element Amplification in the Genomes of Piciformes (Woodpeckers and Allies)

Manthey

Moyle

Boissinot

2018

Genome Biology and Evolution

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The small and conserved genomes of birds are likely a result of flight-related metabolic constraints. Recombination-driven deletions and minimal transposable element (TE) expansions have led to continually shrinking genomes during evolution of many lineages of volant birds. Despite constraints of genome size in birds, we identified multiple waves of amplification of TEs in Piciformes (woodpeckers, honeyguides, toucans, and barbets). Relative to other bird species’ genomic TE abundance (< 10% of genome), we found ∼17–30% TE content in multiple clades within Piciformes. Several families of the retrotransposon superfamily chicken repeat 1 (CR1) expanded in at least three different waves of activity. The most recent CR1 expansions (∼4–7% of genome) preceded bursts of diversification in the woodpecker clade and in the American barbets + toucans clade. Additionally, we identified several thousand polymorphic CR1 insertions (hundreds per individual) in three closely related woodpecker species. Woodpecker CR1 insertion polymorphisms are maintained at lower frequencies than single nucleotide polymorphisms indicating that purifying selection is acting against additional CR1 copies and that these elements impose a fitness cost on their host. These findings provide evidence of large scale and ongoing TE activity in avian genomes despite continual constraint on genome size.

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“…In Vesper bats, for example, over 61% of taxon-specific microRNAs can be traced back to mobile elements, largely from bat-specific DNA transposons [ 549 ]. Mobile DNA-derived microRNAs arise from lineage-specific transposition events [ 550 , 551 ] that can occur in bursts of genome innovation [ 552 ]. From a functional point of view, it should be easy to appreciate that the presence of dispersed mobile DNA sequences in other classes of cellular transcripts, such as mRNAs, provides targets for recognition by complementary microRNAs that are derived from the same mobile element [ 553 ].…”

Section: Genome Writing By Natural Genetic Engineering: Mobile Andmentioning

confidence: 99%

Living Organisms Author Their Read-Write Genomes in Evolution

Shapiro

2017

Biology

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Evolutionary variations generating phenotypic adaptations and novel taxa resulted from complex cellular activities altering genome content and expression: (i) Symbiogenetic cell mergers producing the mitochondrion-bearing ancestor of eukaryotes and chloroplast-bearing ancestors of photosynthetic eukaryotes; (ii) interspecific hybridizations and genome doublings generating new species and adaptive radiations of higher plants and animals; and, (iii) interspecific horizontal DNA transfer encoding virtually all of the cellular functions between organisms and their viruses in all domains of life. Consequently, assuming that evolutionary processes occur in isolated genomes of individual species has become an unrealistic abstraction. Adaptive variations also involved natural genetic engineering of mobile DNA elements to rewire regulatory networks. In the most highly evolved organisms, biological complexity scales with “non-coding” DNA content more closely than with protein-coding capacity. Coincidentally, we have learned how so-called “non-coding” RNAs that are rich in repetitive mobile DNA sequences are key regulators of complex phenotypes. Both biotic and abiotic ecological challenges serve as triggers for episodes of elevated genome change. The intersections of cell activities, biosphere interactions, horizontal DNA transfers, and non-random Read-Write genome modifications by natural genetic engineering provide a rich molecular and biological foundation for understanding how ecological disruptions can stimulate productive, often abrupt, evolutionary transformations.

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Transposable elements and small RNAs: Genomic fuel for species diversity

Cited by 7 publications

References 65 publications

Comparative genomic analysis of the multispecies probiotic-marketed product VSL#3

Comparative genomic analysis of the multispecies probiotic-marketed product VSL#3

Multiple and Independent Phases of Transposable Element Amplification in the Genomes of Piciformes (Woodpeckers and Allies)

Living Organisms Author Their Read-Write Genomes in Evolution

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