Deep sequencing of small RNAs confirms an annelid affinity of Myzostomida

Helm, Conrad; Bernhart, Stephan H.; Siederdissen, Christian Höner zu; Nickel, Birgit; Bleidorn, Christoph

doi:10.1016/j.ympev.2012.03.017

Cited by 29 publications

(26 citation statements)

References 63 publications

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“…Literature search revealed seven publications reporting annelid miRNA identification and or expression (Tessmar-Raible et al, 2007;Sperling et al, 2009;Christodoulou et al, 2010;Gong et al, 2010;Helm et al, 2012;Huang et al, 2012;Kenny et al, 2015). As shown above, annelid miRNAs have an average length 22 nucleotides like other animal miRNAs.…”

Section: Other Factorsmentioning

confidence: 99%

Literature review of baseline information to support the risk assessment of RNAi‐based GM plants

Pačes

Nič²,

Novotný³

et al. 2017

EFSA Supporting Publications

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This report is the outcome of an EFSA procurement aiming at investigating and summarising the state of knowledge on (I) the mode-of-action of dsRNA and miRNA pathways, (II) the potential for nontarget gene regulation by dsRNA-derived siRNAs or miRNAs, (III) the determination of siRNA pools in plant tissues and the importance of individual siRNAs for silencing. The report is based on a comprehensive and systematic literature search, starting with the identification and retrieval of~190,000 publications related to the research area and further filtered down with keywords to produce focused collections used for subsequent screening of titles and abstracts. The report is comprised of an (I) Introduction to the field of small RNAs, (II) a Data and Methodologies section containing strategies used for literature search and study selection, and (III) the Results of the literature review organized according to the three main procurement tasks. The outcome of the first task reviews dsRNA and miRNA pathways in mammals (including humans), birds, fish, arthropods, annelids, molluscs, nematodes, and plants. Eight taxon-dedicated chapters are based on~1,400 cumulative references chosen from~10,000 inspected titles and abstracts. We review conserved and divergent aspects of small RNA pathways and dsRNA responses in animals and plants including structure and function of key proteins as well as four basic mechanisms: genome-encoded posttranscriptional regulations (miRNA), degradation of RNAs by short interfering RNA pools generated from long dsRNA (RNAi), transcriptional silencing, and sequence-independent responses to dsRNA. The outcome of the second task focuses on base pairing between small RNAs and their target RNAs and predictability of biological effects of small RNAs in animals and plants. The outcome of the last task reviews methodology, siRNA pools, and movement of small RNAs in plants. Potential transfer of small RNAs between species and circulating miRNAs in mammals is described in the final chapter.

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Section: Other Factorsmentioning

confidence: 99%

Literature review of baseline information to support the risk assessment of RNAi‐based GM plants

Pačes

Nič²,

Novotný³

et al. 2017

EFSA Supporting Publications

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“…At the time of our analysis, these included five formal phylogenetic analyses of miRNA data focused on identifying the phylogenetic position of turtles within amniotes (19), acoelomorph flatworms within animals (20), lampreys within vertebrates [hagfish and jawed vertebrates (18)], myzostomidan worms within bilaterians (21), and on establishing the monophyly of-and resolving relationships within-annelids (22). [Several additional studies discuss the phylogenetic implications of miRNA data, but do not subject these data to a formal phylogenetic analysis.…”

Section: Significancementioning

confidence: 99%

“…The miRNA study by Sperling et al (22) used "standard" (Wagner) parsimony-in which gains and losses of miRNA families incur equal cost (28)-and the remaining four studies (18)(19)(20)(21) used Dollo parsimony (29). Dollo parsimony allows for the unique evolution of a character and its subsequent loss (both with equal cost), but precludes reevolution of the same character (with effectively infinite cost) once it has been lost.…”

Section: Significancementioning

confidence: 99%

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A critical appraisal of the use of microRNA data in phylogenetics

Thomson

Plachetzki

Mahler

et al. 2014

Proc. Natl. Acad. Sci. U.S.A.

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Recent progress in resolving the tree of life continues to expose relationships that resist resolution, which drives the search for novel sources of information to solve these difficult phylogenetic problems. A recent example, the presence and absence of micro-RNA families, has been vigorously promoted as an ideal source of phylogenetic data and has been applied to several perennial phylogenetic problems. The utility of such data for phylogenetic inference hinges critically both on developing stochastic models that provide a reasonable description of the process that give rise to these data, and also on the careful validation of those models in real inference scenarios. Remarkably, however, the statistical behavior and phylogenetic utility of microRNA data have not yet been rigorously characterized. Here we explore the behavior and performance of microRNA presence/absence data under a variety of evolutionary models and reexamine datasets from several previous studies. We find that highly heterogeneous rates of microRNA gain and loss, pervasive secondary loss, and sampling error collectively render microRNA-based inference of phylogeny difficult. Moreover, our reanalyses fundamentally alter the conclusions for four of the five studies that we reexamined. Our results indicate that the capacity of miRNA data to resolve the tree of life has been overstated, and we urge caution in their application and interpretation.homoplasy | Bayes factor | stochastic Dollo

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“…miRNA sequences, which have been successfully applied to many metazoan phylogenetic studies Heimberg et al, 2010;Sperling et al, 2010;Campbell et al, 2011;Philippe et al, 2011;Rota-Stabelli et al, 2011;Sperling et al, 2011;Wiegmann et al, 2011;Helm et al, 2012;Lyson et al, 2012;Pisani et al, 2012;Fromm et al, 2013;Peterson et al, 2013;Tarver et al, 2013), have five properties making them among the most reliable phylogenetic markers: (i) identification of novel miRNAs does not necessarily require fully sequenced genome sequence, (ii) new lineage-specific miRNA families are continually added to metazoan genomes through time which makes them ideal as phylogenetic markers, (iii) low levels of secondary miRNA loss, (iv) rarity of substitutions to the mature miRNA sequence, and (v) almost impossible scenario of convergent evolution of miRNAs Tarver et al, 2013). Therefore, miRNAs should provide an alternative and valuable evidence for the evolutionary position of Polypteriformes.…”

Section: Introductionmentioning

confidence: 99%