Evolutionary Genomics of microRNAs and Their Relatives

Tanzer, Andrea; Riester, Markus; Hertel, Jana; Bermúdez-Santana, Clara Isabel; Gorodkin, Jan; Hofacker, Ivo L.; Stadler, Peter F.

doi:10.1002/9780470570418.ch15

Cited by 14 publications

(6 citation statements)

References 217 publications

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“…For the mir‐184 family, we found distinct mature sequences that perfectly matched dpu‐miR‐263a and dpu‐miR‐263b from mirBase, respectively. The dataset comprised the majority of the microRNA families known to have been evolved before the split of crustaceans and insects (Hertel et al, ; Tanzer et al, ; Campbell et al, ).…”

Section: Resultsmentioning

confidence: 99%

A first Glimpse at the genome of the Baikalian amphipod Eulimnogammarus verrucosus

Rivarola-Duarte

Otto

Jühling³

et al. 2014

J Exp Zool Pt B

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Eulimnogammarus verrucosus is an amphipod endemic to the unique ecosystem of Lake Baikal and serves in particular as an emerging model in ecotoxicological studies. We report here on a survey sequencing of its genome as a first step to establish sequence resources for this species. From a single lane of paired-end sequencing data we estimated the genome size as nearly 10 Gb and we obtained an overview of the repeat content. At least two thirds of the genome are non-unique DNA, and a third of the genomic DNA is composed of just five families of repetitive elements, including low-complexity sequences. Attempts to use off-the-shelf assembly tools failed on the available low-coverage data both before and after removal of highly repetitive components. Using a seed-based approach we nevertheless assembled short contigs covering 33 pre-microRNAs and the homeodomain-containing exon of nine Hox genes. The absence of clear evidence for paralogs implies that a genome duplication did not contribute to the large genome size. We furthermore report the assembly of the mitochondrial genome using a new, guided "crystallization" procedure. The initial results presented here set the stage for a more complete sequencing and analysis of this large genome.

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Section: Resultsmentioning

confidence: 99%

A first Glimpse at the genome of the Baikalian amphipod Eulimnogammarus verrucosus

Rivarola-Duarte

Otto

Jühling³

et al. 2014

J Exp Zool Pt B

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“…Large-scale comparative analyses of animal miRNA evolution have revealed several bursts of miRNA evolution, most notably one associated with the origin of the vertebrates and another one at the root of the placental mammals [ 11 , 16 , 33 ]. Here, we reevaluate the history of animal miRNAs in light of the recent massive increase in available data.…”

Section: Introductionmentioning

confidence: 99%

The Expansion of Animal MicroRNA Families Revisited

Hertel

Stadler

2015

Life

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MicroRNAs are important regulatory small RNAs in many eukaryotes. Due to their small size and simple structure, they are readily innovated de novo. Throughout the evolution of animals, the emergence of novel microRNA families traces key morphological innovations. Here, we use a computational approach based on homology search and parsimony-based presence/absence analysis to draw a comprehensive picture of microRNA evolution in 159 animal species. We confirm previous observations regarding bursts of innovations accompanying the three rounds of genome duplications in vertebrate evolution and in the early evolution of placental mammals. With a much better resolution for the invertebrate lineage compared to large-scale studies, we observe additional bursts of innovation, e.g., in Rhabditoidea. More importantly, we see clear evidence that loss of microRNA families is not an uncommon phenomenon. The Enoplea may serve as a second dramatic example beyond the tunicates. The large-scale analysis presented here also highlights several generic technical issues in the analysis of very large gene families that will require further research.

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“…They are derived from RNAs with imperfect foldback structures, and can bind to messenger RNAs (mRNAs) that have complementary sequences to the miRNA sequence, causing a reduction of the expression of the target gene through two mechanisms, translation repression and/or transcript cleavage (Bartel, 2004). miRNAs are abundant in a number of eukaryote species, particularly in metazoans and plants (Tanzer et al, 2010). Because miRNAs draw a tremendous amount of attention in molecular biology, miRNAs and their target genes have been well identified in many species.…”

Section: Introductionmentioning

confidence: 99%