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The Expansion of Animal MicroRNA Families Revisited.

Hertel J, Stadler PF - Life (Basel) (2015)

Bottom Line: With a much better resolution for the invertebrate lineage compared to large-scale studies, we observe additional bursts of innovation, e.g., in Rhabditoidea.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.

View Article: PubMed Central - PubMed

Affiliation: Bioinformatics Group, Department of Computer Science, and Interdisciplinary Center for Bioinformatics, University Leipzig, Härtelstrasse 16-18, D-04107 Leipzig, Germany. jana@bioinf.uni-leipzig.de.

ABSTRACT
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.

No MeSH data available.


Related in: MedlinePlus

Relative number of gains and losses of entire miRNA families during metazoan evolution. The relative gain is the number of gained miRNA families compared to the observed number of miRNA families. The relative loss describes the number of lost miRNA families compared to the number of miRNA families in the parent node of the phylogenetic tree.
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life-05-00905-f004: Relative number of gains and losses of entire miRNA families during metazoan evolution. The relative gain is the number of gained miRNA families compared to the observed number of miRNA families. The relative loss describes the number of lost miRNA families compared to the number of miRNA families in the parent node of the phylogenetic tree.

Mentions: In protostomes, we observe further bursts of innovation of novel miRNA families at the ancestor of “free-living” nematodes, Rhabditoidea and at the split of drosophilids. Beyond the massive gains of miRNA families at the ancestral gnathostome, vertebrate and teleost in deuterostomes, additional peaks in miRNA family innovation can be assigned to the ancestral lines of: (1) Amniota, the egg laying animals; (2) Eutheria, the placental mammals; (3) Boreotheria, the group comprising the Superprimates and the Laurasiatheria; (4) Muridae, the group containing mouse, rat and gerbil; and (5) Catarrhini, the Old World Monkeys, including apes and humans; see Figure 4. All of these branches are associated with major increases in morphological complexity in these lineages of animal species [45].


The Expansion of Animal MicroRNA Families Revisited.

Hertel J, Stadler PF - Life (Basel) (2015)

Relative number of gains and losses of entire miRNA families during metazoan evolution. The relative gain is the number of gained miRNA families compared to the observed number of miRNA families. The relative loss describes the number of lost miRNA families compared to the number of miRNA families in the parent node of the phylogenetic tree.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4390885&req=5

life-05-00905-f004: Relative number of gains and losses of entire miRNA families during metazoan evolution. The relative gain is the number of gained miRNA families compared to the observed number of miRNA families. The relative loss describes the number of lost miRNA families compared to the number of miRNA families in the parent node of the phylogenetic tree.
Mentions: In protostomes, we observe further bursts of innovation of novel miRNA families at the ancestor of “free-living” nematodes, Rhabditoidea and at the split of drosophilids. Beyond the massive gains of miRNA families at the ancestral gnathostome, vertebrate and teleost in deuterostomes, additional peaks in miRNA family innovation can be assigned to the ancestral lines of: (1) Amniota, the egg laying animals; (2) Eutheria, the placental mammals; (3) Boreotheria, the group comprising the Superprimates and the Laurasiatheria; (4) Muridae, the group containing mouse, rat and gerbil; and (5) Catarrhini, the Old World Monkeys, including apes and humans; see Figure 4. All of these branches are associated with major increases in morphological complexity in these lineages of animal species [45].

Bottom Line: With a much better resolution for the invertebrate lineage compared to large-scale studies, we observe additional bursts of innovation, e.g., in Rhabditoidea.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.

View Article: PubMed Central - PubMed

Affiliation: Bioinformatics Group, Department of Computer Science, and Interdisciplinary Center for Bioinformatics, University Leipzig, Härtelstrasse 16-18, D-04107 Leipzig, Germany. jana@bioinf.uni-leipzig.de.

ABSTRACT
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.

No MeSH data available.


Related in: MedlinePlus