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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

Map of all miRNA families (y-axis) in all analyzed animal species (x-axis). Each cell (i, j) represents the number of paralogs within miRNA family i in species j. The colors indicate this number. The rows have been clustered by co-occurrence (dendrogram at the left side). Beyond several blocks of lineage-specific miRNA families, e.g., in Rhabditida, Muridae or Cephalochordata, the below described bursts of miRNA innovations are also visible here, e.g., at the origin of vertebrates and Eutheria. The miRNA families in the bottom rows cover nearly the complete range of animal species. Indeed, these families comprise many of the evolutionarily old miRNAs, like mir-10, mir-9 and let-7. Furthermore, few miRNA families have more than eight paralogs.
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life-05-00905-f002: Map of all miRNA families (y-axis) in all analyzed animal species (x-axis). Each cell (i, j) represents the number of paralogs within miRNA family i in species j. The colors indicate this number. The rows have been clustered by co-occurrence (dendrogram at the left side). Beyond several blocks of lineage-specific miRNA families, e.g., in Rhabditida, Muridae or Cephalochordata, the below described bursts of miRNA innovations are also visible here, e.g., at the origin of vertebrates and Eutheria. The miRNA families in the bottom rows cover nearly the complete range of animal species. Indeed, these families comprise many of the evolutionarily old miRNAs, like mir-10, mir-9 and let-7. Furthermore, few miRNA families have more than eight paralogs.

Mentions: The blast search starting from 19,954 pre-miRNA sequences in the set of animal species resulted in a large number of additional homologs not previously documented in miRBase; see Figure 2. We detected 9482 novel miRNA homologs. Of these, 4363 (∼46%) were found in species that were already represented in miRBase. In the additional set of 45 species, we found further 5119 novel homologs. For 452 miRNA families, no additional homologs were found; these seem to be lineage-/species-specific miRNAs. In line with previous studies, we find that miRNAs are continuously integrated into animals’ genomes. There seem to be two dominating types of processes: (i) the de novo emergence of new miRNAs from transcribed sequences leads to new miRNA families; and (ii) gene duplications expand the portfolio of paralogs in a given miRNA family. The two mechanisms are thus readily disentangled by the family-wise census of miRNA families reported here.


The Expansion of Animal MicroRNA Families Revisited.

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

Map of all miRNA families (y-axis) in all analyzed animal species (x-axis). Each cell (i, j) represents the number of paralogs within miRNA family i in species j. The colors indicate this number. The rows have been clustered by co-occurrence (dendrogram at the left side). Beyond several blocks of lineage-specific miRNA families, e.g., in Rhabditida, Muridae or Cephalochordata, the below described bursts of miRNA innovations are also visible here, e.g., at the origin of vertebrates and Eutheria. The miRNA families in the bottom rows cover nearly the complete range of animal species. Indeed, these families comprise many of the evolutionarily old miRNAs, like mir-10, mir-9 and let-7. Furthermore, few miRNA families have more than eight paralogs.
© Copyright Policy
Related In: Results  -  Collection

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

life-05-00905-f002: Map of all miRNA families (y-axis) in all analyzed animal species (x-axis). Each cell (i, j) represents the number of paralogs within miRNA family i in species j. The colors indicate this number. The rows have been clustered by co-occurrence (dendrogram at the left side). Beyond several blocks of lineage-specific miRNA families, e.g., in Rhabditida, Muridae or Cephalochordata, the below described bursts of miRNA innovations are also visible here, e.g., at the origin of vertebrates and Eutheria. The miRNA families in the bottom rows cover nearly the complete range of animal species. Indeed, these families comprise many of the evolutionarily old miRNAs, like mir-10, mir-9 and let-7. Furthermore, few miRNA families have more than eight paralogs.
Mentions: The blast search starting from 19,954 pre-miRNA sequences in the set of animal species resulted in a large number of additional homologs not previously documented in miRBase; see Figure 2. We detected 9482 novel miRNA homologs. Of these, 4363 (∼46%) were found in species that were already represented in miRBase. In the additional set of 45 species, we found further 5119 novel homologs. For 452 miRNA families, no additional homologs were found; these seem to be lineage-/species-specific miRNAs. In line with previous studies, we find that miRNAs are continuously integrated into animals’ genomes. There seem to be two dominating types of processes: (i) the de novo emergence of new miRNAs from transcribed sequences leads to new miRNA families; and (ii) gene duplications expand the portfolio of paralogs in a given miRNA family. The two mechanisms are thus readily disentangled by the family-wise census of miRNA families reported here.

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