Limits...
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

Estimated number of paralogs of miRNA families in the chordate ancestor and after the vertebrate-specific 1R/2R (l.h.s.) and the teleost-specific 3R (r.h.s.) genome duplications. The size of the circles is proportional to the number of miRNA families with given numbers of paralogs in the ancestral state and the node following the gene duplication. The lines have slopes of 1, 2 and 4, respectively.
© Copyright Policy
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC4390885&req=5

life-05-00905-f003: Estimated number of paralogs of miRNA families in the chordate ancestor and after the vertebrate-specific 1R/2R (l.h.s.) and the teleost-specific 3R (r.h.s.) genome duplications. The size of the circles is proportional to the number of miRNA families with given numbers of paralogs in the ancestral state and the node following the gene duplication. The lines have slopes of 1, 2 and 4, respectively.

Mentions: The software ePoPE introduced here implements a variant of Sankoff’s parsimony algorithm using the Dollo variant that excludes the loss and re-gain of an miRNA family along the same lineage. It was designed specifically for studying the evolution of gene families with variable numbers of paralogs, for example miRNAs. With its help, we identify the last common ancestor of each individual miRNA family and find the most parsimonious estimate for the number of paralogs. As expected, we observe a significant increase in the number of miRNA paralogs at the branch leading to the ancestral gnathostome, vertebrate and teleost; see Figure 3.


The Expansion of Animal MicroRNA Families Revisited.

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

Estimated number of paralogs of miRNA families in the chordate ancestor and after the vertebrate-specific 1R/2R (l.h.s.) and the teleost-specific 3R (r.h.s.) genome duplications. The size of the circles is proportional to the number of miRNA families with given numbers of paralogs in the ancestral state and the node following the gene duplication. The lines have slopes of 1, 2 and 4, respectively.
© Copyright Policy
Related In: Results  -  Collection

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

life-05-00905-f003: Estimated number of paralogs of miRNA families in the chordate ancestor and after the vertebrate-specific 1R/2R (l.h.s.) and the teleost-specific 3R (r.h.s.) genome duplications. The size of the circles is proportional to the number of miRNA families with given numbers of paralogs in the ancestral state and the node following the gene duplication. The lines have slopes of 1, 2 and 4, respectively.
Mentions: The software ePoPE introduced here implements a variant of Sankoff’s parsimony algorithm using the Dollo variant that excludes the loss and re-gain of an miRNA family along the same lineage. It was designed specifically for studying the evolution of gene families with variable numbers of paralogs, for example miRNAs. With its help, we identify the last common ancestor of each individual miRNA family and find the most parsimonious estimate for the number of paralogs. As expected, we observe a significant increase in the number of miRNA paralogs at the branch leading to the ancestral gnathostome, vertebrate and teleost; see Figure 3.

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