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Evolution and Phylogeny of MicroRNAs — Protocols, Pitfalls, and Problems

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miRNomics

Part of the book series: Methods in Molecular Biology ((MIMB,volume 2257))

Abstract

MicroRNAs are important regulators in many eukaryotic lineages. Typical miRNAs have a length of about 22nt and are processed from precursors that form a characteristic hairpin structure. Once they appear in a genome, miRNAs are among the best-conserved elements in both animal and plant genomes. Functionally, they play an important role in particular in development. In contrast to protein-coding genes, miRNAs frequently emerge de novo. The genomes of animals and plants harbor hundreds of mutually unrelated families of homologous miRNAs that tend to be persistent throughout evolution. The evolution of their genomic miRNA complement closely correlates with important morphological innovation. In addition, miRNAs have been used as valuable characters in phylogenetic studies. An accurate and comprehensive annotation of miRNAs is required as a basis to understand their impact on phenotypic evolution. Since experimental data on miRNA expression are limited to relatively few species and are subject to unavoidable ascertainment biases, it is inevitable to complement miRNA sequencing by homology based annotation methods. This chapter reviews the state of the art workflows for homology based miRNA annotation, with an emphasis on their limitations and open problems.

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Acknowledgements

This work was funded in part by the German Federal Ministery for Education and Research (BMBF 031A538A, de.NBI/RBC), CAVH was funded by the German Academic Exchange Service (DAAD) (Forschungsstipendien-Promotionen in Deutschland, 2018/19 (Bewerbung 57299294), Ali M. Yazbeck was funded by a doctoral stipend of the National Council for Scientific Research of Lebanon (CNRS-L).

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Authors and Affiliations

  1. Bioinformatics Group, Department of Computer Science, and Interdisciplinary Center for Bioinformatics, University of Leipzig, D-04107, Härtelstraße 16–18, Leipzig, Germany

    Cristian A. Velandia-Huerto, Ali M. Yazbeck & Peter F. Stadler

  2. Doctoral School for Science and Technology, Lebanese University, Rafic Hariri University Campus, Hadath, Lebanon

    Ali M. Yazbeck

  3. Young Investigators Group Bioinformatics & Transcriptomics, Department of Molecular Systems Biology, Helmholtz Centre for Environmental Research GmbH – UFZ, D-04318, Permoserstraße 15, Leipzig, Germany

    Jana Schor

  4. Max Planck Institute for Mathematics in the Sciences, D-04103, Inselstraße 22, Leipzig, Germany

    Peter F. Stadler

  5. Institute for Theoretical Chemistry, University of Vienna, A-1090, Währingerstraße 17, Wien, Austria

    Peter F. Stadler

  6. Santa Fe Institute, Santa Fe, 1399 Hyde Park Rd, NM 87501, USA

    Peter F. Stadler

Authors
  1. Cristian A. Velandia-Huerto
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  2. Ali M. Yazbeck
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  3. Jana Schor
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  4. Peter F. Stadler
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Corresponding authors

Correspondence to Cristian A. Velandia-Huerto , Ali M. Yazbeck or Peter F. Stadler .

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Editors and Affiliations

  1. Medical Informatics and Bioinformatics, Institute for Measurement Engineering and Sensor Technology, Hochschule Ruhr West, University of Applied Sciences, Mülheim adR, Germany

    Jens Allmer

  2. Department of Information System, Galilee Digital Health Research Center (GDH), Zefat Academic College, Zefat, Israel

    Malik Yousef

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Velandia-Huerto, C.A., Yazbeck, A.M., Schor, J., Stadler, P.F. (2022). Evolution and Phylogeny of MicroRNAs — Protocols, Pitfalls, and Problems. In: Allmer, J., Yousef, M. (eds) miRNomics. Methods in Molecular Biology, vol 2257. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-1170-8_11

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  • DOI: https://doi.org/10.1007/978-1-0716-1170-8_11

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  • Publisher Name: Humana, New York, NY

  • Print ISBN: 978-1-0716-1169-2

  • Online ISBN: 978-1-0716-1170-8

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