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As the name suggests, non-LTR retrotransposons lack the long terminal repeats characteristic of the LTR retrotransposons. Additionally, both LTR and non-LTR retrotransposons use distinct mechanisms of mobilization. Non-LTR retrotransposons are further divided into two classes - Long interspersed nuclear elements (LINEs) and short interspersed nuclear elements (SINEs), both of which occur abundantly in most mammals, including humans. Some of the active non-LTR retrotransposons in humans are L1...
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SMORE: Synteny Modulator of Repetitive Elements.

Sarah J Berkemer1,2, Anne Hoffmann3, Cameron R A Murray4

  • 1Bioinformatics Group, Department of Computer Science, and Interdisciplinary Center for Bioinformatics, University of Leipzig, Härtelstraße 16-18, D-04107 Leipzig, Germany. bsarah@bioinf.uni-leipzig.de.

Life (Basel, Switzerland)
|November 1, 2017
PubMed
Summary

Concerted evolution makes distinguishing gene copies difficult. This study introduces a new pipeline using synteny to accurately identify orthologous genes, aiding evolutionary analysis of multicopy gene families.

Keywords:
Y RNAsbioinformaticsconcerted evolutionorthologypipelinesyntenytRNAstandem duplicationsworkflow

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Area of Science:

  • Genomics
  • Evolutionary Biology
  • Bioinformatics

Background:

  • Multicopy gene families like transfer ribonucleic acids (tRNAs) and ribosomal RNAs (rRNAs) undergo concerted evolution.
  • Concerted evolution leads to high sequence similarity among paralogous genes, complicating ortholog identification.
  • Sequence similarity alone is insufficient to distinguish orthologs from paralogs in these cases.

Purpose of the Study:

  • To develop an automated computational pipeline for analyzing evolutionary relationships of multicopy genes.
  • To utilize synteny (preservation of genomic location) as a key feature for ortholog assignment.
  • To provide a freely available tool for evolutionary analysis of challenging gene families.

Main Methods:

  • Genome-wide alignments were used as the initial step.
  • Orthology relationships were assigned based on synteny analysis.
  • The pipeline was tested using transfer RNA (tRNA) evolution in primates and Y RNA evolution in vertebrates and nematodes.

Main Results:

  • The developed pipeline successfully assigns orthology relationships by leveraging synteny.
  • The method effectively handles multicopy gene families where sequence similarity is ambiguous.
  • Case studies on primate tRNAs and vertebrate/nematode Y RNAs demonstrate the pipeline's utility.

Conclusions:

  • Synteny is a crucial factor for resolving orthology in multicopy gene families subject to concerted evolution.
  • The automated pipeline provides a robust and accessible method for evolutionary analysis.
  • This approach enhances our understanding of the evolution of gene families like tRNAs and Y RNAs.