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Ruminant-specific multiple duplication events of PRDM9 before speciation.

Abinash Padhi1, Botong Shen2, Jicai Jiang2

  • 1Department of Animal and Avian Sciences, University of Maryland, College Park, MD, 20742, USA. bshen218@umd.edu.

BMC Evolutionary Biology
|March 16, 2017
PubMed
Summary

The PRDM9 gene in ruminants underwent duplication, creating multiple copies on different chromosomes. These copies, particularly those with zinc finger arrays, show evidence of positive selection and concerted evolution.

Keywords:
Gene duplicationGenetic incompatibilityMolecular evolutionPRDM9Positive selectionRuminantsSpeciation genetics

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Area of Science:

  • Genetics
  • Evolutionary Biology
  • Reproductive Biology

Background:

  • PRDM9 is a key speciation gene regulating meiotic recombination and hybrid incompatibility in sexually reproducing organisms.
  • Understanding the evolution of PRDM9, especially its multiple copies in metazoans, is crucial for insights into mammalian reproduction and fitness.
  • Little is known about the genetic and evolutionary mechanisms behind PRDM9 gene multiplication in metazoan lineages.

Purpose of the Study:

  • To investigate the genetic and evolutionary mechanisms behind PRDM9 gene duplication in ruminants.
  • To identify the number and location of PRDM9 copies in the ruminant genome.
  • To analyze the evolutionary patterns of PRDM9 copies, focusing on zinc finger arrays and selection pressures.

Main Methods:

  • Comparative genomics to identify PRDM9 gene duplication events in ruminants.
  • Chromosomal mapping to determine the location of PRDM9 copies (chr1 and chrX).
  • Sequence analysis of PRDM9 copies to examine zinc finger arrays and identify signatures of positive selection.

Main Results:

  • Evidence of ruminant-specific gene duplication events for PRDM9, occurring after divergence from the common ancestor and before speciation.
  • Identification of three PRDM9 copies: one on chr1 (lineage I) and two on chrX (lineages II & III).
  • Lineages I and II possess variable C2H2 zinc finger arrays, while lineage III lacks them; these arrays in lineages I and II evolved under strong positive selection.

Conclusions:

  • Two distinct gene duplication events shaped the PRDM9 family in ruminants: an inter-chromosomal duplication (chr1-chrX) and an intra-chromosomal X-linked duplication.
  • The duplication between chrX and chr1 is rare, likely resulting from ancient unequal crossing-over events involving ancestral autosomes that formed sex chromosomes.
  • Gene duplication, concerted evolution, and positive selection are identified as the primary drivers for the expansion and evolution of the PRDM9 gene subfamily in ruminants, supporting the Red Queen hypothesis.