Insertion polymorphisms of mobile genetic elements in sexual and asexual populations of daphnia pulex

Xiaoqian Jiang, Haixu Tang, Zhiqiang Ye, Michael Lynch

Research output: Contribution to journalArticle

7 Scopus citations

Abstract

Transposable elements (TEs) constitute a substantial portion of many eukaryotic genomes, and can in principle contribute to evolutionary innovation as well as genomic deterioration. Daphnia pulex serves as a useful model for studying TE dynamics as a potential cause and/or consequence of asexuality. We analyzed insertion polymorphisms of TEs in 20 sexual and 20 asexual isolates of D. pulex across North American from their available whole-genome sequencing data. Our results show that the total fraction of the derived sequences of TEs is not substantially different between asexual and sexual D. pulex isolates. However, in general, sexual clones contain fewer fixed TE insertions but more total insertion polymorphisms than asexual clones, supporting the hypothesis that sexual reproduction facilitates the spread and elimination of TEs. We identified nine asexual-specific fixed TE insertions, eight long terminal repeat retrotransposons, and one DNA transposon. By comparison, no sexual-specific fixed TE insertions were observed in our analysis. Furthermore, except one TE insertion located on a contig from chromosome 7, the other eight asexual-specific insertion sites are located on contigs from chromosome 9 that is known to be associated with obligate asexuality in D. pulex. We found that all nine asexual-specific fixed TE insertions can also be detected in some Daphnia pulicaria isolates, indicating that a substantial number of TE insertions in asexual D. pulex have been directly inherited from D. pulicaria during the origin of obligate asexuals.

Original languageEnglish (US)
Pages (from-to)362-374
Number of pages13
JournalGenome biology and evolution
Volume9
Issue number2
DOIs
StatePublished - 2017
Externally publishedYes

Keywords

  • Asexuality
  • Daphnia pulex
  • Daphnia pulicaria
  • TE insertions
  • Transposable elements

ASJC Scopus subject areas

  • Ecology, Evolution, Behavior and Systematics
  • Genetics

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