A new reference genome assembly for the microcrustacean Daphnia pulex

Zhiqiang Ye, Sen Xu, Ken Spitze, Jana Asselman, Xiaoqian Jiang, Matthew S. Ackerman, Jacqueline Lopez, Brent Harker, R. Taylor Raborn, W. Kelley Thomas, Jordan Ramsdell, Michael E. Pfrender, Michael Lynch

Research output: Contribution to journalArticlepeer-review

73 Scopus citations


Comparing genomes of closely related genotypes from populations with distinct demographic histories can help reveal the impact of effective population size on genome evolution. For this purpose, we present a high quality genome assembly of Daphnia pulex (PA42), and compare this with the first sequenced genome of this species (TCO), which was derived from an isolate from a population with >90% reduction in nucleotide diversity. PA42 has numerous similarities to TCO at the gene level, with an average amino acid sequence identity of 98.8 and >60% of orthologous proteins identical. Nonetheless, there is a highly elevated number of genes in the TCO genome annotation, with 7000 excess genes appearing to be false positives. This view is supported by the high GC content, lack of introns, and short length of these suspicious gene annotations. Consistent with the view that reduced effective population size can facilitate the accumulation of slightly deleterious genomic features, we observe more proliferation of transposable elements (TEs) and a higher frequency of gained introns in the TCO genome.

Original languageEnglish (US)
Pages (from-to)1405-1416
Number of pages12
JournalG3: Genes, Genomes, Genetics
Issue number5
StatePublished - May 1 2017
Externally publishedYes


  • Effective population size
  • Gene number intron
  • Genome annotation
  • Mobile elements

ASJC Scopus subject areas

  • Molecular Biology
  • Genetics
  • Genetics(clinical)


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