Use of HAPPY mapping for the higher order assembly of the Tetrahymena genome

Eileen P. Hamilton, Paul H. Dear, Teisha Rowland, Karen Saks, Jonathan A Eisen, Eduardo Orias

Research output: Contribution to journalArticlepeer-review

12 Scopus citations


Tetrahymena thermophila is the best studied of the ciliates, a diversified and successful lineage of eukaryotic protists. Mirroring the way in which many metazoans partition their germ line and soma into distinct cell types, ciliates separate germ line and soma into two distinct nuclei in a single cell. The diploid, transcriptionally silent micronucleus undergoes meiosis and fertilization during sexual reproduction and determines the genotype of the progeny; in contrast, the expressed macronucleus contains many copies of hundreds of small chromosomes, determines the cell's phenotype, and is inherited only through vegetative reproduction. Here we demonstrate the power of HAPPY physical mapping to aid the complete assembly of T. thermophila macronuclear chromosomes from shotgun sequence scaffolds. The finished genome, one of only two ciliate genomes shotgun sequenced, will shed valuable additional light upon the biology of this extraordinary, diverse, and, from a genomics standpoint, as yet largely unexplored evolutionary branch of eukaryotes.

Original languageEnglish (US)
Pages (from-to)443-451
Number of pages9
Issue number4
StatePublished - Oct 2006
Externally publishedYes


  • Assembly closure
  • Chromosome breakage sequence
  • Germ-line nucleus
  • Internally eliminated sequence
  • Link validation
  • Macronuclear chromosomes
  • Sequence scaffolds
  • Somatic nucleus
  • Telomeres
  • Whole-genome-shotgun sequence

ASJC Scopus subject areas

  • Genetics


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