Multiple and independent phases of transposable element amplification in the genomes of piciformes (woodpeckers and allies)

Joseph D. Manthey, Robert G. Moyle, Stephane Boissinot

Research output: Contribution to journalArticle

Abstract

The small and conserved genomes of birds are likely a result of flight-relatedmetabolic constraints. Recombination-driven deletions andminimal transposable element (TE) expansions have led to continually shrinking genomes during evolution of many lineages of volant birds. Despite constraints of genome size in birds, we identified multiple waves of amplification of TEs in Piciformes (woodpeckers, honeyguides, toucans, and barbets). Relative to other bird species' genomic TE abundance (<10% of genome), we found ∼17-30% TE content inmultiple cladeswithin Piciformes. Several families of the retrotransposon superfamily chicken repeat 1 (CR1) expanded in at least three different waves of activity. The most recent CR1 expansions (∼4-7% of genome) preceded bursts of diversification in the woodpecker clade and in the American barbets + toucans clade. Additionally, we identified several thousand polymorphic CR1 insertions (hundreds per individual) in three closely related woodpecker species. Woodpecker CR1 insertion polymorphisms are maintained at lower frequencies than single nucleotide polymorphisms indicating that purifying selection is acting against additional CR1 copies and that these elements impose a fitness cost on their host. These findings provide evidence of large scale and ongoing TE activity in avian genomes despite continual constraint on genome size.

Original languageEnglish (US)
Pages (from-to)1445-1456
Number of pages12
JournalGenome Biology and Evolution
Volume10
Issue number6
DOIs
StatePublished - Jun 1 2018

Fingerprint

Piciformes
DNA Transposable Elements
woodpeckers
transposons
Chickens
amplification
genome
Birds
Genome
Genome Size
chickens
Ramphastidae
birds
bird
Retroelements
polymorphism
Genetic Recombination
Single Nucleotide Polymorphism
retrotransposons
metsulfuron methyl

Keywords

  • CR1
  • Diversification
  • Genomics
  • Transposable elements
  • Woodpeckers

ASJC Scopus subject areas

  • Ecology, Evolution, Behavior and Systematics
  • Genetics

Cite this

Multiple and independent phases of transposable element amplification in the genomes of piciformes (woodpeckers and allies). / Manthey, Joseph D.; Moyle, Robert G.; Boissinot, Stephane.

In: Genome Biology and Evolution, Vol. 10, No. 6, 01.06.2018, p. 1445-1456.

Research output: Contribution to journalArticle

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