A genome sequence resource for the aye-aye (daubentonia madagascariensis), a nocturnal lemur from madagascar

George H. Perry, Darryl Reeves, Páll Melsted, Aakrosh Ratan, Webb Miller, Katelyn Michelini, Edward E. Louis, Jonathan K. Pritchard, Christopher E. Mason, Yoav Gilad

Research output: Contribution to journalArticle

35 Citations (Scopus)

Abstract

We present a high-coverage draft genome assembly of the aye-aye (Daubentonia madagascariensis), a highly unusual nocturnal primate from Madagascar. Our assembly totals ∼3.0 billion bp (3.0 Gb), roughly the size of the human genome, comprised of ∼2.6 million scaffolds (N50 scaffold size = 13,597 bp) based on short paired-end sequencing reads. We compared the aye-aye genome sequence data with four other published primate genomes (human, chimpanzee, orangutan, and rhesus macaque) as well as with the mouse and dog genomes as nonprimate outgroups. Unexpectedly, we observed strong evidence for a relatively slow substitution rate in the aye-aye lineage compared with these and other primates. In fact, the aye-aye branch length is estimated to be ∼10% shorter than that of the human lineage, which is known for its low substitution rate. This finding may be explained, in part, by the protracted aye-aye life-history pattern, including late weaning and age of first reproduction relative to other lemurs. Additionally, the availability of this draft lemur genome sequence allowed us to polarize nucleotide and protein sequence changes to the ancestral primate lineage - a critical period in primate evolution, for which the relevant fossil record is sparse. Finally, we identified 293,800 high-confidence single nucleotide polymorphisms in the donor individual for our aye-aye genome sequence, a captive-born individual from two wild-born parents. The resulting heterozygosity estimate of 0.051% is the lowest of any primate studied to date, which is understandable considering the aye-aye's extensive home-range size and relatively low population densities. Yet this level of genetic diversity also suggests that conservation efforts benefiting this unusual species should be prioritized, especially in the face of the accelerating degradation and fragmentation of Madagascar's forests.

Original languageEnglish (US)
Pages (from-to)126-135
Number of pages10
JournalGenome biology and evolution
Volume4
Issue number2
DOIs
StatePublished - Sep 24 2012

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Lemur
Madagascar
Primates
primate
genome
Genome
resource
Human Genome
Pongo
Homing Behavior
substitution
genome assembly
Pongo pygmaeus
Lemuridae
Fossils
Pan troglodytes
Population Density
Macaca mulatta
Weaning
weaning

All Science Journal Classification (ASJC) codes

  • Ecology, Evolution, Behavior and Systematics
  • Genetics

Cite this

Perry, George H. ; Reeves, Darryl ; Melsted, Páll ; Ratan, Aakrosh ; Miller, Webb ; Michelini, Katelyn ; Louis, Edward E. ; Pritchard, Jonathan K. ; Mason, Christopher E. ; Gilad, Yoav. / A genome sequence resource for the aye-aye (daubentonia madagascariensis), a nocturnal lemur from madagascar. In: Genome biology and evolution. 2012 ; Vol. 4, No. 2. pp. 126-135.
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abstract = "We present a high-coverage draft genome assembly of the aye-aye (Daubentonia madagascariensis), a highly unusual nocturnal primate from Madagascar. Our assembly totals ∼3.0 billion bp (3.0 Gb), roughly the size of the human genome, comprised of ∼2.6 million scaffolds (N50 scaffold size = 13,597 bp) based on short paired-end sequencing reads. We compared the aye-aye genome sequence data with four other published primate genomes (human, chimpanzee, orangutan, and rhesus macaque) as well as with the mouse and dog genomes as nonprimate outgroups. Unexpectedly, we observed strong evidence for a relatively slow substitution rate in the aye-aye lineage compared with these and other primates. In fact, the aye-aye branch length is estimated to be ∼10{\%} shorter than that of the human lineage, which is known for its low substitution rate. This finding may be explained, in part, by the protracted aye-aye life-history pattern, including late weaning and age of first reproduction relative to other lemurs. Additionally, the availability of this draft lemur genome sequence allowed us to polarize nucleotide and protein sequence changes to the ancestral primate lineage - a critical period in primate evolution, for which the relevant fossil record is sparse. Finally, we identified 293,800 high-confidence single nucleotide polymorphisms in the donor individual for our aye-aye genome sequence, a captive-born individual from two wild-born parents. The resulting heterozygosity estimate of 0.051{\%} is the lowest of any primate studied to date, which is understandable considering the aye-aye's extensive home-range size and relatively low population densities. Yet this level of genetic diversity also suggests that conservation efforts benefiting this unusual species should be prioritized, especially in the face of the accelerating degradation and fragmentation of Madagascar's forests.",
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Perry, GH, Reeves, D, Melsted, P, Ratan, A, Miller, W, Michelini, K, Louis, EE, Pritchard, JK, Mason, CE & Gilad, Y 2012, 'A genome sequence resource for the aye-aye (daubentonia madagascariensis), a nocturnal lemur from madagascar', Genome biology and evolution, vol. 4, no. 2, pp. 126-135. https://doi.org/10.1093/gbe/evr132

A genome sequence resource for the aye-aye (daubentonia madagascariensis), a nocturnal lemur from madagascar. / Perry, George H.; Reeves, Darryl; Melsted, Páll; Ratan, Aakrosh; Miller, Webb; Michelini, Katelyn; Louis, Edward E.; Pritchard, Jonathan K.; Mason, Christopher E.; Gilad, Yoav.

In: Genome biology and evolution, Vol. 4, No. 2, 24.09.2012, p. 126-135.

Research output: Contribution to journalArticle

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T1 - A genome sequence resource for the aye-aye (daubentonia madagascariensis), a nocturnal lemur from madagascar

AU - Perry, George H.

AU - Reeves, Darryl

AU - Melsted, Páll

AU - Ratan, Aakrosh

AU - Miller, Webb

AU - Michelini, Katelyn

AU - Louis, Edward E.

AU - Pritchard, Jonathan K.

AU - Mason, Christopher E.

AU - Gilad, Yoav

PY - 2012/9/24

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N2 - We present a high-coverage draft genome assembly of the aye-aye (Daubentonia madagascariensis), a highly unusual nocturnal primate from Madagascar. Our assembly totals ∼3.0 billion bp (3.0 Gb), roughly the size of the human genome, comprised of ∼2.6 million scaffolds (N50 scaffold size = 13,597 bp) based on short paired-end sequencing reads. We compared the aye-aye genome sequence data with four other published primate genomes (human, chimpanzee, orangutan, and rhesus macaque) as well as with the mouse and dog genomes as nonprimate outgroups. Unexpectedly, we observed strong evidence for a relatively slow substitution rate in the aye-aye lineage compared with these and other primates. In fact, the aye-aye branch length is estimated to be ∼10% shorter than that of the human lineage, which is known for its low substitution rate. This finding may be explained, in part, by the protracted aye-aye life-history pattern, including late weaning and age of first reproduction relative to other lemurs. Additionally, the availability of this draft lemur genome sequence allowed us to polarize nucleotide and protein sequence changes to the ancestral primate lineage - a critical period in primate evolution, for which the relevant fossil record is sparse. Finally, we identified 293,800 high-confidence single nucleotide polymorphisms in the donor individual for our aye-aye genome sequence, a captive-born individual from two wild-born parents. The resulting heterozygosity estimate of 0.051% is the lowest of any primate studied to date, which is understandable considering the aye-aye's extensive home-range size and relatively low population densities. Yet this level of genetic diversity also suggests that conservation efforts benefiting this unusual species should be prioritized, especially in the face of the accelerating degradation and fragmentation of Madagascar's forests.

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