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Biologists routinely use molecular markers to identify conservation units,
to quantify genetic connectivity, to estimate population sizes, and to
identify targets of selection. Many imperiled eagle populations require
such efforts and would benefit from enhanced genomic resources. We
sequenced, assembled, and annotated the first eagle genome using DNA from
a male golden eagle (Aquila chrysaetos) captured in western North America.
We constructed genomic libraries that were sequenced using Illumina
technology and assembled the high-quality data to a depth of ~40x
coverage. The genome assembly includes 2,552 scaffolds >10 Kb and
415 scaffolds >1.2 Mb. We annotated 16,571 genes that are involved
in myriad biological processes, including such disparate traits as beak
formation and color vision. We also identified repetitive regions spanning
92 Mb (~6% of the assembly), including LINES, SINES, LTR-RTs and DNA
transposons. The mitochondrial genome encompasses 17,332 bp and is ~91%
identical to the Mountain Hawk-Eagle (Nisaetus nipalensis). Finally, the
data reveal that several anonymous microsatellites commonly used for
population studies are embedded within protein-coding genes and thus may
not have evolved in a neutral fashion. Because the genome sequence
includes ~800,000 novel polymorphisms, markers can now be chosen based on
their proximity to functional genes involved in migration, carnivory, and
other biological processes.
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