Abstract
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.
Highlights
Eagles have been cultural icons emblematic of nations, religions, and peoples around the world ([1,2]; Figure S1)
Modest suites of microsatellite markers are available for a few species (e.g., Aquila adalberti, [14]); A. heliaca, [15]; Haliaeetus albicilla, [16]; Nisaetus nipalensis, [17]), and complete mitochondrial genome sequences are available for three species (Spilornis cheela [18], N. nipalensis, and Spizaetus alboniger [19])
Quality control filtering yielded 24.5 Gb and 21.0 Gb from the paired-end and mate-paired libraries, respectively, so about one-third of the raw data fell to the cutting-room floor [56]
Summary
Eagles have been cultural icons emblematic of nations, religions, and peoples around the world ([1,2]; Figure S1). In contemporary North America, native cultures incorporate eagle feathers into medicines and religious ceremonies. Many eagle species are of worldwide conservation concern due to direct threats to individuals (e.g., poaching and collisions with wind turbines) and indirect threats to populations (e.g., habitat loss and environmental toxins) [2,8,9,10,11]. Conservation efforts have often been hampered by the generally secretive nature and remote habitats of eagles, but recently described molecular markers have provided new tools for population monitoring [12,13]. Modest suites of microsatellite markers are available for a few species (e.g., Aquila adalberti, [14]); A. heliaca, [15]; Haliaeetus albicilla, [16]; Nisaetus nipalensis, [17]), and complete mitochondrial genome sequences are available for three species (Spilornis cheela [18], N. nipalensis, and Spizaetus alboniger [19])
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