The genome sequence of a widespread apex predator, the golden eagle (Aquila chrysaetos).
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.
Department of Forestry and Natural Resources, Purdue University, West Lafayette, Indiana, United States of America.
Jacqueline M
JM
Doyle
Division of Forestry and Natural Resources, West Virginia University, Morgantown, West Virginia, United States of America; Northern Research Station, USDA Forest Service, Parsons, West Virginia, United States of America.
Todd E
TE
Katzner
Western Foundation of Vertebrate Zoology, Camarillo, California, United States of America.
Peter H
PH
Bloom
Department of Forestry and Natural Resources, Purdue University, West Lafayette, Indiana, United States of America.
Yanzhu
Y
Ji
Department of Forestry and Natural Resources, Purdue University, West Lafayette, Indiana, United States of America; Department of Biological Sciences, Purdue University, West Lafayette, Indiana, United States of America.
Bhagya K
BK
Wijayawardena
Department of Forestry and Natural Resources, Purdue University, West Lafayette, Indiana, United States of America; Department of Biological Sciences, Purdue University, West Lafayette, Indiana, United States of America.
J Andrew
JA
DeWoody
D000818:Animals; D004251:DNA Transposable Elements / Q000235:genetics; D020307:Eagles / Q000235:genetics*; D016678:Genome / Q000235:genetics*; D008297:Male; D009656:North America
D004251:DNA Transposable Elements