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, asse...

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Autores principales:	Jacqueline M Doyle, Todd E Katzner, Peter H Bloom, Yanzhu Ji, Bhagya K Wijayawardena, J Andrew DeWoody
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2014
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/b13a86758bb14696bf0fae57de4ce961
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spelling	oai:doaj.org-article:b13a86758bb14696bf0fae57de4ce9612021-11-18T08:21:50ZThe genome sequence of a widespread apex predator, the golden eagle (Aquila chrysaetos).1932-620310.1371/journal.pone.0095599https://doaj.org/article/b13a86758bb14696bf0fae57de4ce9612014-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/24759626/pdf/?tool=EBIhttps://doaj.org/toc/1932-6203Biologists 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.Jacqueline M DoyleTodd E KatznerPeter H BloomYanzhu JiBhagya K WijayawardenaJ Andrew DeWoodyPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 9, Iss 4, p e95599 (2014)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Jacqueline M Doyle Todd E Katzner Peter H Bloom Yanzhu Ji Bhagya K Wijayawardena J Andrew DeWoody The genome sequence of a widespread apex predator, the golden eagle (Aquila chrysaetos).
description	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.
format	article
author	Jacqueline M Doyle Todd E Katzner Peter H Bloom Yanzhu Ji Bhagya K Wijayawardena J Andrew DeWoody
author_facet	Jacqueline M Doyle Todd E Katzner Peter H Bloom Yanzhu Ji Bhagya K Wijayawardena J Andrew DeWoody
author_sort	Jacqueline M Doyle
title	The genome sequence of a widespread apex predator, the golden eagle (Aquila chrysaetos).
title_short	The genome sequence of a widespread apex predator, the golden eagle (Aquila chrysaetos).
title_full	The genome sequence of a widespread apex predator, the golden eagle (Aquila chrysaetos).
title_fullStr	The genome sequence of a widespread apex predator, the golden eagle (Aquila chrysaetos).
title_full_unstemmed	The genome sequence of a widespread apex predator, the golden eagle (Aquila chrysaetos).
title_sort	genome sequence of a widespread apex predator, the golden eagle (aquila chrysaetos).
publisher	Public Library of Science (PLoS)
publishDate	2014
url	https://doaj.org/article/b13a86758bb14696bf0fae57de4ce961
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The genome sequence of a widespread apex predator, the golden eagle (Aquila chrysaetos).

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