DOI: 10.5061/dryad.d0md6
title: Data from: 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 &gt;10 Kb and
 415 scaffolds &gt;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.
description: annotated
 genes_proteins16,571 genes were
 annotated in the golden eagle genome, this fasta file describes the
 protein sequences (see readme.pdf for more information). Corresponding
 file archived in fortress is
 kmer70_min10000_scaffolds_revisedassembly.all.maker.proteins.kmer70_min10000_scaffolds_revisedassembly.all.maker.proteins.fastaannotated genes_transcripts16,571 genes were annotated in the golden eagle genome, this fasta files describes the transcripts (see readme.pdf for additional information). Corresponding file archived in fortress is kmer70_min10000_scaffolds_revisedassembly.all.maker.transcripts.kmer70_min10000_scaffolds_revisedassembly.all.maker.transcripts.fastamitochondrial genome_GE_MITObim_revisedGolden eagle mitochondrial genome sequence assembled with MITObim vs. 1.6 and MIRA MIRA 3.4.1.1.GE_MITObim_revised.fastaxenobiotic sequences_Golden_Eagle_BLASTN_outputblastn (DiaGrid) Input Options Query File: GoldenEagle sequences with no significant match (E&lt;10-6) to chicken genome Database Selection: nt Custom Database Format: N Expectation Value: 1.0E-6 Word Size: 28 Search and Result Restriction Options Max Target Seqs: 1000 Output Formatting Options Format: 6 Custom Selection: qseqid sseqid qstart qend sstart send evalue bitscore pident length mismatch gapopen staxids sscinames scomnames sblastnames sskingdoms stitleGolden_Eagle_BLASTN_output.txttransposable elements_RepeatProteinMask output_ge_v2_all############################ ##### RepeatProteinMask #### ############################ ## version: 4.0.2 ## command: RepeatProteinMask -noLowSimple -pvalue 1e-4 -engine abblast kmer70-v2-min200-scaffolds.fa ## output files: ge_v2_all.annotge_v2_all.annottransposable elements_repeatmasker_kmer70-v2-min200-scaffolds.fa############################ ###### RepeatMasker ######## ############################ ## RepeatMasker version 4.0.2 ## RepeatMaskerLibrary-20130422 version ## command: RepeatMasker -nolow -no_is -norna -dir . \ -lib RepeatMaskerLib.embl.lib \ kmer70-v2-min200-scaffolds.fa ## output files: repeatmasker_kmer70-v2-min200-scaffolds.fa.masked repeatmasker_kmer70-v2-min200-scaffolds.fa.tblrepeatmasker_kmer70-v2-min200-scaffolds.fa.tar.gztransposable elements_repeatmasker_kmer70-v2-min200-scaffolds.fa############################ ###### RepeatMasker ######## ############################ ## RepeatMasker version 4.0.2 ## RepeatMaskerLibrary-20130422 version ## command: RepeatMasker -nolow -no_is -norna -dir . \ -lib RepeatMaskerLib.embl.lib \ kmer70-v2-min200-scaffolds.fa ## output files: repeatmasker_kmer70-v2-min200-scaffolds.fa.masked repeatmasker_kmer70-v2-min200-scaffolds.fa.tblrepeatmasker_kmer70-v2-min200-scaffolds.fa.tblannotated genes_gff16,571 genes were annotated in the golden eagle genome, this is the .gff file associated with the annotations (see readme.pdf for additional information).genome.all.gfftransposable elements_repeatmodeler_kmer70-v2-min200-scaffolds.fa.tar############################ ####### RepeatModeler ###### ############################ ## version: 1.0.7 ## command: BuildDatabase -name goldenEagle_v2_tmp -engine ncbi kmer70-v2-min200-scaffolds.fa RepeatModeler -database goldenEagle_v2_tmp RepeatMasker -nolow -no_is -norna -dir . -lib Ach-v2.consensi.fa.classified kmer70-v2-min200-scaffolds.fa ## output files: Ach-v2.consensi.fa.classified repeatmodeler_kmer70-v2-min200-scaffolds.fa.masked repeatmodeler_kmer70-v2-min200-scaffolds.fa.tblrepeatmodeler_kmer70-v2-min200-scaffolds.fa.tar.gztransposable elements_repeatmodeler_kmer70-v2-min200-scaffolds.fa############################ ####### RepeatModeler ###### ############################ ## version: 1.0.7 ## command: BuildDatabase -name goldenEagle_v2_tmp -engine ncbi kmer70-v2-min200-scaffolds.fa RepeatModeler -database goldenEagle_v2_tmp RepeatMasker -nolow -no_is -norna -dir . -lib Ach-v2.consensi.fa.classified kmer70-v2-min200-scaffolds.fa ## output files: Ach-v2.consensi.fa.classified repeatmodeler_kmer70-v2-min200-scaffolds.fa.masked repeatmodeler_kmer70-v2-min200-scaffolds.fa.tblrepeatmodeler_kmer70-v2-min200-scaffolds.fa.tbltransposable elements_Ach-v2.consensi.fa############################ ####### RepeatModeler ###### ############################ ## version: 1.0.7 ## command: BuildDatabase -name goldenEagle_v2_tmp -engine ncbi kmer70-v2-min200-scaffolds.fa RepeatModeler -database goldenEagle_v2_tmp RepeatMasker -nolow -no_is -norna -dir . -lib Ach-v2.consensi.fa.classified kmer70-v2-min200-scaffolds.fa ## output files: Ach-v2.consensi.fa.classified repeatmodeler_kmer70-v2-min200-scaffolds.fa.masked repeatmodeler_kmer70-v2-min200-scaffolds.fa.tblAch-v2.consensi.fa.classifiedtransposable elements_kmer70-v2-min200-scaffolds.fa.2.7.7.80.10.50.200############################ ########### trf ############ ############################ ## version: 4.04 ## command: trf kmer70-v2-min200-scaffolds.fa 2 7 7 80 10 50 200 -f -h ## output files: kmer70-v2-min200-scaffolds.fa.2.7.7.80.10.50.200.datkmer70-v2-min200-scaffolds.fa.2.7.7.80.10.50.200.datmicrosatellites_kmer70_min200_scaffolds_revisedassembly_allmicrosatellites.fastaI used the MISA.pl script (http://pgrc.ipk-gatersleben.de/misa/misa.html) to identify all microsatellites present in scaffolds greater than 200 bp. Misa.pl kmer70_min200_scaffolds_revisedassembly.fastakmer70_min200_scaffolds_revisedassembly_allmicrosatellites.fasta.misagenome assembly_kmer70_min10000_scaffolds_revisedassemblyThe golden eagle genome was assembled in ABySS with the following parameters: abyss-pe s=202 n=10 k=70 l=30; followed by file specifications for 1) 'lib' -- the paired-end and mate-pair reads, 2) 'se' -- the unpaired and mate-pair reads used as single-end reads in assembly and 3) 'mp' -- the paired-end and mate-pair reads used in scaffolding.kmer70_min10000_scaffolds_revisedassembly.tar.gz