Jarvis ED, Mirarab S, Aberer AJ, Li B, Houde P, Li C, et al. Whole-genome analyses resolve early branches in the tree of life of modern birds. Science. 2014;346:1320–31.
Article
CAS
PubMed
PubMed Central
Google Scholar
Fowler DW, Freedman EA, Scannella JB. Predatory functional morphology in raptors: interdigital variation in talon size is related to prey restraint and immobilisation technique. PLoS One. 2009;4:e7999.
Article
PubMed
PubMed Central
Google Scholar
Zhan X, Pan S, Wang J, Dixon A, He J, Muller MG, et al. Peregrine and saker falcon genome sequences provide insights into evolution of a predatory lifestyle. Nat Genet. 2013;45:563–6.
Article
CAS
PubMed
Google Scholar
Wu Y, Hadly EA, Teng W, Hao Y, Liang W, Liu Y, et al. Retinal transcriptome sequencing sheds light on the adaptation to nocturnal and diurnal lifestyles in raptors. Sci Rep. 2016;6:33578.
Article
CAS
PubMed
PubMed Central
Google Scholar
Le Duc D, Schöneberg T. Adaptation to nocturnality - learning from avian genomes. Bioessays. 2016;38:694–703.
Article
PubMed
Google Scholar
Zhang G, Li C, Li Q, Li B, Larkin DM, Lee C, et al. Comparative genomics reveals insights into avian genome evolution and adaptation. Science. 2014;346:1311–20.
Article
CAS
PubMed
PubMed Central
Google Scholar
Van Den Bussche RA, Judkins ME, Montague MJ, Warren WC. A resource of genome-wide single nucleotide polymorphisms (Snps) for the conservation and management of golden eagles. J Raptor Res. 2017;51:368–77.
Article
Google Scholar
Hanna ZR, Henderson JB, Wall JD, Emerling CA, Fuchs J, Runckel C, et al. Northern spotted owl (Strix occidentalis caurina) genome: divergence with the barred owl (Strix varia) and characterization of light-associated genes. Genome Biol Evol. 2017;9:2522–45.
Article
CAS
PubMed
PubMed Central
Google Scholar
Mueller JC, Kuhl H, Boerno S, Tella JL, Carrete M, Kempenaers B. Evolution of genomic variation in the burrowing owl in response to recent colonization of urban areas. Proc Biol Sci. 2018;285:20180206.
Article
PubMed
PubMed Central
Google Scholar
Luo R, Liu B, Xie Y, Li Z, Huang W, Yuan J, et al. SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler. Gigascience. 2012;1:18.
Article
PubMed
PubMed Central
Google Scholar
Kajitani R, Toshimoto K, Noguchi H, Toyoda A, Ogura Y, Okuno M, et al. Efficient de novo assembly of highly heterozygous genomes from whole-genome shotgun short reads. Genome Res. 2014;24:1384–95.
Article
CAS
PubMed
PubMed Central
Google Scholar
Le Duc D, Renaud G, Krishnan A, Almén MS, Huynen L, Prohaska SJ, et al. Kiwi genome provides insights into evolution of a nocturnal lifestyle. Genome Biol. 2015;16:147.
Article
PubMed
PubMed Central
Google Scholar
Ganapathy G, Howard JT, Ward JM, Li J, Li B, Li Y, et al. High-coverage sequencing and annotated assemblies of the budgerigar genome. Gigascience. 2014;3:11.
Article
PubMed
PubMed Central
Google Scholar
Warren WC, Clayton DF, Ellegren H, Arnold AP, Hillier LW, Künstner A, et al. The genome of a songbird. Nature. 2010;464:757–62.
Article
CAS
PubMed
PubMed Central
Google Scholar
Shapiro MD, Kronenberg Z, Li C, Domyan ET, Pan H, Campbell M, et al. Genomic diversity and evolution of the head crest in the rock pigeon. Science. 2013;339:1063–7.
Article
CAS
PubMed
PubMed Central
Google Scholar
International Chicken Genome Sequencing Consortium. Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution. Nature. 2004;432:695–716.
Article
Google Scholar
Yang Z. PAML 4: phylogenetic analysis by maximum likelihood. Mol Biol Evol. 2017;24:1586–91.
Article
Google Scholar
Zhang J, Nielsen R, Yang Z. Evaluation of an improved branch-site likelihood method for detecting positive selection at the molecular level. Mol Biol Evol. 2005;22:2472–9.
Article
CAS
PubMed
Google Scholar
Safran M, Dalah I, Alexander J, Rosen N, Iny Stein T, Shmoish M, et al. GeneCards version 3: the human gene integrator. Database (Oxford). 2010;2010:baq020.
Article
Google Scholar
Engevik K, Aihara E, Matthis A, Montrose M. TFF2, CXCR4 and EGF-R mediated gastric wound repair in vitro in gastric organoids. FASEB J. 2017;31(Suppl 1):1043–8.
Google Scholar
Saada A, Vogel RO, Hoefs SJ, van den Brand MA, Wessels HJ, Willems PH, et al. Mutations in NDUFAF3 (C3ORF60), encoding an NDUFAF4 (C6ORF66)-interacting complex I assembly protein, cause fatal neonatal mitochondrial disease. Am J Hum Genet. 2009;84:718–27.
Article
CAS
PubMed
PubMed Central
Google Scholar
Kersten S, Seydoux J, Peters JM, Gonzalez FJ, Desvergne B, Wahli W. Peroxisome proliferator–activated receptor α mediates the adaptive response to fasting. J Clin Invest. 1999;103:1489–98.
Article
CAS
PubMed
PubMed Central
Google Scholar
Tatarinova TV, Alexandrov NN, Bouck JB, Feldmann KA. GC3 biology in corn, rice, sorghum and other grasses. BMC Genomics. 2010;11:308.
Article
PubMed
PubMed Central
Google Scholar
Borges R, Khan I, Johnson WE, Gilbert MT, Zhang G, Jarvis ED, et al. Gene loss, adaptive evolution and the co-evolution of plumage coloration genes with opsins in birds. BMC Genomics. 2015;16:751.
Article
PubMed
PubMed Central
Google Scholar
Yu G, Zhang Y, Xiang Y, Jiang P, Chen Z, Lee W, et al. Cell migration-promoting and apoptosis-inhibiting activities of Bm-TFF2 require distinct structure basis. Biochem Biophys Res Commun. 2010;400:724–8.
Article
CAS
PubMed
Google Scholar
Crane NJ, Brown TS, Evans KN, Hawksworth JS, Hussey S, Tadaki DK, et al. Monitoring the healing of combat wounds using Raman spectroscopic mapping. Wound Repair Regen. 2010;18:409–16.
Article
PubMed
Google Scholar
Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, et al. Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet. 2000;25:25–9.
Article
CAS
PubMed
PubMed Central
Google Scholar
Zhao H, Ru B, Teeling EC, Faulkes CG, Zhang S, Rossiter SJ. Rhodopsin molecular evolution in mammals inhabiting low light environments. PLoS One. 2009;4:e8326.
Article
PubMed
PubMed Central
Google Scholar
Dawson PA, Hubbert M, Haywood J, Craddock AL, Zerangue N, Christian WV, et al. The heteromeric organic solute transporter α-β, Ostα-Ostβ, is an ileal basolateral bile acid transporter. J Biol Chem. 2005;280:6960–8.
Article
CAS
PubMed
Google Scholar
Govindarajan K, MacSharry J, Casey PG, Shanahan F, Joyce SA, Gahan CG. Unconjugated bile acids influence expression of circadian genes: a potential mechanism for microbe-host crosstalk. PLoS One. 2016;11:e0167319.
Article
PubMed
PubMed Central
Google Scholar
Zhang F, Duan Y, Xi L, Wei M, Shi A, Zhou Y, et al. The influences of cholecystectomy on the circadian rhythms of bile acids as well as the enterohepatic transporters and enzymes systems in mice. Chronobiol Int. 2018;35:673–90.
Article
CAS
PubMed
Google Scholar
Khan I, Yang Z, Maldonado E, Li C, Zhang G, Gilbert MT, et al. Olfactory receptor subgenomes linked with broad ecological adaptations in Sauropsida. Mol Biol Evol. 2015;32:2832–43.
Article
CAS
PubMed
Google Scholar
Hasin-Brumshtein Y, Lancet D, Olender T. Human olfaction: from genomic variation to phenotypic diversity. Trends Genet. 2009;25:178–84.
Article
CAS
PubMed
Google Scholar
Emery NJ. Cognitive ornithology: the evolution of avian intelligence. Philos Trans R Soc Lond Ser B Biol Sci. 2006;361:23–43.
Article
Google Scholar
Brawand D, Soumillon M, Necsulea A, Julien P, Csárdi G, Harrigan P, et al. The evolution of gene expression levels in mammalian organs. Nature. 2011;478:343–8.
Article
CAS
PubMed
Google Scholar
Alkan C, Sajjadian S, Eichler EE. Limitations of next-generation genome sequence assembly. Nat Methods. 2011;8:61–5.
Article
CAS
PubMed
Google Scholar
Korlach J, Gedman G, Kingan SB, Chin CS, Howard JT, Audet JN, et al. De novo PacBio long-read and phased avian genome assemblies correct and add to reference genes generated with intermediate and short reads. Gigascience. 2017;6:1–6.
Article
CAS
PubMed
PubMed Central
Google Scholar
Li H. Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM. ArXiv. 2013;1303:3997.
Google Scholar
Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, et al. The sequence alignment/map format and SAMtools. Bioinformatics. 2009;25:2078–9.
Article
PubMed
PubMed Central
Google Scholar
Benson G. Tandem repeats finder: a program to analyze DNA sequences. Nucleic Acids Res. 1999;27:573–80.
Article
CAS
PubMed
PubMed Central
Google Scholar
Jurka J, Kapitonov VV, Pavlicek A, Klonowski P, Kohany O, Walichiewicz J. Repbase update, a database of eukaryotic repetitive elements. Cytogenet Genome Res. 2005;110:462–7.
Article
CAS
PubMed
Google Scholar
Bedell JA, Korf I, Gish W. MaskerAid: a performance enhancement to RepeatMasker. Bioinformatics. 2000;16:1040–1.
Article
CAS
PubMed
Google Scholar
RMBlast. http://www.repeatmasker.org/RMBlast.html. Accessed 16 Aug 2016.
Abrusán G, Grundmann N, DeMester L, Makalowski W. TEclass--a tool for automated classification of unknown eukaryotic transposable elements. Bioinformatics. 2009;25:1329–30.
Article
PubMed
Google Scholar
Camacho C, Coulouris G, Avagyan V, Ma N, Papadopoulos J, Bealer K, et al. BLAST+: architecture and applications. BMC Bioinformatics. 2009;10:421.
Article
PubMed
PubMed Central
Google Scholar
She R, Chu JS, Wang K, Pei J, Chen N. GenBlastA: enabling BLAST to identify homologous gene sequences. Genome Res. 2009;19:143–9.
Article
CAS
PubMed
PubMed Central
Google Scholar
Slater GS, Birney E. Automated generation of heuristics for biological sequence comparison. BMC Bioinformatics. 2005;6:31.
Article
PubMed
PubMed Central
Google Scholar
Stanke M, Keller O, Gunduz I, Hayes A, Waack S, Morgenstern B. AUGUSTUS: ab initio prediction of alternative transcripts. Nucleic Acids Res. 2006;34:W435–9.
Article
CAS
PubMed
PubMed Central
Google Scholar
Grabherr MG, Haas BJ, Yassour M, Levin JZ, Thompson DA, Amit I, et al. Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nat Biotechnol. 2011;29:644–52.
Article
CAS
PubMed
PubMed Central
Google Scholar
Simão FA, Waterhouse RM, Ioannidis P, Kriventseva EV, Zdobnov EM. BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs. Bioinformatics. 2015;31:3210–2.
Article
PubMed
Google Scholar
Li L, Stoeckert CJ Jr, Roos DS. OrthoMCL: identification of ortholog groups for eukaryotic genomes. Genome Res. 2003;13:2178–89.
Article
CAS
PubMed
PubMed Central
Google Scholar
Edgar RC. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 2004;32:1792–7.
Article
CAS
PubMed
PubMed Central
Google Scholar
Capella-Gutiérrez S, Silla-Martínez JM, Gabaldón T. trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses. Bioinformatics. 2009;25:1972–3.
Article
PubMed
PubMed Central
Google Scholar
Kumar S, Stecher G, Tamura K. MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets. Mol Biol Evol. 2016;33:1870–4.
Article
CAS
PubMed
PubMed Central
Google Scholar
Hedges SB, Dudley J, Kumar S. TimeTree: a public knowledge-base of divergence times among organisms. Bioinformatics. 2006;22:2971–2.
Article
CAS
PubMed
Google Scholar
Han MV, Thomas GW, Lugo-Martinez J, Hahn MW. Estimating gene gain and loss rates in the presence of error in genome assembly and annotation using CAFE 3. Mol Biol Evol. 2013;30:1987–97.
Article
CAS
PubMed
Google Scholar
Löytynoja A, Goldman N. An algorithm for progressive multiple alignment of sequences with insertions. Proc Natl Acad Sci U S A. 2005;102:10557–62.
Article
PubMed
PubMed Central
Google Scholar
Weber JA, Aldana R, Gallagher BD, Edwards JS. Sentieon DNA pipeline for variant detection—software-only solution, over 20× faster than GATK 3.3 with identical results. PeerJ PrePrints. 2016;4:e1672v2.
Google Scholar
Kim S, Cho YS, Kim HM, Chung O, Kim H, Jho S, et al. Comparison of carnivore, omnivore, and herbivore mammalian genomes with a new leopard assembly. Genome Biol. 2016;17:211.
Article
PubMed
PubMed Central
Google Scholar
Storey JD. A direct approach to false discovery rates. J R Stat Soc Series B Stat Methodol. 2002;64:479–98.
Article
Google Scholar
Aken BL, Achuthan P, Akanni W, Amode MR, Bernsdorff F, Bhai J, et al. Ensembl 2017. Nucleic Acids Res. 2017;45:D635–42.
Article
CAS
PubMed
Google Scholar
Moriya Y, Itoh M, Okuda S, Yoshizawa AC, Kanehisa M. KAAS: an automatic genome annotation and pathway reconstruction server. Nucleic Acids Res. 2007;35:W182–5.
Article
PubMed
PubMed Central
Google Scholar
The UniProt Consortium. UniProt: the universal protein knowledgebase. Nucleic Acids Res. 2017;45:D158–69.
Article
Google Scholar
Haas BJ, Papanicolaou A, Yassour M, Grabherr M, Blood PD, Bowden J, et al. De novo transcript sequence reconstruction from RNA-seq using the trinity platform for reference generation and analysis. Nat Protoc. 2013;8:1494–512.
Article
CAS
PubMed
Google Scholar
Kim D, Pertea G, Trapnell C, Pimentel H, Kelley R, Salzberg SL. TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions. Genome Biol. 2013;14:R36.
Article
PubMed
PubMed Central
Google Scholar
Anders S, Pyl PT, Huber W. HTSeq–a Python framework to work with high-throughput sequencing data. Bioinformatics. 2015;31:166–9.
Article
CAS
PubMed
Google Scholar
Robinson MD, Oshlack A. A scaling normalization method for differential expression analysis of RNA-seq data. Genome Biol. 2010;11:R25.
Article
PubMed
PubMed Central
Google Scholar
Robinson MD, McCarthy DJ, Smyth GK. edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics. 2010;26:139–40.
Article
CAS
PubMed
Google Scholar
McCarthy DJ, Smyth GK. Testing significance relative to a fold-change threshold is a TREAT. Bioinformatics. 2009;25:765–71.
Article
CAS
PubMed
PubMed Central
Google Scholar
Ritchie ME, Phipson B, Wu D, Hu Y, Law CW, Shi W, et al. limma powers differential expression analyses for RNA-sequencing and microarray studies. Nucleic Acids Res. 2015;43:e47.
Article
PubMed
PubMed Central
Google Scholar
Steiger SS, Kuryshev VY, Stensmyr MC, Kempenaers B, Mueller JC. A comparison of reptilian and avian olfactory receptor gene repertoires: species-specific expansion of group gamma genes in birds. BMC Genomics. 2009;10:446.
Article
PubMed
PubMed Central
Google Scholar
Li W, Godzik A. Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences. Bioinformatics. 2006;22:1658–9.
Article
CAS
PubMed
Google Scholar
Finn RD, Coggill P, Eberhardt RY, Eddy SR, Mistry J, Mitchell AL, et al. The Pfam protein families database: towards a more sustainable future. Nucleic Acids Res. 2016;44:D279–85.
Article
CAS
PubMed
Google Scholar
Mistry J, Finn RD, Eddy SR, Bateman A, Punta M. Challenges in homology search: HMMER3 and convergent evolution of coiled-coil regions. Nucleic Acids Res. 2013;41:e121.
Article
CAS
PubMed
PubMed Central
Google Scholar
Niimura Y. On the origin and evolution of vertebrate olfactory receptor genes: comparative genome analysis among 23 chordate species. Genome Biol Evol. 2009;1:34–44.
Article
PubMed
PubMed Central
Google Scholar
Chenna R, Sugawara H, Koike T, Lopez R, Gibson TJ, Higgins DG, et al. Multiple sequence alignment with the Clustal series of programs. Nucleic Acids Res. 2009;31:3497–500.
Article
Google Scholar
Niimura Y, Nei M. Evolution of olfactory receptor genes in the human genome. Proc Natl Acad Sci U S A. 2003;100:12235–40.
Article
CAS
PubMed
PubMed Central
Google Scholar
Newman T, Trask BJ. Complex evolution of 7E olfactory receptor genes in segmental duplications. Genome Res. 2003;13:781–93.
Article
CAS
PubMed
PubMed Central
Google Scholar
Shannon CE. The mathematical theory of communication. Bell Syst Tech J. 1948;27:379–423.
Article
Google Scholar
Hall TA. BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symp Ser. 1999;41:95–8.
CAS
Google Scholar
Carbon S, Ireland A, Mungall CJ, Shu S, Marshall B, Lewis S. AmiGO: online access to ontology and annotation data. Bioinformatics. 2009;25:288–9.
Article
CAS
PubMed
Google Scholar
Cho YS, Jun J, Kim JA, Kim HM, Chung O, Kang SG, et al. Birds of prey genome. Sequence Read Archive. 2019. https://www.ncbi.nlm.nih.gov/bioproject/PRJNA431699.