{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,15]],"date-time":"2026-06-15T10:36:04Z","timestamp":1781519764607,"version":"3.54.1"},"reference-count":119,"publisher":"Elsevier BV","issue":"6","license":[{"start":{"date-parts":[[2022,11,1]],"date-time":"2022-11-01T00:00:00Z","timestamp":1667260800000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/tdm\/userlicense\/1.0\/"},{"start":{"date-parts":[[2022,11,1]],"date-time":"2022-11-01T00:00:00Z","timestamp":1667260800000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/legal\/tdmrep-license"},{"start":{"date-parts":[[2022,11,4]],"date-time":"2022-11-04T00:00:00Z","timestamp":1667520000000},"content-version":"vor","delay-in-days":3,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc-nd\/4.0\/"}],"content-domain":{"domain":["elsevier.com","sciencedirect.com"],"crossmark-restriction":true},"short-container-title":["Genomics"],"published-print":{"date-parts":[[2022,11]]},"DOI":"10.1016\/j.ygeno.2022.110518","type":"journal-article","created":{"date-parts":[[2022,11,5]],"date-time":"2022-11-05T19:51:57Z","timestamp":1667677917000},"page":"110518","update-policy":"https:\/\/doi.org\/10.1016\/elsevier_cm_policy","source":"Crossref","is-referenced-by-count":15,"title":["Chromosome-level genome assembly of the Muscovy duck provides insight into fatty liver susceptibility"],"prefix":"10.1016","volume":"114","author":[{"given":"Ming-Min","family":"Xu","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Li-Hong","family":"Gu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Wan-Yue","family":"Lv","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sheng-Chang","family":"Duan","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lian-Wei","family":"Li","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yuan","family":"Du","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Li-Zhi","family":"Lu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tao","family":"Zeng","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zhuo-Cheng","family":"Hou","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zhanshan Sam","family":"Ma","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Wei","family":"Chen","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Adeniyi C.","family":"Adeola","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jian-Lin","family":"Han","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tie-Shan","family":"Xu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yang","family":"Dong","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ya-Ping","family":"Zhang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Min-Sheng","family":"Peng","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"78","reference":[{"key":"10.1016\/j.ygeno.2022.110518_bb0005","doi-asserted-by":"crossref","first-page":"633","DOI":"10.1079\/WPS200575","article-title":"Welfare of ducks in European duck husbandry systems","volume":"61","author":"Rodenburg","year":"2019","journal-title":"World's Poult. Sci. J."},{"key":"10.1016\/j.ygeno.2022.110518_bb0010","doi-asserted-by":"crossref","first-page":"915","DOI":"10.1016\/j.jas.2005.01.009","article-title":"An exploratory osteological study of the muscovy duck (Cairina moschata) (Aves: Anatidae) with implications for neotropical archaeology","volume":"32","author":"Stahl","year":"2005","journal-title":"J. Archaeol. Sci."},{"key":"10.1016\/j.ygeno.2022.110518_bb0015","series-title":"The Cambridge World History of Food","first-page":"559","article-title":"Muscovy ducks","author":"Gade","year":"2000"},{"key":"10.1016\/j.ygeno.2022.110518_bb0020","doi-asserted-by":"crossref","first-page":"453","DOI":"10.2307\/3670998","article-title":"Ecological studies of Muscovy ducks in Mexico","volume":"29","author":"Woodyard","year":"1984","journal-title":"Southwest. Nat."},{"key":"10.1016\/j.ygeno.2022.110518_bb0025","doi-asserted-by":"crossref","DOI":"10.5252\/anthropozoologica2019v54a13","article-title":"The modern ontological natures of the Cairina moschata (Linnaeus, 1758) duck. Cases from Per\u00fa, the northern hemisphere, and digital communities","volume":"54","author":"Gamboa","year":"2019","journal-title":"Anthropozoologica"},{"key":"10.1016\/j.ygeno.2022.110518_bb0030","series-title":"The Handbook of South American Archaeology","first-page":"121","article-title":"Animal domestication in South America","author":"Stahl","year":"2008"},{"key":"10.1016\/j.ygeno.2022.110518_bb0035","doi-asserted-by":"crossref","first-page":"229","DOI":"10.3923\/ijps.2012.229.236","article-title":"Amino acid and fatty acid profiles of Peking and Muscovy duck meat","volume":"11","author":"Aronal","year":"2012","journal-title":"Int. J. Poult. Sci."},{"key":"10.1016\/j.ygeno.2022.110518_bb0040","doi-asserted-by":"crossref","first-page":"483","DOI":"10.1007\/s12192-015-0573-4","article-title":"De novo assembly and characterization of Muscovy duck liver transcriptome and analysis of differentially regulated genes in response to heat stress","volume":"20","author":"Zeng","year":"2015","journal-title":"Cell Stress Chaperones"},{"key":"10.1016\/j.ygeno.2022.110518_bb0045","doi-asserted-by":"crossref","first-page":"931","DOI":"10.1017\/S0043933913000937","article-title":"Characterisation of the local Muscovy duck in Nigeria and its potential for egg and meat production","volume":"69","author":"Yakubu","year":"2013","journal-title":"World's Poult. Sci. J."},{"key":"10.1016\/j.ygeno.2022.110518_bb0050","doi-asserted-by":"crossref","first-page":"565","DOI":"10.1080\/00439339.2021.1921668","article-title":"A review on the productive potential of the Muscovy duck","volume":"77","author":"Arias-Sosa","year":"2021","journal-title":"World\u2019s Poult. Sci. J."},{"key":"10.1016\/j.ygeno.2022.110518_bb0055","doi-asserted-by":"crossref","first-page":"134","DOI":"10.1007\/s11515-012-1206-2","article-title":"Avian metabolism: its control and evolution","volume":"8","author":"Scanes","year":"2012","journal-title":"Front. Biol."},{"key":"10.1016\/j.ygeno.2022.110518_bb0060","doi-asserted-by":"crossref","first-page":"331","DOI":"10.1007\/BF02537194","article-title":"Plasma lipoproteins and liver lipids in two breeds of geese with different susceptibility to hepatic steatosis: changes induced by development and force-feeding","volume":"26","author":"Hermier","year":"1991","journal-title":"Lipids"},{"key":"10.1016\/j.ygeno.2022.110518_bb0065","doi-asserted-by":"crossref","first-page":"581","DOI":"10.1186\/s12864-021-07897-4","article-title":"A chromosome-level genome assembly of Cairina moschata and comparative genomic analyses","volume":"22","author":"Jiang","year":"2021","journal-title":"BMC Genomics"},{"key":"10.1016\/j.ygeno.2022.110518_bb0070","doi-asserted-by":"crossref","first-page":"13","DOI":"10.1186\/s12864-018-5415-1","article-title":"RNA-seq analysis of hepatic gene expression of common Pekin, Muscovy, mule and hinny ducks fed ad libitum or overfed","volume":"20","author":"H\u00e9rault","year":"2019","journal-title":"BMC Genomics"},{"key":"10.1016\/j.ygeno.2022.110518_bb0075","doi-asserted-by":"crossref","first-page":"390","DOI":"10.1016\/j.cbpa.2006.07.014","article-title":"Does overfeeding enhance genotype effects on liver ability for lipogenesis and lipid secretion in ducks?","volume":"145","author":"Chartrin","year":"2006","journal-title":"Comp. Biochem. Physiol. A Mol. Integr. Physiol."},{"key":"10.1016\/j.ygeno.2022.110518_bb0080","doi-asserted-by":"crossref","first-page":"663","DOI":"10.1016\/S1096-4959(03)00146-5","article-title":"Differential channelling of liver lipids in relation to susceptibility to hepatic steatosis in two species of ducks","volume":"135","author":"Hermier","year":"2003","journal-title":"Comp. Biochem. Physiol. B Biochem. Mol. Biol."},{"key":"10.1016\/j.ygeno.2022.110518_bb0085","first-page":"403","article-title":"The animal health and welfare consequences of foie gras production","volume":"54","author":"Skippon","year":"2013","journal-title":"Can. Vet. J."},{"key":"10.1016\/j.ygeno.2022.110518_bb0090","doi-asserted-by":"crossref","first-page":"11","DOI":"10.1038\/nrgastro.2017.109","article-title":"Global burden of NAFLD and NASH: trends, predictions, risk factors and prevention","volume":"15","author":"Younossi","year":"2018","journal-title":"Nat. Rev. Gastroenterol. Hepatol."},{"key":"10.1016\/j.ygeno.2022.110518_bb0095","doi-asserted-by":"crossref","first-page":"73","DOI":"10.1002\/hep.28431","article-title":"Global epidemiology of nonalcoholic fatty liver disease-Meta-analytic assessment of prevalence, incidence, and outcomes","volume":"64","author":"Younossi","year":"2016","journal-title":"Hepatology"},{"key":"10.1016\/j.ygeno.2022.110518_bb0100","doi-asserted-by":"crossref","first-page":"656","DOI":"10.1038\/nrgastro.2013.183","article-title":"NAFLD, NASH and liver cancer","volume":"10","author":"Michelotti","year":"2013","journal-title":"Nat. Rev. Gastroenterol. Hepatol."},{"key":"10.1016\/j.ygeno.2022.110518_bb0105","doi-asserted-by":"crossref","first-page":"2188","DOI":"10.1002\/hep.26986","article-title":"Nonalcoholic steatohepatitis is the most rapidly growing indication for liver transplantation in patients with hepatocellular carcinoma in the U.S","volume":"59","author":"Wong","year":"2014","journal-title":"Hepatology"},{"key":"10.1016\/j.ygeno.2022.110518_bb0110","doi-asserted-by":"crossref","first-page":"1148","DOI":"10.1016\/j.jhep.2014.11.034","article-title":"Evidence of NAFLD progression from steatosis to fibrosing-steatohepatitis using paired biopsies: implications for prognosis and clinical management","volume":"62","author":"McPherson","year":"2015","journal-title":"J. Hepatol."},{"key":"10.1016\/j.ygeno.2022.110518_bb0115","doi-asserted-by":"crossref","first-page":"1","DOI":"10.2141\/jpsa.0130090","volume":"51","author":"Islam","year":"2014","journal-title":"J. Poult. Sci."},{"key":"10.1016\/j.ygeno.2022.110518_bb0120","doi-asserted-by":"crossref","first-page":"giaa142","DOI":"10.1093\/gigascience\/giaa142","article-title":"A new duck genome reveals conserved and convergently evolved chromosome architectures of birds and mammals","volume":"10","author":"Li","year":"2021","journal-title":"Gigascience"},{"key":"10.1016\/j.ygeno.2022.110518_bb0125","article-title":"Highly conserved non-coding sequences are associated with vertebrate development","volume":"3","author":"Woolfe","year":"2005","journal-title":"PLoS Biol."},{"key":"10.1016\/j.ygeno.2022.110518_bb0130","doi-asserted-by":"crossref","first-page":"476","DOI":"10.1038\/nature10530","article-title":"A high-resolution map of human evolutionary constraint using 29 mammals","volume":"478","author":"Lindblad-Toh","year":"2011","journal-title":"Nature"},{"key":"10.1016\/j.ygeno.2022.110518_bb0135","doi-asserted-by":"crossref","DOI":"10.1016\/j.celrep.2021.110280","article-title":"Convergent and lineage-specific genomic differences in limb regulatory elements in limbless reptile lineages","volume":"38","author":"Roscito","year":"2022","journal-title":"Cell Rep."},{"key":"10.1016\/j.ygeno.2022.110518_bb0140","doi-asserted-by":"crossref","first-page":"526","DOI":"10.1016\/j.ydbio.2008.10.044","article-title":"Systematic human\/zebrafish comparative identification of cis-regulatory activity around vertebrate developmental transcription factor genes","volume":"327","author":"Navratilova","year":"2009","journal-title":"Dev. Biol."},{"key":"10.1016\/j.ygeno.2022.110518_bb0145","doi-asserted-by":"crossref","first-page":"158","DOI":"10.1038\/ng.2007.55","article-title":"Ultraconservation identifies a small subset of extremely constrained developmental enhancers","volume":"40","author":"Visel","year":"2008","journal-title":"Nat. Genet."},{"key":"10.1016\/j.ygeno.2022.110518_bb0150","doi-asserted-by":"crossref","first-page":"4737","DOI":"10.1038\/s41467-018-07122-z","article-title":"Phenotype loss is associated with widespread divergence of the gene regulatory landscape in evolution","volume":"9","author":"Roscito","year":"2018","journal-title":"Nat. Commun."},{"key":"10.1016\/j.ygeno.2022.110518_bb0155","doi-asserted-by":"crossref","first-page":"1362","DOI":"10.1016\/j.cell.2021.01.047","article-title":"African lungfish genome sheds light on the vertebrate water-to-land transition","volume":"184","author":"Wang","year":"2021","journal-title":"Cell"},{"key":"10.1016\/j.ygeno.2022.110518_bb0160","doi-asserted-by":"crossref","first-page":"74","DOI":"10.1126\/science.aat7244","article-title":"Convergent regulatory evolution and loss of flight in paleognathous birds","volume":"364","author":"Sackton","year":"2019","journal-title":"Science"},{"key":"10.1016\/j.ygeno.2022.110518_bb0165","doi-asserted-by":"crossref","first-page":"115","DOI":"10.1007\/s00795-007-0364-9","article-title":"Adiponectin receptors, with special focus on the role of the third receptor, T-cadherin, in vascular disease","volume":"40","author":"Takeuchi","year":"2007","journal-title":"Med. Mol. Morphol."},{"key":"10.1016\/j.ygeno.2022.110518_bb0170","doi-asserted-by":"crossref","first-page":"402","DOI":"10.1002\/humu.21652","article-title":"CDH13 gene coding T-cadherin influences variations in plasma adiponectin levels in the Japanese population","volume":"33","author":"Morisaki","year":"2012","journal-title":"Hum. Mutat."},{"key":"10.1016\/j.ygeno.2022.110518_bb0175","doi-asserted-by":"crossref","first-page":"4955","DOI":"10.1093\/hmg\/ddq423","article-title":"Genome-wide association study for adiponectin levels in Filipino women identifies CDH13 and a novel uncommon haplotype at KNG1-ADIPOQ","volume":"19","author":"Wu","year":"2010","journal-title":"Hum. Mol. Genet."},{"key":"10.1016\/j.ygeno.2022.110518_bb0180","doi-asserted-by":"crossref","first-page":"2417","DOI":"10.2337\/db10-1321","article-title":"A genome-wide association study reveals a quantitative trait locus of adiponectin on CDH13 that predicts cardiometabolic outcomes","volume":"60","author":"Chung","year":"2011","journal-title":"Diabetes"},{"key":"10.1016\/j.ygeno.2022.110518_bb0185","doi-asserted-by":"crossref","first-page":"1288","DOI":"10.1038\/nm788","article-title":"Adiponectin stimulates glucose utilization and fatty-acid oxidation by activating AMP-activated protein kinase","volume":"8","author":"Yamauchi","year":"2002","journal-title":"Nat. Med."},{"key":"10.1016\/j.ygeno.2022.110518_bb0190","doi-asserted-by":"crossref","first-page":"2562","DOI":"10.2337\/db05-1322","article-title":"Adiponectin increases fatty acid oxidation in skeletal muscle cells by sequential activation of AMP-activated protein kinase, p38 mitogen-activated protein kinase, and peroxisome proliferator-activated receptor alpha","volume":"55","author":"Yoon","year":"2006","journal-title":"Diabetes"},{"key":"10.1016\/j.ygeno.2022.110518_bb0195","doi-asserted-by":"crossref","first-page":"E253","DOI":"10.1152\/ajpendo.00331.2016","article-title":"Overexpression of PGC-1\u03b1 increases peroxisomal activity and mitochondrial fatty acid oxidation in human primary myotubes","volume":"312","author":"Huang","year":"2017","journal-title":"Am. J. Physiol. Endocrinol. Metab."},{"key":"10.1016\/j.ygeno.2022.110518_bb0200","doi-asserted-by":"crossref","first-page":"139","DOI":"10.1006\/mgme.2000.3055","article-title":"Genomics of the human carnitine acyltransferase genes","volume":"71","author":"van der Leij","year":"2000","journal-title":"Mol. Genet. Metab."},{"key":"10.1016\/j.ygeno.2022.110518_bb0205","doi-asserted-by":"crossref","first-page":"195","DOI":"10.1016\/j.bbrc.2013.11.036","article-title":"Identification of acyl-CoA synthetases involved in the mammalian sphingosine 1-phosphate metabolic pathway","volume":"442","author":"Ohkuni","year":"2013","journal-title":"Biochem. Biophys. Res. Commun."},{"key":"10.1016\/j.ygeno.2022.110518_bb0210","doi-asserted-by":"crossref","first-page":"1293","DOI":"10.1021\/bi801879z","article-title":"The mechanisms of human hotdog-fold thioesterase 2 (hTHEM2) substrate recognition and catalysis illuminated by a structure and function based analysis","volume":"48","author":"Cao","year":"2009","journal-title":"Biochemistry"},{"key":"10.1016\/j.ygeno.2022.110518_bb0215","doi-asserted-by":"crossref","first-page":"527","DOI":"10.1172\/JCI2927","article-title":"Molecular basis of hepatic carnitine palmitoyltransferase I deficiency","volume":"102","author":"L","year":"1998","journal-title":"J. Clin. Invest."},{"key":"10.1016\/j.ygeno.2022.110518_bb0220","doi-asserted-by":"crossref","first-page":"12402","DOI":"10.1021\/bi960785e","article-title":"Medium-long-chain chimeric human Acyl-CoA dehydrogenase: medium-chain enzyme with the active center base arrangement of long-chain Acyl-CoA dehydrogenase","volume":"35","author":"Nandy","year":"1996","journal-title":"Biochemistry"},{"key":"10.1016\/j.ygeno.2022.110518_bb0225","doi-asserted-by":"crossref","first-page":"401","DOI":"10.1016\/S0021-9258(18)51692-6","article-title":"Hormone-sensitive lipase and monoglyceride lipase activities in adipose tissue","volume":"239","author":"Vaughan","year":"1964","journal-title":"J. Biol. Chem."},{"key":"10.1016\/j.ygeno.2022.110518_bb0230","doi-asserted-by":"crossref","first-page":"G852","DOI":"10.1152\/ajpgi.00521.2005","article-title":"Lipid metabolism and liver inflammation. II. Fatty liver disease and fatty acid oxidation","volume":"290","author":"Reddy","year":"2006","journal-title":"Am. J. Physiol. Gastrointest. Liver Physiol."},{"key":"10.1016\/j.ygeno.2022.110518_bb0235","doi-asserted-by":"crossref","first-page":"E11285","DOI":"10.1073\/pnas.1716990115","article-title":"Mechanism by which arylamine N-acetyltransferase 1 ablation causes insulin resistance in mice","volume":"114","author":"Camporez","year":"2017","journal-title":"Proc. Natl. Acad. Sci. U. S. A."},{"key":"10.1016\/j.ygeno.2022.110518_bb0240","doi-asserted-by":"crossref","first-page":"527","DOI":"10.1016\/j.celrep.2016.09.005","article-title":"Nat1 deficiency is associated with mitochondrial dysfunction and exercise intolerance in mice","volume":"17","author":"Chennamsetty","year":"2016","journal-title":"Cell Rep."},{"key":"10.1016\/j.ygeno.2022.110518_bb0245","doi-asserted-by":"crossref","first-page":"343","DOI":"10.1038\/nrgastro.2017.32","article-title":"Lipid droplets and liver disease: from basic biology to clinical implications","volume":"14","author":"Gluchowski","year":"2017","journal-title":"Nat. Rev. Gastroenterol. Hepatol."},{"key":"10.1016\/j.ygeno.2022.110518_bb0250","doi-asserted-by":"crossref","first-page":"1383","DOI":"10.1126\/science.1100747","article-title":"Fat mobilization in adipose tissue is promoted by adipose triglyceride lipase","volume":"306","author":"Zimmermann","year":"2004","journal-title":"Science"},{"key":"10.1016\/j.ygeno.2022.110518_bb0255","doi-asserted-by":"crossref","first-page":"309","DOI":"10.1016\/j.cmet.2006.03.005","article-title":"Adipose triglyceride lipase-mediated lipolysis of cellular fat stores is activated by CGI-58 and defective in Chanarin-Dorfman Syndrome","volume":"3","author":"Lass","year":"2006","journal-title":"Cell Metab."},{"key":"10.1016\/j.ygeno.2022.110518_bb0260","doi-asserted-by":"crossref","first-page":"14229","DOI":"10.1038\/ncomms14229","article-title":"Functional roles of Aves class-specific cis-regulatory elements on macroevolution of bird-specific features","volume":"8","author":"Seki","year":"2017","journal-title":"Nat. Commun."},{"key":"10.1016\/j.ygeno.2022.110518_bb0265","doi-asserted-by":"crossref","first-page":"2382","DOI":"10.3382\/ps.2009-00208","article-title":"Gene expression and protein content in relation to intramuscular fat content in Muscovy and Pekin ducks","volume":"88","author":"Saez","year":"2009","journal-title":"Poult. Sci."},{"key":"10.1016\/j.ygeno.2022.110518_bb0270","doi-asserted-by":"crossref","first-page":"746","DOI":"10.1126\/science.1158997","article-title":"Is genetic evolution predictable?","volume":"323","author":"Stern","year":"2009","journal-title":"Science"},{"key":"10.1016\/j.ygeno.2022.110518_bb0275","doi-asserted-by":"crossref","DOI":"10.2307\/3677171","article-title":"Fuel supply and metabolic constraints in migrating birds","volume":"29","author":"Jenni","year":"1998","journal-title":"J. Avian Biol."},{"key":"10.1016\/j.ygeno.2022.110518_bb0280","series-title":"Some Aspects in the Ecology of Muscovy Ducks in Mexico","author":"Woodyard","year":"1982"},{"key":"10.1016\/j.ygeno.2022.110518_bb0285","doi-asserted-by":"crossref","first-page":"176","DOI":"10.1016\/j.gexplo.2009.02.008","article-title":"Distinguishing breeding populations of mallards (Anas platyrhynchos) using trace elements","volume":"102","author":"Kaimal","year":"2009","journal-title":"J. Geochem. Explor."},{"key":"10.1016\/j.ygeno.2022.110518_bb0290","doi-asserted-by":"crossref","first-page":"2648","DOI":"10.1038\/s41467-018-04868-4","article-title":"An intercross population study reveals genes associated with body size and plumage color in ducks","volume":"9","author":"Zhou","year":"2018","journal-title":"Nat. Commun."},{"key":"10.1016\/j.ygeno.2022.110518_bb0295","doi-asserted-by":"crossref","first-page":"267","DOI":"10.1016\/S0044-8486(98)00413-X","article-title":"Comparative study of digestive enzymes in fish with different nutritional habits. Proteolytic and amylase activities","volume":"170","author":"Hidalgo","year":"1999","journal-title":"Aquaculture"},{"issue":"1980","key":"10.1016\/j.ygeno.2022.110518_bb0300","doi-asserted-by":"crossref","first-page":"1217","DOI":"10.1051\/rnd:19800713","article-title":"The adaptation of digestive enzymes to the diet: its physiological significance","volume":"20","author":"Corring","year":"1980","journal-title":"Reprod. Nutr. Dev."},{"key":"10.1016\/j.ygeno.2022.110518_bb0305","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1016\/j.anifeedsci.2003.09.007","article-title":"Carbohydrate fermentation in the avian ceca: a review","volume":"113","author":"J\u00f3zefiak","year":"2004","journal-title":"Anim. Feed Sci. Technol."},{"key":"10.1016\/j.ygeno.2022.110518_bb0310","doi-asserted-by":"crossref","first-page":"2756","DOI":"10.1038\/s41467-019-10682-3","article-title":"Convergent genomic signatures of flight loss in birds suggest a switch of main fuel","volume":"10","author":"Pan","year":"2019","journal-title":"Nat. Commun."},{"key":"10.1016\/j.ygeno.2022.110518_bb0315","first-page":"351","article-title":"Re-evaluation of fatty acid metabolism-related gene expression in nonalcoholic fatty liver disease","volume":"20","author":"Kohjima","year":"2007","journal-title":"Int. J. Mol. Med."},{"key":"10.1016\/j.ygeno.2022.110518_bb0320","doi-asserted-by":"crossref","first-page":"31","DOI":"10.2337\/db21-0363","article-title":"Hepatic CPT1A facilitates liver\u2013adipose cross talk via induction of FGF21 in mice","volume":"71","author":"Sun","year":"2022","journal-title":"Diabetes"},{"key":"10.1016\/j.ygeno.2022.110518_bb0325","doi-asserted-by":"crossref","first-page":"122","DOI":"10.1002\/hep.24338","article-title":"Deficiency of liver adipose triglyceride lipase in mice causes progressive hepatic steatosis","volume":"54","author":"Wu","year":"2011","journal-title":"Hepatology"},{"key":"10.1016\/j.ygeno.2022.110518_bb0330","doi-asserted-by":"crossref","first-page":"44597","DOI":"10.1038\/srep44597","article-title":"FOXO transcription factors protect against the diet-induced fatty liver disease","volume":"7","author":"Pan","year":"2017","journal-title":"Sci. Rep."},{"key":"10.1016\/j.ygeno.2022.110518_bb0335","doi-asserted-by":"crossref","first-page":"1213","DOI":"10.1038\/nmeth.2688","article-title":"Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position","volume":"10","author":"Buenrostro","year":"2013","journal-title":"Nat. Methods"},{"key":"10.1016\/j.ygeno.2022.110518_bb0340","doi-asserted-by":"crossref","first-page":"1896","DOI":"10.1016\/j.ygeno.2018.12.013","article-title":"Hybrid assembly of ultra-long nanopore reads augmented with 10x-genomics contigs: demonstrated with a human genome","volume":"111","author":"Ma","year":"2019","journal-title":"Genomics"},{"key":"10.1016\/j.ygeno.2022.110518_bb0345","doi-asserted-by":"crossref","first-page":"31900","DOI":"10.1038\/srep31900","article-title":"DBG2OLC: efficient assembly of large genomes using long erroneous reads of the third generation sequencing technologies","volume":"6","author":"Ye","year":"2016","journal-title":"Sci. Rep."},{"key":"10.1016\/j.ygeno.2022.110518_bb0350","doi-asserted-by":"crossref","DOI":"10.7717\/peerj.2016","article-title":"Sparc: a sparsity-based consensus algorithm for long erroneous sequencing reads","volume":"4","author":"Ye","year":"2016","journal-title":"PeerJ"},{"key":"10.1016\/j.ygeno.2022.110518_bb0355","doi-asserted-by":"crossref","first-page":"2253","DOI":"10.1093\/bioinformatics\/btz891","article-title":"NextPolish: a fast and efficient genome polishing tool for long-read assembly","volume":"36","author":"Hu","year":"2020","journal-title":"Bioinformatics"},{"key":"10.1016\/j.ygeno.2022.110518_bb0360","doi-asserted-by":"crossref","first-page":"99","DOI":"10.1016\/j.cels.2015.07.012","article-title":"Juicebox provides a visualization system for hi-C contact maps with unlimited zoom","volume":"3","author":"Durand","year":"2016","journal-title":"Cell. Syst."},{"key":"10.1016\/j.ygeno.2022.110518_bb0365","doi-asserted-by":"crossref","first-page":"92","DOI":"10.1126\/science.aal3327","article-title":"De novo assembly of the Aedes aegypti genome using Hi-C yields chromosome-length scaffolds","volume":"356","author":"Dudchenko","year":"2017","journal-title":"Science"},{"key":"10.1016\/j.ygeno.2022.110518_bb0370","doi-asserted-by":"crossref","DOI":"10.1002\/0471250953.bi0410s25","article-title":"Using RepeatMasker to identify repetitive elements in genomic sequences","volume":"25","author":"Tarailo-Graovac","year":"2009","journal-title":"Curr. Protoc. Bioinformatics"},{"key":"10.1016\/j.ygeno.2022.110518_bb0375","doi-asserted-by":"crossref","first-page":"11","DOI":"10.1186\/s13100-015-0041-9","article-title":"Repbase update, a database of repetitive elements in eukaryotic genomes","volume":"6","author":"Bao","year":"2015","journal-title":"Mob. DNA"},{"key":"10.1016\/j.ygeno.2022.110518_bb0380","doi-asserted-by":"crossref","first-page":"W265","DOI":"10.1093\/nar\/gkm286","article-title":"LTR_FINDER: an efficient tool for the prediction of full-length LTR retrotransposons","volume":"35","author":"Xu","year":"2007","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.ygeno.2022.110518_bb0385","doi-asserted-by":"crossref","first-page":"R7","DOI":"10.1186\/gb-2008-9-1-r7","article-title":"Automated eukaryotic gene structure annotation using EVidenceModeler and the program to assemble spliced alignments","volume":"9","author":"Haas","year":"2008","journal-title":"Genome Biol."},{"key":"10.1016\/j.ygeno.2022.110518_bb0390","doi-asserted-by":"crossref","first-page":"2114","DOI":"10.1093\/bioinformatics\/btu170","article-title":"Trimmomatic: a flexible trimmer for Illumina sequence data","volume":"30","author":"Bolger","year":"2014","journal-title":"Bioinformatics"},{"key":"10.1016\/j.ygeno.2022.110518_bb0395","doi-asserted-by":"crossref","first-page":"R36","DOI":"10.1186\/gb-2013-14-4-r36","article-title":"TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions","volume":"14","author":"Kim","year":"2013","journal-title":"Genome Biol."},{"key":"10.1016\/j.ygeno.2022.110518_bb0400","doi-asserted-by":"crossref","first-page":"562","DOI":"10.1038\/nprot.2012.016","article-title":"Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and cufflinks","volume":"7","author":"Trapnell","year":"2012","journal-title":"Nat. Protoc."},{"key":"10.1016\/j.ygeno.2022.110518_bb0405","doi-asserted-by":"crossref","first-page":"644","DOI":"10.1038\/nbt.1883","article-title":"Full-length transcriptome assembly from RNA-Seq data without a reference genome","volume":"29","author":"Grabherr","year":"2011","journal-title":"Nat. Biotechnol."},{"key":"10.1016\/j.ygeno.2022.110518_bb0410","doi-asserted-by":"crossref","first-page":"637","DOI":"10.1093\/bioinformatics\/btn013","article-title":"Using native and syntenically mapped cDNA alignments to improve de novo gene finding","volume":"24","author":"Stanke","year":"2008","journal-title":"Bioinformatics"},{"key":"10.1016\/j.ygeno.2022.110518_bb0415","doi-asserted-by":"crossref","first-page":"547","DOI":"10.1101\/gr.10.4.547","article-title":"Using GeneWise in the Drosophila annotation experiment","volume":"10","author":"Birney","year":"2000","journal-title":"Genome Res."},{"key":"10.1016\/j.ygeno.2022.110518_bb0420","doi-asserted-by":"crossref","first-page":"365","DOI":"10.1093\/nar\/gkg095","article-title":"The SWISS-PROT protein knowledgebase and its supplement TrEMBL in 2003","volume":"31","author":"Boeckmann","year":"2003","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.ygeno.2022.110518_bb0425","doi-asserted-by":"crossref","first-page":"27","DOI":"10.1093\/nar\/28.1.27","article-title":"KEGG: Kyoto encyclopedia of genes and genomes","volume":"28","author":"Kanehisa","year":"2000","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.ygeno.2022.110518_bb0430","doi-asserted-by":"crossref","first-page":"847","DOI":"10.1093\/bioinformatics\/17.9.847","article-title":"InterProScan--an integration platform for the signature-recognition methods in InterPro","volume":"17","author":"Zdobnov","year":"2001","journal-title":"Bioinformatics"},{"key":"10.1016\/j.ygeno.2022.110518_bb0435","doi-asserted-by":"crossref","first-page":"955","DOI":"10.1093\/nar\/25.5.955","article-title":"tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence","volume":"25","author":"Lowe","year":"1997","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.ygeno.2022.110518_bb0440","doi-asserted-by":"crossref","first-page":"D226","DOI":"10.1093\/nar\/gks1005","article-title":"Rfam 11.0: 10 years of RNA families","volume":"41","author":"Burge","year":"2013","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.ygeno.2022.110518_bb0445","doi-asserted-by":"crossref","first-page":"2933","DOI":"10.1093\/bioinformatics\/btt509","article-title":"Infernal 1.1: 100-fold faster RNA homology searches","volume":"29","author":"Nawrocki","year":"2013","journal-title":"Bioinformatics"},{"key":"10.1016\/j.ygeno.2022.110518_bb0450","doi-asserted-by":"crossref","first-page":"3210","DOI":"10.1093\/bioinformatics\/btv351","article-title":"BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs","volume":"31","author":"Sim\u00e3o","year":"2015","journal-title":"Bioinformatics"},{"key":"10.1016\/j.ygeno.2022.110518_bb0455","doi-asserted-by":"crossref","first-page":"R12","DOI":"10.1186\/gb-2004-5-2-r12","article-title":"Versatile and open software for comparing large genomes","volume":"5","author":"Kurtz","year":"2004","journal-title":"Genome Biol."},{"key":"10.1016\/j.ygeno.2022.110518_bb0460","doi-asserted-by":"crossref","first-page":"giaa114","DOI":"10.1093\/gigascience\/giaa114","article-title":"Pacific biosciences assembly with Hi-C mapping generates an improved, chromosome-level goose genome","volume":"9","author":"Li","year":"2020","journal-title":"Gigascience"},{"key":"10.1016\/j.ygeno.2022.110518_bb0465","article-title":"Genomic analyses of unveil helmeted guinea fowl (Numida meleagris) domestication in West Africa","volume":"13","author":"Shen","year":"2021","journal-title":"Genome Biol. Evol."},{"key":"10.1016\/j.ygeno.2022.110518_bb0470","doi-asserted-by":"crossref","first-page":"155","DOI":"10.1007\/978-1-62703-646-7_10","article-title":"Phylogeny-aware alignment with PRANK","volume":"1079","author":"L\u00f6ytynoja","year":"2014","journal-title":"Methods Mol. Biol."},{"key":"10.1016\/j.ygeno.2022.110518_bb0475","doi-asserted-by":"crossref","first-page":"540","DOI":"10.1093\/oxfordjournals.molbev.a026334","article-title":"Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis","volume":"17","author":"Castresana","year":"2000","journal-title":"Mol. Biol. Evol."},{"key":"10.1016\/j.ygeno.2022.110518_bb0480","doi-asserted-by":"crossref","first-page":"1312","DOI":"10.1093\/bioinformatics\/btu033","article-title":"RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies","volume":"30","author":"Stamatakis","year":"2014","journal-title":"Bioinformatics"},{"key":"10.1016\/j.ygeno.2022.110518_bb0485","doi-asserted-by":"crossref","first-page":"238","DOI":"10.1186\/s13059-019-1832-y","article-title":"OrthoFinder: phylogenetic orthology inference for comparative genomics","volume":"20","author":"Emms","year":"2019","journal-title":"Genome Biol."},{"key":"10.1016\/j.ygeno.2022.110518_bb0490","doi-asserted-by":"crossref","first-page":"301","DOI":"10.1093\/bioinformatics\/19.2.301","article-title":"r8s: inferring absolute rates of molecular evolution and divergence times in the absence of a molecular clock","volume":"19","author":"Sanderson","year":"2003","journal-title":"Bioinformatics"},{"key":"10.1016\/j.ygeno.2022.110518_bb0495","doi-asserted-by":"crossref","first-page":"1987","DOI":"10.1093\/molbev\/mst100","article-title":"Estimating gene gain and loss rates in the presence of error in genome assembly and annotation using CAFE 3","volume":"30","author":"Han","year":"2013","journal-title":"Mol. Biol. Evol."},{"key":"10.1016\/j.ygeno.2022.110518_bb0500","doi-asserted-by":"crossref","first-page":"284","DOI":"10.1089\/omi.2011.0118","article-title":"clusterProfiler: an R package for comparing biological themes among gene clusters","volume":"16","author":"Yu","year":"2012","journal-title":"OMICS"},{"key":"10.1016\/j.ygeno.2022.110518_bb0505","doi-asserted-by":"crossref","first-page":"eaav6202","DOI":"10.1126\/science.aav6202","article-title":"Large-scale ruminant genome sequencing provides insights into their evolution and distinct traits","volume":"364","author":"Chen","year":"2019","journal-title":"Science"},{"key":"10.1016\/j.ygeno.2022.110518_bb0510","doi-asserted-by":"crossref","first-page":"1586","DOI":"10.1093\/molbev\/msm088","article-title":"PAML 4: phylogenetic analysis by maximum likelihood","volume":"24","author":"Yang","year":"2007","journal-title":"Mol. Biol. Evol."},{"key":"10.1016\/j.ygeno.2022.110518_bb0515","first-page":"D498","article-title":"The reactome pathway knowledgebase","volume":"48","author":"Jassal","year":"2020","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.ygeno.2022.110518_bb0520","doi-asserted-by":"crossref","first-page":"487","DOI":"10.1101\/gr.113985.110","article-title":"Adaptive seeds tame genomic sequence comparison","volume":"21","author":"Kielbasa","year":"2011","journal-title":"Genome Res."},{"key":"10.1016\/j.ygeno.2022.110518_bb0525","doi-asserted-by":"crossref","first-page":"708","DOI":"10.1101\/gr.1933104","article-title":"Aligning multiple genomic sequences with the threaded blockset aligner","volume":"14","author":"Blanchette","year":"2004","journal-title":"Genome Res."},{"key":"10.1016\/j.ygeno.2022.110518_bb0530","doi-asserted-by":"crossref","first-page":"41","DOI":"10.1093\/bib\/bbq072","article-title":"PHAST and RPHAST: phylogenetic analysis with space\/time models","volume":"12","author":"Hubisz","year":"2011","journal-title":"Brief. Bioinform."},{"key":"10.1016\/j.ygeno.2022.110518_bb0535","doi-asserted-by":"crossref","first-page":"1034","DOI":"10.1101\/gr.3715005","article-title":"Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes","volume":"15","author":"Siepel","year":"2005","journal-title":"Genome Res."},{"key":"10.1016\/j.ygeno.2022.110518_bb0540","doi-asserted-by":"crossref","first-page":"1086","DOI":"10.1093\/molbev\/msz049","article-title":"Bayesian detection of convergent rate changes of conserved noncoding elements on phylogenetic trees","volume":"36","author":"Hu","year":"2019","journal-title":"Mol. Biol. Evol."},{"key":"10.1016\/j.ygeno.2022.110518_bb0545","doi-asserted-by":"crossref","first-page":"97","DOI":"10.1101\/gr.789803","article-title":"AVID: a global alignment program","volume":"13","author":"Bray","year":"2003","journal-title":"Genome Res."},{"key":"10.1016\/j.ygeno.2022.110518_bb0550","doi-asserted-by":"crossref","first-page":"W273","DOI":"10.1093\/nar\/gkh458","article-title":"VISTA: computational tools for comparative genomics","volume":"32","author":"Frazer","year":"2004","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.ygeno.2022.110518_bb0555","doi-asserted-by":"crossref","first-page":"10","DOI":"10.14806\/ej.17.1.200","article-title":"Cutadapt removes adapter sequences from high-throughput sequencing reads","volume":"17","author":"Martin","year":"2011","journal-title":"EMBnet.journal"},{"key":"10.1016\/j.ygeno.2022.110518_bb0560","doi-asserted-by":"crossref","first-page":"357","DOI":"10.1038\/nmeth.1923","article-title":"Fast gapped-read alignment with bowtie 2","volume":"9","author":"Langmead","year":"2012","journal-title":"Nat. Methods"},{"key":"10.1016\/j.ygeno.2022.110518_bb0565","doi-asserted-by":"crossref","first-page":"giab008","DOI":"10.1093\/gigascience\/giab008","article-title":"Twelve years of SAMtools and BCFtools","volume":"10","author":"Danecek","year":"2021","journal-title":"Gigascience"},{"key":"10.1016\/j.ygeno.2022.110518_bb0570","doi-asserted-by":"crossref","first-page":"R137","DOI":"10.1186\/gb-2008-9-9-r137","article-title":"Model-based analysis of ChIP-Seq (MACS)","volume":"9","author":"Zhang","year":"2008","journal-title":"Genome Biol."},{"key":"10.1016\/j.ygeno.2022.110518_bb0575","doi-asserted-by":"crossref","first-page":"259","DOI":"10.1186\/s13059-015-0831-x","article-title":"HiC-pro: an optimized and flexible pipeline for Hi-C data processing","volume":"16","author":"Servant","year":"2015","journal-title":"Genome Biol."},{"key":"10.1016\/j.ygeno.2022.110518_bb0580","doi-asserted-by":"crossref","first-page":"189","DOI":"10.1038\/s41467-017-02525-w","article-title":"High-resolution TADs reveal DNA sequences underlying genome organization in flies","volume":"9","author":"Ram\u00edrez","year":"2018","journal-title":"Nat. Commun."},{"key":"10.1016\/j.ygeno.2022.110518_bb0585","doi-asserted-by":"crossref","first-page":"991","DOI":"10.1038\/s41596-019-0273-0","article-title":"Identifying statistically significant chromatin contacts from Hi-C data with FitHiC2","volume":"15","author":"Kaul","year":"2020","journal-title":"Nat. Protoc."},{"key":"10.1016\/j.ygeno.2022.110518_bb0590","doi-asserted-by":"crossref","first-page":"559","DOI":"10.1186\/1471-2105-9-559","article-title":"WGCNA: an R package for weighted correlation network analysis","volume":"9","author":"Langfelder","year":"2008","journal-title":"BMC Bioinform."},{"key":"10.1016\/j.ygeno.2022.110518_bb0595","doi-asserted-by":"crossref","first-page":"2498","DOI":"10.1101\/gr.1239303","article-title":"Cytoscape: a software environment for integrated models of biomolecular interaction networks","volume":"13","author":"Shannon","year":"2003","journal-title":"Genome Res."}],"container-title":["Genomics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S0888754322002634?httpAccept=text\/xml","content-type":"text\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S0888754322002634?httpAccept=text\/plain","content-type":"text\/plain","content-version":"vor","intended-application":"text-mining"}],"deposited":{"date-parts":[[2025,10,11]],"date-time":"2025-10-11T06:42:15Z","timestamp":1760164935000},"score":1,"resource":{"primary":{"URL":"https:\/\/linkinghub.elsevier.com\/retrieve\/pii\/S0888754322002634"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2022,11]]},"references-count":119,"journal-issue":{"issue":"6","published-print":{"date-parts":[[2022,11]]}},"alternative-id":["S0888754322002634"],"URL":"https:\/\/doi.org\/10.1016\/j.ygeno.2022.110518","relation":{},"ISSN":["0888-7543"],"issn-type":[{"value":"0888-7543","type":"print"}],"subject":[],"published":{"date-parts":[[2022,11]]},"assertion":[{"value":"Elsevier","name":"publisher","label":"This article is maintained by"},{"value":"Chromosome-level genome assembly of the Muscovy duck provides insight into fatty liver susceptibility","name":"articletitle","label":"Article Title"},{"value":"Genomics","name":"journaltitle","label":"Journal Title"},{"value":"https:\/\/doi.org\/10.1016\/j.ygeno.2022.110518","name":"articlelink","label":"CrossRef DOI link to publisher maintained version"},{"value":"article","name":"content_type","label":"Content Type"},{"value":"\u00a9 2022 Published by Elsevier Inc.","name":"copyright","label":"Copyright"}],"article-number":"110518"}}