{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,8]],"date-time":"2026-04-08T23:14:05Z","timestamp":1775690045304,"version":"3.50.1"},"reference-count":86,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2023,2,1]],"date-time":"2023-02-01T00:00:00Z","timestamp":1675209600000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"},{"start":{"date-parts":[[2023,2,1]],"date-time":"2023-02-01T00:00:00Z","timestamp":1675209600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"}],"funder":[{"name":"National Key Research and Development Program of China","award":["2018YFD0900200"],"award-info":[{"award-number":["2018YFD0900200"]}]},{"name":"the Funamental Research Funds for the Central University of China","award":["2662020SCPY002"],"award-info":[{"award-number":["2662020SCPY002"]}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["32172962"],"award-info":[{"award-number":["32172962"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["31872579"],"award-info":[{"award-number":["31872579"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["BMC Biol"],"abstract":"<jats:title>Abstract<\/jats:title><jats:sec>\n                <jats:title>Background<\/jats:title>\n                <jats:p>The loach (<jats:italic>Misgurnus anguillicaudatus<\/jats:italic>), the most widely distributed species of the family Cobitidae, displays a mud-dwelling behavior and intestinal air-breathing, inhabiting the muddy bottom of extensive freshwater habitats. However, lack of high-quality reference genome seriously limits the interpretation of the genetic basis of specialized adaptations of the loach to the adverse environments including but not limited to the extreme water temperature, hypoxic and noxious mud environment.<\/jats:p>\n              <\/jats:sec><jats:sec>\n                <jats:title>Results<\/jats:title>\n                <jats:p>This study generated a 1.10-Gb high-quality, chromosome-anchored genome assembly, with a contig N50 of 3.83 Mb. Multiple comparative genomic analyses found that proto-oncogene c-Fos (<jats:italic>fos<\/jats:italic>), a regulator of bone development, is positively selected in loach. Knockout of <jats:italic>fos<\/jats:italic> (ID: Mis0086400.1) led to severe osteopetrosis and movement difficulties, combined with the comparison results of bone mineral density, supporting the hypothesis that <jats:italic>fos<\/jats:italic> is associated with loach mud-dwelling behavior. Based on genomic and transcriptomic analysis, we identified two key elements involved in the intestinal air-breathing of loach: a novel gene (ID: mis0158000.1) and heat shock protein beta-1 (<jats:italic>hspb1<\/jats:italic>). The flavin-containing monooxygenase 5 (<jats:italic>fmo5<\/jats:italic>) genes, central to xenobiotic metabolism, undergone expansion in loach and were identified as differentially expressed genes in a drug stress trial. A <jats:italic>fmo5<\/jats:italic><jats:sup><jats:italic>\u2212\/\u2212<\/jats:italic><\/jats:sup> (ID: Mis0185930.1) loach displayed liver and intestine injury, indicating the importance of this gene to the adaptation of the loach to the noxious mud.<\/jats:p>\n              <\/jats:sec><jats:sec>\n                <jats:title>Conclusions<\/jats:title>\n                <jats:p>Our work provides valuable insights into the genetic basis of biological adaptation to adverse environments.<\/jats:p>\n              <\/jats:sec>","DOI":"10.1186\/s12915-023-01517-1","type":"journal-article","created":{"date-parts":[[2023,2,1]],"date-time":"2023-02-01T21:02:46Z","timestamp":1675285366000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":15,"title":["The chromosome-level genome and key genes associated with mud-dwelling behavior and adaptations of hypoxia and noxious environments in loach (Misgurnus anguillicaudatus)"],"prefix":"10.1186","volume":"21","author":[{"given":"Bing","family":"Sun","sequence":"first","affiliation":[]},{"given":"Yuwei","family":"Huang","sequence":"additional","affiliation":[]},{"given":"L. Filipe C.","family":"Castro","sequence":"additional","affiliation":[]},{"given":"Su","family":"Yang","sequence":"additional","affiliation":[]},{"given":"Songqian","family":"Huang","sequence":"additional","affiliation":[]},{"given":"Wu","family":"Jin","sequence":"additional","affiliation":[]},{"given":"He","family":"Zhou","sequence":"additional","affiliation":[]},{"given":"Shigeho","family":"Ijiri","sequence":"additional","affiliation":[]},{"given":"Yi","family":"Luo","sequence":"additional","affiliation":[]},{"given":"Jian","family":"Gao","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9676-5838","authenticated-orcid":false,"given":"Xiaojuan","family":"Cao","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2023,2,1]]},"reference":[{"key":"1517_CR1","doi-asserted-by":"publisher","first-page":"47","DOI":"10.1146\/annurev-animal-030117-014821","volume":"6","author":"V Ravi","year":"2018","unstructured":"Ravi V, Venkatesh B. The divergent genomes of teleosts. Annu Rev Anim Biosci. 2018;6:47\u201368.","journal-title":"Annu Rev Anim Biosci"},{"key":"1517_CR2","doi-asserted-by":"publisher","first-page":"823","DOI":"10.1038\/s41559-019-0864-8","volume":"3","author":"K Wang","year":"2019","unstructured":"Wang K, Shen Y, Yang Y, Gan X, Liu G, Hu K, et al. Morphology and genome of a snailfish from the Mariana Trench provide insights into deep-sea adaptation. Nat Ecol Evol. 2019;3:823\u201333.","journal-title":"Nat Ecol Evol"},{"key":"1517_CR3","doi-asserted-by":"publisher","first-page":"304","DOI":"10.1016\/j.aquaculture.2014.02.022","volume":"426-427","author":"J Gao","year":"2014","unstructured":"Gao J, Koshio S, Wang WM, Li Y, Huang SQ, Cao XJ. Effects of dietary phospholipid levels on growth performance, fatty acid composition and antioxidant responses of Dojo loach Misgurnus anguillicaudatus larvae. Aquaculture. 2014;426-427:304\u20139.","journal-title":"Aquaculture."},{"key":"1517_CR4","first-page":"45","volume":"21","author":"J Wang","year":"2016","unstructured":"Wang J. Research on cave dwelling behavior ecology of loach. J Shanghai Agricult. 2016;21:45.","journal-title":"J Shanghai Agricult"},{"key":"1517_CR5","doi-asserted-by":"publisher","first-page":"680","DOI":"10.1016\/j.acthis.2018.08.013","volume":"120","author":"YK Ip","year":"2018","unstructured":"Ip YK, Chew SF. Air-breathing and excretory nitrogen metabolism in fishes. Acta Histochem. 2018;120:680\u201390.","journal-title":"Acta Histochem"},{"key":"1517_CR6","doi-asserted-by":"publisher","first-page":"185","DOI":"10.1007\/s10641-007-9188-7","volume":"81","author":"Y Fujimoto","year":"2008","unstructured":"Fujimoto Y, Ouchi Y, Hakuba T, Chiba H, Iwata M. Influence of modern irrigation, drainage system and water management on spawning migration of mud loach, Misgurnus anguillicaudatus C. Environ Biol Fishes. 2008;81:185\u201394.","journal-title":"Environ Biol Fishes"},{"key":"1517_CR7","volume-title":"RCA III, Effects of sediment on the aquatic environment","author":"JM Castro","year":"1995","unstructured":"Castro JM, Reckendorf F. RCA III, Effects of sediment on the aquatic environment. Washington: Natural Resources Conservation Service; 1995."},{"key":"1517_CR8","doi-asserted-by":"publisher","first-page":"141","DOI":"10.1016\/j.ibiod.2017.03.020","volume":"128","author":"Y Du","year":"2017","unstructured":"Du Y, Ma T, Xiao C, Liu YJ, Chen LZ, Yu HT. Water-rock interaction during the diagenesis of mud and its prospect in hydrogeology. Int Biodeter Biodegr. 2017;128:141\u20137.","journal-title":"Int Biodeter Biodegr"},{"key":"1517_CR9","doi-asserted-by":"publisher","first-page":"1362","DOI":"10.1016\/j.cell.2021.01.047","volume":"184","author":"K Wang","year":"2021","unstructured":"Wang K, Wang J, Zhu C, Yang L, Wang W. African lungfish genome sheds light on the vertebrate water-to-land transition. Cell. 2021;184:1362\u201376.","journal-title":"Cell."},{"key":"1517_CR10","doi-asserted-by":"publisher","first-page":"521","DOI":"10.1007\/s10126-016-9713-9","volume":"18","author":"S Huang","year":"2016","unstructured":"Huang S, Cao X, Tian X. Transcriptomic Analysis of Compromise between air-breathing and nutrient uptake of posterior intestine in loach (Misgurnus anguillicaudatus), an air-breathing fish. Marine Biotechnol. 2016;18:521\u201333.","journal-title":"Marine Biotechnol"},{"key":"1517_CR11","doi-asserted-by":"publisher","first-page":"89","DOI":"10.1016\/j.margen.2016.06.002","volume":"29","author":"Y Jiang","year":"2016","unstructured":"Jiang Y, Feng S, Xu J, Zhang S, Li S, Sun X, et al. Comparative transcriptome analysis between aquatic and aerial breathing organs of Channa argus to reveal the genetic basis underlying bimodal respiration. Mar Genomics. 2016;29:89\u201396.","journal-title":"Mar Genomics"},{"key":"1517_CR12","doi-asserted-by":"publisher","first-page":"11928","DOI":"10.3390\/ijms222111928","volume":"22","author":"B Sun","year":"2021","unstructured":"Sun B, Huang S, Huang L, Yang L, Gao J, Cao X. Fibronectin 1B gene plays an important role in loach barbel air-breathing. Int J Mol Sci. 2021;22:11928.","journal-title":"Int J Mol Sci"},{"key":"1517_CR13","doi-asserted-by":"publisher","first-page":"39","DOI":"10.1016\/j.cbpb.2016.07.006","volume":"202","author":"W Luo","year":"2016","unstructured":"Luo W, Liang X, Huang S, Cao X. Molecular cloning, expression analysis and miRNA prediction of vascular endothelial growth factor A (VEGFAa and VEGFAb) in pond loach Misgurnus anguillicaudatus, an air-breathing fish. Comp Biochem Physiol B Biochem Mol Biol. 2016;202:39\u201347.","journal-title":"Comp Biochem Physiol B Biochem Mol Biol"},{"key":"1517_CR14","doi-asserted-by":"publisher","first-page":"65","DOI":"10.1007\/s10142-021-00822-8","volume":"22","author":"S Huang","year":"2022","unstructured":"Huang S, Yang L, Zhang L, Sun B, Gao J, Chen Z, et al. Endogenic upregulations of HIF\/VEGF signaling pathway genes promote air breathing organ angiogenesis in bimodal respiration fish. Funct Integr Genomics. 2022;22:65\u201376.","journal-title":"Funct Integr Genomics"},{"key":"1517_CR15","doi-asserted-by":"publisher","first-page":"336","DOI":"10.1016\/j.chemosphere.2011.04.006","volume":"84","author":"B Zheng","year":"2011","unstructured":"Zheng B, Zhao X, Liu L, Li Z, Lei K, Zhang L, et al. Effects of hydrodynamics on the distribution of trace persistent organic pollutants and macrobenthic communities in Bohai Bay. Chemosphere. 2011;84:336\u201341.","journal-title":"Chemosphere."},{"key":"1517_CR16","doi-asserted-by":"publisher","first-page":"13685","DOI":"10.1007\/s11356-014-3161-8","volume":"21","author":"X Cousin","year":"2014","unstructured":"Cousin X, Cachot J. PAHs and fish-exposure monitoring and adverse effects--from molecular to individual level. Environ Sci Pollut Res Int. 2014;21:13685\u20138.","journal-title":"Environ Sci Pollut Res Int"},{"key":"1517_CR17","first-page":"62","volume":"35","author":"BH Liu","year":"2013","unstructured":"Liu BH, Shi YJ, Yuan JY, Hu XS, Zhang H, Li ZY, et al. Estimation of genomic characteristics by analyzing k-mer frequency in de novo genome projects. Quant Biol. 2013;35:62\u20137.","journal-title":"Quant Biol"},{"key":"1517_CR18","doi-asserted-by":"publisher","first-page":"31","DOI":"10.1093\/bioinformatics\/btt310","volume":"30","author":"R Chikhi","year":"2014","unstructured":"Chikhi R, Medvedev P. Informed and automated k-mer size selection for genome assembly. Bioinformatics. 2014;30:31\u20137.","journal-title":"Bioinformatics."},{"key":"1517_CR19","doi-asserted-by":"publisher","first-page":"1027","DOI":"10.1111\/1755-0998.13021","volume":"19","author":"X Yang","year":"2019","unstructured":"Yang X, Liu H, Ma Z, Zou Y, Zou M, Mao Y, et al. Chromosome-level genome assembly of Triplophysa tibetana, a fish adapted to the harsh high-altitude environment of the Tibetan Plateau. Mol Ecol Resour. 2019;19:1027\u201336.","journal-title":"Mol Ecol Resour"},{"key":"1517_CR20","first-page":"1027","volume":"19","author":"Y Deng","year":"2021","unstructured":"Deng Y, Meng M, Fang J, Jiang H, Sun N, Lv W, et al. Genome of the butterfly hillstream loach provides insights into adaptations to torrential mountain stream life. Mol Ecol Resour. 2021;19:1027\u201336.","journal-title":"Mol Ecol Resour"},{"key":"1517_CR21","doi-asserted-by":"publisher","first-page":"625","DOI":"10.1038\/ng.3280","volume":"47","author":"Y Wang","year":"2015","unstructured":"Wang Y, Lu Y, Zhang Y, Ning Z, Li Y, Zhao Q, et al. The draft genome of the grass carp (Ctenopharyngodon idellus) provides insights into its evolution and vegetarian adaptation. Nat Genet. 2015;47:625\u201331.","journal-title":"Nat Genet"},{"key":"1517_CR22","doi-asserted-by":"publisher","first-page":"3210","DOI":"10.1093\/bioinformatics\/btv351","volume":"31","author":"FA Sim\u00e3o","year":"2015","unstructured":"Sim\u00e3o FA, Waterhouse RM, Ioannidis P, Kriventseva EV, Zdobnov EM. BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs. Bioinformatics. 2015;31:3210\u20132.","journal-title":"Bioinformatics."},{"key":"1517_CR23","doi-asserted-by":"publisher","first-page":"74","DOI":"10.22540\/JFSF-03-074","volume":"3","author":"DA Skelton","year":"2018","unstructured":"Skelton DA, Mavroeidi A. How do muscle and bone strengthening and balance activities (MBSBA) vary across the life course, and are there particular ages where MBSBA are most important? J Frailty Sarcopenia Falls. 2018;3:74\u201384.","journal-title":"J Frailty Sarcopenia Falls"},{"key":"1517_CR24","first-page":"65","volume":"19","author":"A Yuki","year":"2012","unstructured":"Yuki A, Yotani K, Ishido M, Tamaki H, Kasuga N. Relationship between tibia bone and plantaris muscle developments in running and jump trained rat. Janpan. 2012;19:65\u201373.","journal-title":"Janpan."},{"key":"1517_CR25","doi-asserted-by":"publisher","first-page":"271","DOI":"10.1016\/S1546-5098(01)19008-4","volume":"19","author":"MW Westneat","year":"2001","unstructured":"Westneat MW, Wainwright SA. Mechanical design for swimming: muscle, tendon, and bone. Fish Physiol. 2001;19:271\u2013311.","journal-title":"Fish Physiol"},{"key":"1517_CR26","doi-asserted-by":"publisher","first-page":"1740","DOI":"10.1101\/gr.158105.113","volume":"23","author":"M Nikaido","year":"2013","unstructured":"Nikaido M, Noguchi H, Nishihara H, Toyoda A, Suzuki Y, Kajitani R, et al. Coelacanth genomes reveal signatures for evolutionary transition from water to land. Genome Res. 2013;23:1740\u20138.","journal-title":"Genome Res"},{"key":"1517_CR27","doi-asserted-by":"publisher","first-page":"311","DOI":"10.1038\/nature12027","volume":"496","author":"CT Amemiya","year":"2013","unstructured":"Amemiya CT, Alf\u00f6ldi J, Lee AP, Fan S, Philippe H, Maccallum I, et al. The African coelacanth genome provides insights into tetrapod evolution. Nature. 2013;496:311\u20136.","journal-title":"Nature."},{"key":"1517_CR28","doi-asserted-by":"publisher","first-page":"1377","DOI":"10.1016\/j.cell.2021.01.046","volume":"184","author":"X Bi","year":"2021","unstructured":"Bi X, Wang K, Yang L, Pan H, Jiang H, Wei Q, et al. Tracing the genetic footprints of vertebrate landing in non-teleost ray-finned fishes. Cell. 2021;184:1377\u201391.","journal-title":"Cell."},{"key":"1517_CR29","doi-asserted-by":"publisher","first-page":"872","DOI":"10.3390\/ijms9050872","volume":"9","author":"M Toshio","year":"2008","unstructured":"Toshio M, Hiroyuki O. Remarks on muscle contraction mechanism. Int J Mol Sci. 2008;9:872\u2013904.","journal-title":"Int J Mol Sci"},{"key":"1517_CR30","doi-asserted-by":"publisher","first-page":"58","DOI":"10.1126\/science.8316858","volume":"261","author":"I Rayment","year":"1993","unstructured":"Rayment I, Holden HM, Whittaker M, Yohn CB, Lorenz M, Holmes KC, et al. Structure of the actin-myosin complex and its implications for muscle contraction. Science. 1993;261:58\u201365.","journal-title":"Science."},{"key":"1517_CR31","doi-asserted-by":"publisher","first-page":"ii40","DOI":"10.1136\/ard.61.suppl_2.ii40","volume":"61 Suppl 2","author":"EF Wagner","year":"2002","unstructured":"Wagner EF. Functions of AP1 (Fos\/Jun) in bone development. Ann Rheum Dis. 2002;61 Suppl 2:ii40\u20132.","journal-title":"Ann Rheum Dis"},{"key":"1517_CR32","doi-asserted-by":"publisher","first-page":"277","DOI":"10.1002\/bies.950170402","volume":"17","author":"O Jacenko","year":"1995","unstructured":"Jacenko O. c-fos and bone loss: a proto-oncogene regulates osteoclast lineage determination. Bioessays. 1995;17:277\u201381.","journal-title":"Bioessays."},{"key":"1517_CR33","doi-asserted-by":"publisher","first-page":"3994","DOI":"10.1073\/pnas.94.8.3994","volume":"94","author":"H Watanabe","year":"1997","unstructured":"Watanabe H, Saitoh K, Kameda T, Murakami M, Niikura Y, Okazaki S, et al. Chondrocytes as a specific target of ectopic Fos expression in early development. Proc Natl Acad Sci U S A. 1997;94:3994\u20139.","journal-title":"Proc Natl Acad Sci U S A"},{"key":"1517_CR34","doi-asserted-by":"publisher","first-page":"577","DOI":"10.1016\/0092-8674(92)90592-Z","volume":"71","author":"RS Johnson","year":"1992","unstructured":"Johnson RS, Spiegelman BM, Papaioannou V. Pleiotropic effects of a null mutation in the c-fos proto-oncogene. Cell. 1992;71:577\u201386.","journal-title":"Cell."},{"key":"1517_CR35","doi-asserted-by":"publisher","first-page":"741","DOI":"10.1038\/360741a0","volume":"360","author":"ZQ Wang","year":"1992","unstructured":"Wang ZQ, Ovitt C, Grigoriadis AE, M\u00f6hle-Steinlein U, R\u00fcther U, Wagner EF. Bone and haematopoietic defects in mice lacking c-fos. Nature. 1992;360:741\u20135.","journal-title":"Nature."},{"key":"1517_CR36","doi-asserted-by":"publisher","first-page":"2437","DOI":"10.1002\/j.1460-2075.1991.tb07783.x","volume":"10","author":"ZQ Wang","year":"1991","unstructured":"Wang ZQ, Grigoriadis AE, M\u00f6hle-Steinlein U, Wagner EF. A novel target cell for c-fos-induced oncogenesis: development of chondrogenic tumours in embryonic stem cell chimeras. EMBO J. 1991;10:2437\u201350.","journal-title":"EMBO J"},{"key":"1517_CR37","first-page":"1294","volume":"10","author":"S Huang","year":"2021","unstructured":"Huang S, Sun B, Huang L, Yang L, Liu C, Zhu J, et al. Comparative transcriptomic analysis of regenerated skins provides insights into cutaneous air-breathing formation in fish. Biology (Basel). 2021;10:1294.","journal-title":"Biology (Basel)"},{"key":"1517_CR38","doi-asserted-by":"publisher","first-page":"148","DOI":"10.1089\/ham.2007.1079","volume":"9","author":"JF Storz","year":"2008","unstructured":"Storz JF, Moriyama H. Mechanisms of hemoglobin adaptation to high altitude hypoxia. High Alt Med Biol. 2008;9:148\u201357.","journal-title":"High Alt Med Biol"},{"key":"1517_CR39","doi-asserted-by":"publisher","first-page":"255","DOI":"10.1016\/S1546-5098(08)00006-X","volume":"27","author":"R Wells","year":"2009","unstructured":"Wells R. Chapter 6 Blood-Gas as Transport and hemoglobin function: adaptations for functional and environmental hypoxia. Fish Physiol. 2009;27:255\u201399.","journal-title":"Fish Physiol"},{"key":"1517_CR40","doi-asserted-by":"publisher","first-page":"952","DOI":"10.1186\/s12864-018-5355-9","volume":"19","author":"N Li","year":"2018","unstructured":"Li N, Bao L, Zhou T, Yuan Z, Liu S, Dunham R, et al. Genome sequence of walking catfish (Clarias batrachus) provides insights into terrestrial adaptation. BMC Genomics. 2018;19:952.","journal-title":"BMC Genomics"},{"key":"1517_CR41","doi-asserted-by":"publisher","first-page":"1149","DOI":"10.1007\/s11427-020-1809-0","volume":"64","author":"Y Lei","year":"2021","unstructured":"Lei Y, Yang LD, Jiang HF, Chen J, Sun N, Lv WQ, et al. Recent genome duplications facilitate the phenotypic diversity of Hb repertoire in the Cyprinidae. Sci China Life Sci. 2021;64:1149\u201364.","journal-title":"Sci China Life Sci"},{"key":"1517_CR42","doi-asserted-by":"publisher","first-page":"31845","DOI":"10.1038\/srep31845","volume":"6","author":"W Luo","year":"2016","unstructured":"Luo W, Cao X, Xu X, Huang S, Liu C, Tomljanovic T. Developmental transcriptome analysis and identification of genes involved in formation of intestinal air-breathing function of Dojo loach, Misgurnus anguillicaudatus. Sci Rep. 2016;6:31845.","journal-title":"Sci Rep"},{"key":"1517_CR43","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0149123","volume":"11","author":"S Huang","year":"2016","unstructured":"Huang S, Cao X, Tian X, Wang W. High-throughput sequencing identifies microRNAs from posterior intestine of loach (Misgurnus anguillicaudatus) and their response to intestinal air-breathing inhibition. PLoS One. 2016;11:e0149123.","journal-title":"PLoS One"},{"key":"1517_CR44","doi-asserted-by":"publisher","first-page":"E405","DOI":"10.1152\/ajpendo.90874.2008","volume":"296","author":"JA Williams","year":"2009","unstructured":"Williams JA, Chen X, Sabbatini ME. Small G proteins as key regulators of pancreatic digestive enzyme secretion. Am J Physiol Endocrinol Metab. 2009;296:E405\u201314.","journal-title":"Am J Physiol Endocrinol Metab"},{"key":"1517_CR45","doi-asserted-by":"publisher","first-page":"1545","DOI":"10.1111\/1755-0998.13560","volume":"22","author":"X Hu","year":"2022","unstructured":"Hu X, Jiang Z, Ming Y, Jian J, Jiang S, Zhang D, et al. A chromosomal level genome sequence for Quasipaa spinosa (Dicroglossidae) reveals chromosomal evolution and population diversity. Mol Ecol Resour. 2022;22:1545\u201358.","journal-title":"Mol Ecol Resour"},{"key":"1517_CR46","doi-asserted-by":"publisher","first-page":"231","DOI":"10.1080\/09593330.2011.560615","volume":"32","author":"A Bhatnagar","year":"2011","unstructured":"Bhatnagar A, Vilar VJ, Botelho CM, Boaventura RA. A review of the use of red mud as adsorbent for the removal of toxic pollutants from water and wastewater. Environ Technol. 2011;32:231\u201349.","journal-title":"Environ Technol"},{"key":"1517_CR47","doi-asserted-by":"publisher","first-page":"367","DOI":"10.1016\/j.ygeno.2018.02.011","volume":"111","author":"S Yi","year":"2019","unstructured":"Yi S, Wang W, Zhou X. Genomic evidence for the population genetic differentiation of Misgurnus anguillicaudatus in the Yangtze River basin of China. Genomics. 2019;111:367\u201374.","journal-title":"Genomics."},{"key":"1517_CR48","doi-asserted-by":"publisher","first-page":"1837","DOI":"10.1016\/j.bcp.2013.04.012","volume":"85","author":"Y Uno","year":"2013","unstructured":"Uno Y, Shimizu M, Yamazaki H. Molecular and functional characterization of flavin-containing monooxygenases in cynomolgus macaque. Biochem Pharmacol. 2013;85:1837\u201347.","journal-title":"Biochem Pharmacol"},{"key":"1517_CR49","doi-asserted-by":"publisher","first-page":"357","DOI":"10.1016\/j.pharmthera.2005.01.001","volume":"106","author":"SK Krueger","year":"2005","unstructured":"Krueger SK, Williams DE. Mammalian flavin-containing monooxygenases: structure\/function, genetic polymorphisms and role in drug metabolism. Pharmacol Ther. 2005;106:357\u201387.","journal-title":"Pharmacol Ther"},{"key":"1517_CR50","doi-asserted-by":"publisher","first-page":"1616","DOI":"10.1124\/dmd.113.052613","volume":"41","author":"M Perreault","year":"2013","unstructured":"Perreault M, Gauthier-Landry L, Trottier J, Verreault M, Caron P, Finel M, et al. The Human UDP-glucuronosyltransferase UGT2A1 and UGT2A2 enzymes are highly active in bile acid glucuronidation. Drug Metab Dispos. 2013;41:1616\u201320.","journal-title":"Drug Metab Dispos"},{"key":"1517_CR51","doi-asserted-by":"publisher","first-page":"261","DOI":"10.1016\/0163-7258(89)90122-8","volume":"43","author":"B Burchell","year":"1989","unstructured":"Burchell B, Coughtrie MW. UDP-glucuronosyltransferases. Pharmacol Ther. 1989;43:261\u201389.","journal-title":"Pharmacol Ther"},{"key":"1517_CR52","doi-asserted-by":"publisher","first-page":"237","DOI":"10.1016\/0025-326X(95)00174-L","volume":"31","author":"G Witt","year":"1995","unstructured":"Witt G. Polycyclic aromatic hydrocarbons in water and sediment of the Baltic Sea. Mar Pollut Bull. 1995;31:237\u201348.","journal-title":"Mar Pollut Bull"},{"key":"1517_CR53","doi-asserted-by":"publisher","DOI":"10.1016\/j.chemosphere.2021.129812","volume":"274","author":"N Esfandiar","year":"2021","unstructured":"Esfandiar N, Suri R, McKenzie ER. Simultaneous removal of multiple polycyclic aromatic hydrocarbons (PAHs) from urban stormwater using low-cost agricultural\/industrial byproducts as sorbents. Chemosphere. 2021;274:129812.","journal-title":"Chemosphere."},{"key":"1517_CR54","doi-asserted-by":"publisher","first-page":"265","DOI":"10.1016\/0048-9697(95)05026-4","volume":"181","author":"CD Simpson","year":"1996","unstructured":"Simpson CD, Mosi AA, Cullen WR, Reimer KJ. Composition and distribution of polycyclic aromatic hydrocarbon contamination in surficial marine sediments from Kitimat Harbor, Canada. Sci Total Environ. 1996;181:265\u201378.","journal-title":"Sci Total Environ"},{"key":"1517_CR55","doi-asserted-by":"publisher","first-page":"999","DOI":"10.1016\/S0025-326X(00)00044-8","volume":"40","author":"S Mccready","year":"2000","unstructured":"Mccready S, Slee DJ, Birch GF, Taylor SE. The distribution of polycyclic aromatic hydrocarbons in surficial sediments of Sydney Harbour, Australia. Mar Pollut Bull. 2000;40:999\u20131006.","journal-title":"Mar Pollut Bull"},{"key":"1517_CR56","doi-asserted-by":"publisher","first-page":"914","DOI":"10.1016\/j.envpol.2018.07.048","volume":"242","author":"QS Huang","year":"2018","unstructured":"Huang QS, Liu YY, Chen YJ, Fang C, Chi YL, Zhu HM, et al. New insights into the metabolism and toxicity of bisphenol A on marine fish under long-term exposure. Environ Pollut. 2018;242:914\u201321.","journal-title":"Environ Pollut"},{"key":"1517_CR57","doi-asserted-by":"publisher","first-page":"9","DOI":"10.1016\/0043-1354(92)90105-D","volume":"26","author":"F Beltr\u00e1n","year":"1992","unstructured":"Beltr\u00e1n F, G\u00f3mez-Serrano V, Dur\u00e1n A. Degradation kinetics of p-Nitrophenol ozonation in water. Water Res. 1992;26:9\u201317.","journal-title":"Water Res"},{"key":"1517_CR58","doi-asserted-by":"publisher","first-page":"2383","DOI":"10.1139\/b86-315","volume":"64","author":"RK Antibus","year":"1986","unstructured":"Antibus RK, Kroehler CJ, Linkins AE. The effects of external pH, temperature, and substrate concentration on acid phosphatase activity of ectomycorrhizal fungi. Can J Bot. 1986;64:2383\u20137.","journal-title":"Can J Bot"},{"key":"1517_CR59","doi-asserted-by":"publisher","first-page":"262","DOI":"10.1111\/j.1600-0773.1976.tb03178.x","volume":"39","author":"U Lidman","year":"1976","unstructured":"Lidman U, F\u00f6rlin L, Molander O, Axelson G. Induction of the drug metabolizing system in rainbow trout (Salmo gairdnerii) liver by polychlorinated biphenyls (PCBs). Acta Pharmacol Toxicol (Copenh). 1976;39:262\u201372.","journal-title":"Acta Pharmacol Toxicol (Copenh)"},{"key":"1517_CR60","doi-asserted-by":"publisher","first-page":"644","DOI":"10.1016\/j.fsi.2019.10.044","volume":"95","author":"XB Bai","year":"2019","unstructured":"Bai XB, Shi YH, Tarique I, Vistro WA, Huang YF, Chen H, et al. Multivesicular bodies containing exosomes in immune-related cells of the intestine in zebrafish (Danio rerio): Ultrastructural evidence. Fish Shellfish Immunol. 2019;95:644\u20139.","journal-title":"Fish Shellfish Immunol"},{"key":"1517_CR61","doi-asserted-by":"publisher","first-page":"267","DOI":"10.1016\/j.bcp.2015.05.013","volume":"96","author":"SG Gonzalez Malagon","year":"2015","unstructured":"Gonzalez Malagon SG, Melidoni AN, Hernandez D, Omar BA, Houseman L, Veeravalli S, et al. The phenotype of a knockout mouse identifies flavin-containing monooxygenase 5 (FMO5) as a regulator of metabolic ageing. Biochem Pharmacol. 2015;96:267\u201377.","journal-title":"Biochem Pharmacol"},{"key":"1517_CR62","doi-asserted-by":"publisher","first-page":"1354","DOI":"10.1016\/j.ajpath.2018.02.007","volume":"188","author":"A Tawiah","year":"2018","unstructured":"Tawiah A, Cornick S, Moreau F, Gorman H, Kumar M, Tiwari S, et al. High MUC2 mucin expression and misfolding induce cellular stress, reactive oxygen production, and apoptosis in goblet cells. Am J Pathol. 2018;188:1354\u201373.","journal-title":"Am J Pathol"},{"key":"1517_CR63","doi-asserted-by":"publisher","first-page":"259","DOI":"10.1186\/s13059-015-0831-x","volume":"16","author":"N Servant","year":"2015","unstructured":"Servant N, Varoquaux N, Lajoie BR, Viara E, Chen CJ, Vert JP, et al. HiC-Pro: an optimized and flexible pipeline for Hi-C data processing. Genome Biol. 2015;16:259.","journal-title":"Genome Biol"},{"key":"1517_CR64","doi-asserted-by":"publisher","first-page":"722","DOI":"10.1101\/gr.215087.116","volume":"27","author":"S Koren","year":"2017","unstructured":"Koren S, Walenz BP, Berlin K, Miller JR, Bergman NH, Phillippy AM. Canu: scalable and accurate long-read assembly via adaptive k-mer weighting and repeat separation. Genome Res. 2017;27:722\u201336.","journal-title":"Genome Res"},{"key":"1517_CR65","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0112963","volume":"9","author":"BJ Walker","year":"2014","unstructured":"Walker BJ, Abeel T, Shea T, Priest M, Abouelliel A, Sakthikumar S, et al. Pilon: an integrated tool for comprehensive microbial variant detection and genome assembly improvement. PLoS One. 2014;9:e112963.","journal-title":"PLoS One"},{"key":"1517_CR66","doi-asserted-by":"publisher","first-page":"95","DOI":"10.1016\/j.cels.2016.07.002","volume":"3","author":"NC Durand","year":"2016","unstructured":"Durand NC, Shamim MS, Machol I, Rao SS, Huntley MH, Lander ES, et al. Juicer provides a one-click system for analyzing loop-resolution Hi-C experiments. Cell Syst. 2016;3:95\u20138.","journal-title":"Cell Syst"},{"key":"1517_CR67","doi-asserted-by":"publisher","first-page":"92","DOI":"10.1126\/science.aal3327","volume":"356","author":"O Dudchenko","year":"2017","unstructured":"Dudchenko O, Batra SS, Omer AD, Nyquist SK, Hoeger M, Durand NC, et al. De novo assembly of the Aedes aegypti genome using Hi-C yields chromosome-length scaffolds. Science. 2017;356:92\u20135.","journal-title":"Science."},{"key":"1517_CR68","doi-asserted-by":"publisher","first-page":"573","DOI":"10.1093\/nar\/27.2.573","volume":"27","author":"G Benson","year":"1999","unstructured":"Benson G. Tandem repeats finder: a program to analyze DNA sequences. Nucleic Acids Res. 1999;27:573\u201380.","journal-title":"Nucleic Acids Res"},{"key":"1517_CR69","doi-asserted-by":"publisher","first-page":"462","DOI":"10.1159\/000084979","volume":"110","author":"J Jurka","year":"2005","unstructured":"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\u20137.","journal-title":"Cytogenet Genome Res"},{"key":"1517_CR70","doi-asserted-by":"crossref","unstructured":"Tarailo-Graovac M, Chen N. Using RepeatMasker to identify repetitive elements in genomic sequences. Curr Protoc Bioinformatics. 2009;4:4.10.1\u20134.10.14.","DOI":"10.1002\/0471250953.bi0410s25"},{"key":"1517_CR71","doi-asserted-by":"publisher","first-page":"W435","DOI":"10.1093\/nar\/gkl200","volume":"34","author":"M Stanke","year":"2006","unstructured":"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\u20139.","journal-title":"Nucleic Acids Res"},{"key":"1517_CR72","doi-asserted-by":"publisher","first-page":"78","DOI":"10.1006\/jmbi.1997.0951","volume":"268","author":"C Burge","year":"1997","unstructured":"Burge C, Karlin S. Prediction of complete gene structures in human genomic DNA. J Mol Biol. 1997;268:78\u201394.","journal-title":"J Mol Biol"},{"key":"1517_CR73","doi-asserted-by":"publisher","first-page":"R7","DOI":"10.1186\/gb-2008-9-1-r7","volume":"9","author":"BJ Haas","year":"2008","unstructured":"Haas BJ, Salzberg SL, Zhu W, Pertea M, Allen JE, Orvis J, et al. Automated eukaryotic gene structure annotation using EVidenceModeler and the Program to Assemble Spliced Alignments. Genome Biol. 2008;9:R7.","journal-title":"Genome Biol"},{"key":"1517_CR74","doi-asserted-by":"publisher","first-page":"2178","DOI":"10.1101\/gr.1224503","volume":"13","author":"L Li","year":"2003","unstructured":"Li L, Stoeckert CJ Jr, Roos DS. OrthoMCL: identification of ortholog groups for eukaryotic genomes. Genome Res. 2003;13:2178\u201389.","journal-title":"Genome Res"},{"key":"1517_CR75","doi-asserted-by":"publisher","first-page":"1312","DOI":"10.1093\/bioinformatics\/btu033","volume":"30","author":"A Stamatakis","year":"2014","unstructured":"Stamatakis A. RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics. 2014;30:1312\u20133.","journal-title":"Bioinformatics."},{"key":"1517_CR76","doi-asserted-by":"publisher","first-page":"1586","DOI":"10.1093\/molbev\/msm088","volume":"24","author":"ZH Yang","year":"2007","unstructured":"Yang ZH. PAML 4: phylogenetic analysis by maximum likelihood. Mol Biol Evol. 2007;24:1586\u201391.","journal-title":"Mol Biol Evol"},{"key":"1517_CR77","doi-asserted-by":"publisher","first-page":"E5018","DOI":"10.1073\/pnas.1718603115","volume":"115","author":"T Zhou","year":"2018","unstructured":"Zhou T, Li N, Jin YL, Zeng QF, Prabowo W, Liu Y, et al. Chemokine C-C motif ligand 33 is a key regulator of teleost fish barbel development. Proc Natl Acad Sci U S A. 2018;115:E5018\u201327.","journal-title":"Proc Natl Acad Sci U S A"},{"key":"1517_CR78","doi-asserted-by":"publisher","first-page":"414","DOI":"10.1016\/j.bbrc.2020.08.074","volume":"532","author":"SX Sun","year":"2020","unstructured":"Sun SX, Ren TY, Li X, Cao XJ, Gao J. Polyunsaturated fatty acids synthesized by freshwater fish: A new insight to the roles of elovl2 and elovl5 in vivo. Biochem Biophys Res Commun. 2020;532:414\u20139.","journal-title":"Biochem Biophys Res Commun"},{"key":"1517_CR79","doi-asserted-by":"publisher","first-page":"2011","DOI":"10.1007\/s11033-008-9412-3","volume":"36","author":"JX Liu","year":"2009","unstructured":"Liu JX, Zhai YH, Gui JF. Molecular characterization and expression pattern of AFPIV during embryogenesis in gibel carp (Carassiu auratus gibelio). Mol Biol Rep. 2009;36:2011\u20138.","journal-title":"Mol Biol Rep"},{"key":"1517_CR80","doi-asserted-by":"publisher","first-page":"254","DOI":"10.1111\/j.1439-0264.2009.00932.x","volume":"38","author":"XJ Cao","year":"2009","unstructured":"Cao XJ, Wang WM. Histology and mucin histochemistry of the digestive tract of yellow catfish, Pelteobagrus fulvidraco. Anat Histol Embryol. 2009;38:254\u201361.","journal-title":"Anat Histol Embryol"},{"key":"1517_CR81","doi-asserted-by":"publisher","first-page":"76","DOI":"10.1016\/j.jtherbio.2017.06.006","volume":"69","author":"YY Wang","year":"2017","unstructured":"Wang YY, Sun LX, Zhu JJ, Zhao Y, Wang H, Liu HJ, et al. Epigenetic control of cyp19a1a expression is critical for high temperature induced Nile tilapia masculinization. J Therm Biol. 2017;69:76\u201384.","journal-title":"J Therm Biol"},{"key":"1517_CR82","doi-asserted-by":"publisher","first-page":"22908","DOI":"10.1074\/jbc.271.37.22908","volume":"271","author":"N Ida","year":"1996","unstructured":"Ida N, Hartmann T, Pantel J, Schr\u00f6der J, Zerfass R, F\u00f6rstl H, et al. Analysis of heterogeneous A4 peptides in human cerebrospinal fluid and blood by a newly developed sensitive Western blot assay. J Biol Chem. 1996;271:22908\u201314.","journal-title":"J Biol Chem"},{"key":"1517_CR83","doi-asserted-by":"publisher","first-page":"5280","DOI":"10.1167\/iovs.14-15513","volume":"56","author":"T Van Bergen","year":"2015","unstructured":"Van Bergen T, Spangler R, Marshall D, Hollanders K, Van de Veire S, Vandewalle E, et al. The role of LOX and LOXL2 in the pathogenesis of an experimental model of choroidal neovascularization. Invest Ophthalmol Vis Sci. 2015;56:5280\u20139.","journal-title":"Invest Ophthalmol Vis Sci"},{"key":"1517_CR84","volume-title":"Misgurnus anguillicaudatus Genome sequencing","author":"B Sun","year":"2022","unstructured":"Sun B. Misgurnus anguillicaudatus Genome sequencing. Bethesda: NCBI; 2022. https:\/\/submit.ncbi.nlm.nih.gov\/subs\/wgs\/SUB11149465\/overview."},{"key":"1517_CR85","volume-title":"Posterior intestine sequencing of loach under air exposure","author":"B Sun","year":"2022","unstructured":"Sun B. posterior intestine sequencing of loach under air exposure. Bethesda: NCBI; 2022. https:\/\/submit.ncbi.nlm.nih.gov\/subs\/sra\/SUB11136602\/overview."},{"key":"1517_CR86","volume-title":"Loach liver drug stress","author":"B Sun","year":"2022","unstructured":"Sun B. loach liver drug stress. Bethesda: NCBI; 2022. https:\/\/submit.ncbi.nlm.nih.gov\/subs\/sra\/SUB12389508\/overview."}],"container-title":["BMC Biology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/s12915-023-01517-1.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/article\/10.1186\/s12915-023-01517-1\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/s12915-023-01517-1.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,2,4]],"date-time":"2023-02-04T04:56:11Z","timestamp":1675486571000},"score":1,"resource":{"primary":{"URL":"https:\/\/bmcbiol.biomedcentral.com\/articles\/10.1186\/s12915-023-01517-1"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2023,2,1]]},"references-count":86,"journal-issue":{"issue":"1","published-online":{"date-parts":[[2023,12]]}},"alternative-id":["1517"],"URL":"https:\/\/doi.org\/10.1186\/s12915-023-01517-1","relation":{},"ISSN":["1741-7007"],"issn-type":[{"value":"1741-7007","type":"electronic"}],"subject":[],"published":{"date-parts":[[2023,2,1]]},"assertion":[{"value":"21 September 2022","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"18 January 2023","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"1 February 2023","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"order":1,"name":"Ethics","group":{"name":"EthicsHeading","label":"Declarations"}},{"value":"All experimental protocols in this study were approved by the Animal Experimental Ethical Inspection of Laboratory Animal Center, Huazhong Agricultural University, Wuhan, China (HZAUFI-2021-0032). All efforts were made to minimize the suffering of the fish.","order":2,"name":"Ethics","group":{"name":"EthicsHeading","label":"Ethics approval and consent to participate"}},{"value":"Not applicable.","order":3,"name":"Ethics","group":{"name":"EthicsHeading","label":"Consent for publication"}},{"value":"The authors declare that they have no competing interests.","order":4,"name":"Ethics","group":{"name":"EthicsHeading","label":"Competing interests"}}],"article-number":"18"}}