[1] EISENSTEIN M.Closing in on a complete human genome[J].Nature,2021,590(7847):679-681. [2] WU Z H,GUI S T,QUAN Z W,et al.A precise chloroplast genome of Nelumbo nucifera (Nelumbonaceae) evaluated with Sanger,Illumina MiSeq,and PacBio RS II sequencing platforms:insight into the plastid evolution of basal eudicots[J].BMC Plant Biol,2014,14(1):289. [3] HASIN Y,SELDIN M,LUSIS A.Multi-omics approaches to disease[J].Genome Biol,2017,18(1):83. [4] ZHANG W W,LI F,NIE L.Integrating multiple 'omics’ analysis for microbial biology:application and methodologies[J]. Microbiology,2010,156(2):287-301. [5] 冯 勉,张 莉.多组学联合分析在畜禽研究中的应用[J].中国畜牧杂志,2022,58(3):1-6. FENG M,ZHANG L.Application of multi-omics joint analysis in the research of livestock and poultry[J].Chinese Journal of Animal Science,2022,58(3):1-6.(in Chinese) [6] MARDIS E R.DNA sequencing technologies:2006-2016[J].Nat Protoc,2017,12(2):213-218. [7] CHEN P,SUN Z P,WANG J W,et al.Portable nanopore-sequencing technology:trends in development and applications[J].Front Microbiol,2023,14:1043967. [8] HU T S,CHITNIS N,MONOS D,et al.Next-generation sequencing technologies:an overview[J].Human Immunol,2021, 82(11): 801-811. [9] SANGER F,NICKLEN S,COULSON A R.DNA sequencing with chain-terminating inhibitors[J].Proc Natl Acad Sci USA,1977, 74(12):5463-5467. [10] HAAS R,ZELEZNIAK A,IACOVACCI J,et al.Designing and interpreting 'multi-omic’ experiments that may change our understanding of biology[J].Curr Opin Syst Biol,2017,6:37-45. [11] WANG C S,HAN B.Twenty years of rice genomics research:From sequencing and functional genomics to quantitative genomics[J].Mol Plant,2022,15(4):593-619. [12] International Chicken Genome Sequencing Consortium.Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution[J].Nature,2004,432(7018):695-716. [13] GROENEN M A M,ARCHIBALD A L,UENISHI H,et al.Analyses of pig genomes provide insight into porcine demography and evolution[J].Nature,2012,491(7424):393-398. [14] WANG K C,CHANG H Y.Epigenomics:technologies and applications[J].Circ Res,2018,122(9):1191-1199. [15] LI H Y,XI Q Y,XIONG Y Y,et al.Identification and comparison of microRNAs from skeletal muscle and adipose tissues from two porcine breeds[J].Anim Genet,2012,43(6):704-713. [16] LIU X F,DING X B,LI X,et al.An atlas and analysis of bovine skeletal muscle long noncoding RNAs[J].Anim Genet, 2017,48(3):278-286. [17] LOWE R,SHIRLEY N,BLEACKLEY M,et al.Transcriptomics technologies[J].PLoS Comput Biol,2017,13(5):e1005457. [18] HARPER A L,HE Z,LANGER S,et al.Validation of an associative transcriptomics platform in the polyploid crop species Brassica juncea by dissection of the genetic architecture of agronomic and quality traits[J].Plant J,2020,103(5):1885-1893. [19] LIAO Y H,LIU Z Y,ZHANG Y,et al.High-throughput and high-sensitivity full-length single-cell RNA-seq analysis on third-generation sequencing platform[J].Cell Discov,2023,9(1):5. [20] SANGWAN R S,TRIPATHI S,SINGH J,et al.De novo sequencing and assembly of Centella asiatica leaf transcriptome for mapping of structural,functional and regulatory genes with special reference to secondary metabolism[J].Gene,2013,525(1):58-76. [21] JIN L,TANG Q Z,HU S L,et al.A pig BodyMap transcriptome reveals diverse tissue physiologies and evolutionary dynamics of transcription[J].Nat Commun,2021,12(1):3715. [22] ZHAO Y X,HOU Y,XU Y Y,et al.A compendium and comparative epigenomics analysis of cis-regulatory elements in the pig genome[J].Nat Commun,2021,12(1):2217. [23] HARPER J W,BENNETT E J.Proteome complexity and the forces that drive proteome imbalance[J].Nature,2016, 537(7620):328-338. [24] MOOTHA V.The mitochondrial proteome and human disease[J].Pathology,2015,47(S1):S28. [25] GONZÁLEZ-GOMARIZ J,GURUCEAGA E,LÓPEZ-SÁNCHEZ M,et al.Proteogenomics in the context of the Human Proteome Project (HPP)[J].Expert Rev Proteomics,2019,16(3):267-275. [26] PARK J,PIEHOWSKI P D,WILKINS C,et al.Informed-Proteomics:open-source software package for top-down proteomics[J]. Nat Methods,2017,14(9):909-914. [27] WANG Z X,SHANG P,LI Q G,et al.iTRAQ-based proteomic analysis reveals key proteins affecting muscle growth and lipid deposition in pigs[J].Sci Rep,2017,7(1):46717. [28] ZAMBONI N,SAGHATELIAN A,PATTI G J.Defining the metabolome:size,flux,and regulation[J].Mol Cell,2015,58(4): 699-706. [29] DAMIANI C,GAGLIO D,SACCO E,et al.Systems metabolomics:from metabolomic snapshots to design principles[J].Curr Opin Biotechnol,2020,63:190-199. [30] WELZENBACH J,NEUHOFF C,HEIDT H,et al.Integrative analysis of metabolomic,proteomic and genomic data to reveal functional pathways and candidate genes for drip loss in pigs[J].Int J Mol Sci,2016,17(9):1426. [31] BOVO S,MAZZONI G,GALIMBERTI G,et al.Metabolomics evidences plasma and serum biomarkers differentiating two heavy pig breeds[J].Animal,2016,10(10):1741-1748. [32] XIE F,XU L,WANG Y,et al.Metagenomic sequencing reveals that high-grain feeding alters the composition and metabolism of Cecal microbiota and induces Cecal mucosal injury in sheep[J].mSystems,2021,6(5):e0091521. [33] BI Y L,TU Y,ZHANG N F,et al.Multiomics analysis reveals the presence of a microbiome in the gut of fetal lambs[J].Gut,2021,70(5):853-864. [34] BOIX C A,JAMES B T,PARK Y P,et al.Regulatory genomic circuitry of human disease loci by integrative epigenomics[J]. Nature,2021,590(7845):300-307. [35] PREISSL S,GAULTON K J,REN B.Characterizing cis-regulatory elements using single-cell epigenomics[J].Nat Rev Genet,2023, 24(1): 21-43. [36] ALDRIDGE S,TEICHMANN S A.Single cell transcriptomics comes of age[J].Nat Commun,2020,11(1):4307. [37] RUSK N.Spatial transcriptomics[J].Nat Methods,2016,13(9):710. [38] LIU X J,LOCASALE J W.Metabolomics:a primer[J].Trends Biochem Sci,2017,42(4):274-284. [39] KNIGHT R,VRBANAC A,TAYLOR B C,et al.Best practices for analysing microbiomes[J].Nat Rev Microbiol,2018, 16(7):410-422. [40] MOHAMMADI-SHEMIRANI P,SOOD T,PARÉ G.From 'omics to multi-omics technologies:the discovery of novel causal mediators[J].Curr Atheroscler Rep,2023,25(2):55-65. [41] ZHANG H W,LV C,ZHANG L J,et al.Application of omics- and multi-omics-based techniques for natural product target discovery[J].Biomed Pharmacother,2021,141:111833. [42] 商 鹏.基于胚胎肌肉组织转录组和蛋白质组数据鉴定猪生长性状相关基因[D].北京:中国农业大学,2017. SHANG P.Identification of candidate genes on growth traits intergrating transcriptome and proteome of embryonic muscle in pigs[D].Beijing:China Agricultural University,2017.(in Chinese) [43] LI X,YANG J,SHEN M,et al.Whole-genome resequencing of wild and domestic sheep identifies genes associated with morphological and agronomic traits[J].Nat Commun,2020,11(1):2815. [44] ZHANG D,DENG Y X,KUKANJA P,et al.Spatial epigenome-transcriptome co-profiling of mammalian tissues[J].Nature,2023, 616(7955):113-122. [45] 蒋可人,马 峥,郑 航,等.转录组与蛋白质组整合分析在生物学研究中的应用[J].生物技术通报,2018,34(12):50-55. JIANG K R,MA Z,ZHENG H,et al.Review on the application of integrated transcriptome and proteome analysis in biology[J].Biotechnol Bull,2018,34(12):50-55.(in Chinese) [46] PONSUKSILI S,TRAKOOLJUL N,HADLICH F,et al.Genetic regulation of liver metabolites and transcripts linking to biochemical-clinical parameters[J].Front Genet,2019,10:348. [47] LIU R X,HONG J,XU X Q,et al.Gut microbiome and serum metabolome alterations in obesity and after weight-loss intervention[J].Nat Med,2017,23(7):859-868. [48] LI Q,WANG Y H,HU X,et al.Transcriptional states and chromatin accessibility during bovine myoblasts proliferation and myogenic differentiation[J].Cell Prolif,2022,55(5):e13219. [49] YU T Y,TIAN X K,LI D,et al.Transcriptome,proteome and metabolome analysis provide insights on fat deposition and meat quality in pig[J].Food Res Int,2023,166:112550. [50] TIAN X K,LI D,ZHAO X,et al.Dietary grape pomace extract supplementation improved meat quality,antioxidant capacity,and immune performance in finishing pigs[J].Front Microbiol,2023,14:1116022. [51] TEKOLA-AYELE F,ZENG X H,CHATTERJEE S,et al.Placental multi-omics integration identifies candidate functional genes for birthweight[J].Nat Commun,2022,13(1):2384. [52] JIN C,LEE B,SHEN L,et al.Integrating multi-omics summary data using a Mendelian randomization framework[J].Brief Bioinform,2022,23(6):bbac376. [53] BODEIN A,SCOTT-BOYER M P,PERIN O,et al.Interpretation of network-based integration from multi-omics longitudinal data[J].Nucleic Acids Res,2022,50(5):e27. [54] REEL P S,REEL S,PEARSON E,et al.Using machine learning approaches for multi-omics data analysis:a review[J].Biotechnol Adv,2021,49:107739. [55] SHANG P,WANG Z X,CHAMBA Y,et al.A comparison of prenatal muscle transcriptome and proteome profiles between pigs with divergent growth phenotypes[J].J Cell Biochem,2019,120(4):5277-5286. [56] HUANG X,ZHANG H Y,CAO H Y,et al.Transcriptomics and metabolomics analysis of the ovaries of high and low egg production chickens[J].Animals,2022,12(16):2010. [57] 喇永富.利用转录组和蛋白质组测序筛选绵羊多羔基因的研究[D].兰州:甘肃农业大学,2020. LA Y F.Study on screening polytocous genes in sheep based on transcriptome and proteomics sequencing[D].Lanzhou:Gansu Agricultural University,2020.(in Chinese) [58] SUN Z P,LIU Y F,HE X Y,et al.Integrative proteomics and transcriptomics profiles of the oviduct reveal the prolificacy-related candidate biomarkers of goats (Capra hircus) in estrous periods[J].Int J Mol Sci,2022,23(23):14888. [59] 张壮彪.基于下丘脑多组学分析筛选小尾寒羊多羔候选基因[D].北京:中国农业科学院,2020. ZHANG Z B. Screening polytocous candidate genes in small tail han sheep based on hypothalamic multi-omics analysis[D]. Beijing:Chinese Academy of Agricultural Sciences,2020.(in Chinese) [60] CHANG J Y,FAN D,LIU J X,et al.Transcriptomic and chromatin landscape analysis reveals that involvement of pituitary level transcription factors modulate incubation behaviors of magang geese[J].Genes (Basel),2023,14(4):815. [61] LI J J,XIANG Y,ZHANG L,et al.Enhancer-promoter interaction maps provide insights into skeletal muscle-related traits in pig genome[J].BMC Biol,2022,20(1):136. [62] WANG L Y,ZHANG Y W,ZHANG B,et al.Candidate gene screening for lipid deposition using combined transcriptomic and proteomic data from Nanyang black pigs[J].BMC Genomics,2021,22(1):441. [63] ZHAN H W,XIONG Y C,WANG Z C,et al.Integrative analysis of transcriptomic and metabolomic profiles reveal the complex molecular regulatory network of meat quality in Enshi black pigs[J].Meat Sci,2022,183:108642. [64] LI J J,ZHANG D H,YIN L Q,et al.Integration analysis of metabolome and transcriptome profiles revealed the age-dependent dynamic change in chicken meat[J].Food Res Int,2022,156:111171. [65] WANG W L,HU H F,ZIJLSTRA R T,et al.Metagenomic reconstructions of gut microbial metabolism in weanling pigs[J]. Microbiome,2019,7(1):48. [66] REVERTER A,BALLESTER M,ALEXANDRE P A,et al.A gene co-association network regulating gut microbial communities in a Duroc pig population[J].Microbiome,2021,9(1):52. [67] SAELAO P,WANG Y,CHANTHAVIXAY G,et al.Integrated proteomic and transcriptomic analysis of differential expression of chicken lung tissue in response to NDV infection during heat stress[J].Genes (Basel),2018,9(12):579. [68] YU H L,WANG Q,TANG J Q,et al.Comprehensive analysis of gut microbiome and host transcriptome in chickens after Eimeria tenella infection[J].Front Cell Infect Microbiol,2023,13:1191939. [69] 许秋实.基于多组学水平的酮病奶牛脂肪组织代谢适应分析[D].长春:吉林大学,2019. XU Q S. Integrated analysis of metabolic adaptation on adipose tissue in ketotic dairy cows based on multi-omics data[D]. Changchun:Jilin University,2019.(in Chinese) [70] ZHANG B,CHAMBA Y,SHANG P,et al.Comparative transcriptomic and proteomic analyses provide insights into the key genes involved in high-altitude adaptation in the Tibetan pig[J].Sci Rep,2017,7(1):3654. [71] LIU S L,GAO Y H,CANELA-XANDRI O,et al.A multi-tissue atlas of regulatory variants in cattle[J].Nat Genet,2022,54(9): 1438-1447. [72] THE GTEX CONSORTIUM,ARDLIE K G,DELUCA D S,et al.The Genotype-Tissue Expression (GTEx) pilot analysis:multitissue gene regulation in humans[J].Science,2015,348(6235):648-660. |