How to Cite

If you use data from this website in your publication, please cite the genome and data sources for the tracks you used. For tissue-specific tracks, you should look up the associated BioProject accession in the JBrowse faceted track selector and then find the corresponding publication in the table below. PubMed ids in the table link are linked to the PubMed pages at NCBI.

Genome, Data Set or BioProject

Publication

 

ARS-UCD1.2

 

Rosen BD, Bickhart DM, Schnabel RD, Koren S, Elsik CG, Tseng E, Rowan TN, Low WY, Zimin A, Couldrey C, Hall R, Li W, Rhie A, Ghurye J, McKay SD, Thibaud-Nissen F, Hoffman J, Murdoch BM, Snelling WM, McDaneld TG, Hammond JA, Schwartz JC, Nandolo W, Hagen DE, Dreischer C, Schultheiss SJ, Schroeder SG, Phillippy AM, Cole JB, Van Tassell CP, Liu G, Smith TPL, Medrano JF. De novo assembly of the cattle reference genome with single-molecule sequencing. Gigascience. 2020 Mar 1;9(3):giaa021. doi: 10.1093/gigascience/giaa021. PMID: 32191811; PMCID: PMC7081964.

 

 

ARS1

 

Bickhart DM, Rosen BD, Koren S, Sayre BL, Hastie AR, Chan S, Lee J, Lam ET, Liachko I, Sullivan ST, Burton JN, Huson HJ, Nystrom JC, Kelley CM, Hutchison JL, Zhou Y, Sun J, Crisà A, Ponce de León FA, Schwartz JC, Hammond JA, Waldbieser GC, Schroeder SG, Liu GE, Dunham MJ, Shendure J, Sonstegard TS, Phillippy AM, Van Tassell CP, Smith TP. Single-molecule sequencing and chromatin conformation capture enable de novo reference assembly of the domestic goat genome. Nat Genet. 2017 Apr;49(4):643-650. doi: 10.1038/ng.3802. Epub 2017 Mar 6. PMID: 28263316; PMCID: PMC5909822.

 

 

EquCab3.0

 

Kalbfleisch TS, Rice ES, DePriest MS Jr, Walenz BP, Hestand MS, Vermeesch JR, O Connell BL, Fiddes IT, Vershinina AO, Saremi NF, Petersen JL, Finno CJ, Bellone RR, McCue ME, Brooks SA, Bailey E, Orlando L, Green RE, Miller DC, Antczak DF, MacLeod JN. Improved reference genome for the domestic horse increases assembly contiguity and composition. Commun Biol. 2018 Nov 16;1:197. doi: 10.1038/s42003-018-0199-z. PMID: 30456315; PMCID: PMC6240028.

 

 

GRCg6a

 

Warren WC, Hillier LW, Tomlinson C, Minx P, Kremitzki M, Graves T, Markovic C, Bouk N, Pruitt KD, Thibaud-Nissen F, Schneider V, Mansour TA, Brown CT, Zimin A, Hawken R, Abrahamsen M, Pyrkosz AB, Morisson M, Fillon V, Vignal A, Chow W, Howe K, Fulton JE, Miller MM, Lovell P, Mello CV, Wirthlin M, Mason AS, Kuo R, Burt DW, Dodgson JB, Cheng HH. A New Chicken Genome Assembly Provides Insight into Avian Genome Structure. G3 (Bethesda). 2017 Jan 5;7(1):109-117. doi: 10.1534/g3.116.035923. PMID: 27852011; PMCID: PMC5217101.

 

 

Oar_v3.1

 

Jiang Y, Xie M, Chen W, Talbot R, Maddox JF, Faraut T, Wu C, Muzny DM, Li Y, Zhang W, Stanton JA, Brauning R, Barris WC, Hourlier T, Aken BL, Searle SMJ, Adelson DL, Bian C, Cam GR, Chen Y, Cheng S, DeSilva U, Dixen K, Dong Y, Fan G, Franklin IR, Fu S, Guan R, Highland MA, Holder ME, Huang G, Ingham AB, Jhangiani SN, Kalra D, Kovar CL, Lee SL, Liu W, Liu X, Lu C, Lv T, Mathew T, McWilliam S, Menzies M, Pan S, Robelin D, Servin B, Townley D, Wang W, Wei B, White SN, Yang X, Ye C, Yue Y, Zeng P, Zhou Q, Hansen JB, Kristensen K, Gibbs RA, Flicek P, Warkup CC, Jones HE, Oddy VH, Nicholas FW, McEwan JC, Kijas J, Wang J, Worley KC, Archibald AL, Cockett N, Xu X, Wang W, Dalrymple BP. The sheep genome illuminates biology of the rumen and lipid metabolism. Science. 2014 Jun 6;344(6188):1168-1173. doi: 10.1126/science.1252806. PMID: 24904168; PMCID: PMC4157056.

 

 

Sscrofa11.1

 

Warr A, Affara N, Aken B, Beiki H, Bickhart DM, Billis K, Chow W, Eory L, Finlayson HA, Flicek P, Girón CG, Griffin DK, Hall R, Hannum G, Hourlier T, Howe K, Hume DA, Izuogu O, Kim K, Koren S, Liu H, Manchanda N, Martin FJ, Nonneman DJ, O'Connor RE, Phillippy AM, Rohrer GA, Rosen BD, Rund LA, Sargent CA, Schook LB, Schroeder SG, Schwartz AS, Skinner BM, Talbot R, Tseng E, Tuggle CK, Watson M, Smith TPL, Archibald AL. An improved pig reference genome sequence to enable pig genetics and genomics research. Gigascience. 2020 Jun 1;9(6):giaa051. doi: 10.1093/gigascience/giaa051. PMID: 32543654; PMCID: PMC7448572.

 

 

UOA_WB_1

 

Low WY, Tearle R, Bickhart DM, Rosen BD, Kingan SB, Swale T, Thibaud-Nissen F, Murphy TD, Young R, Lefevre L, Hume DA, Collins A, Ajmone-Marsan P, Smith TPL, Williams JL. Chromosome-level assembly of the water buffalo genome surpasses human and goat genomes in sequence contiguity. Nat Commun. 2019 Jan 16;10(1):260. doi: 10.1038/s41467-018-08260-0. PMID: 30651564; PMCID: PMC6335429.

 

 

Ensembl Genes

 

Howe KL, Achuthan P, Allen J, Allen J, Alvarez-Jarreta J, Amode MR, Armean IM, Azov AG, Bennett R, Bhai J, Billis K, Boddu S, Charkhchi M, Cummins C, Da Rin Fioretto L, Davidson C, Dodiya K, El Houdaigui B, Fatima R, Gall A, Garcia Giron C, Grego T, Guijarro-Clarke C, Haggerty L, Hemrom A, Hourlier T, Izuogu OG, Juettemann T, Kaikala V, Kay M, Lavidas I, Le T, Lemos D, Gonzalez Martinez J, Marugán JC, Maurel T, McMahon AC, Mohanan S, Moore B, Muffato M, Oheh DN, Paraschas D, Parker A, Parton A, Prosovetskaia I, Sakthivel MP, Salam AIA, Schmitt BM, Schuilenburg H, Sheppard D, Steed E, Szpak M, Szuba M, Taylor K, Thormann A, Threadgold G, Walts B, Winterbottom A, Chakiachvili M, Chaubal A, De Silva N, Flint B, Frankish A, Hunt SE, IIsley GR, Langridge N, Loveland JE, Martin FJ, Mudge JM, Morales J, Perry E, Ruffier M, Tate J, Thybert D, Trevanion SJ, Cunningham F, Yates AD, Zerbino DR, Flicek P. Ensembl 2021. Nucleic Acids Res. 2021 Jan 8;49(D1):D884-D891. doi: 10.1093/nar/gkaa942. PMID: 33137190; PMCID: PMC7778975.

 

 

RefSeq Genes

 

O'Leary NA, Wright MW, Brister JR, Ciufo S, Haddad D, McVeigh R, Rajput B, Robbertse B, Smith-White B, Ako-Adjei D, Astashyn A, Badretdin A, Bao Y, Blinkova O, Brover V, Chetvernin V, Choi J, Cox E, Ermolaeva O, Farrell CM, Goldfarb T, Gupta T, Haft D, Hatcher E, Hlavina W, Joardar VS, Kodali VK, Li W, Maglott D, Masterson P, McGarvey KM, Murphy MR, O'Neill K, Pujar S, Rangwala SH, Rausch D, Riddick LD, Schoch C, Shkeda A, Storz SS, Sun H, Thibaud-Nissen F, Tolstoy I, Tully RE, Vatsan AR, Wallin C, Webb D, Wu W, Landrum MJ, Kimchi A, Tatusova T, DiCuccio M, Kitts P, Murphy TD, Pruitt KD. Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion, and functional annotation. Nucleic Acids Res. 2016 Jan 4;44(D1):D733-45. doi: 10.1093/nar/gkv1189. Epub 2015 Nov 8. PMID: 26553804; PMCID: PMC4702849.

 

 

SNP

 

Howe KL, Achuthan P, Allen J, Allen J, Alvarez-Jarreta J, Amode MR, Armean IM, Azov AG, Bennett R, Bhai J, Billis K, Boddu S, Charkhchi M, Cummins C, Da Rin Fioretto L, Davidson C, Dodiya K, El Houdaigui B, Fatima R, Gall A, Garcia Giron C, Grego T, Guijarro-Clarke C, Haggerty L, Hemrom A, Hourlier T, Izuogu OG, Juettemann T, Kaikala V, Kay M, Lavidas I, Le T, Lemos D, Gonzalez Martinez J, Marugán JC, Maurel T, McMahon AC, Mohanan S, Moore B, Muffato M, Oheh DN, Paraschas D, Parker A, Parton A, Prosovetskaia I, Sakthivel MP, Salam AIA, Schmitt BM, Schuilenburg H, Sheppard D, Steed E, Szpak M, Szuba M, Taylor K, Thormann A, Threadgold G, Walts B, Winterbottom A, Chakiachvili M, Chaubal A, De Silva N, Flint B, Frankish A, Hunt SE, IIsley GR, Langridge N, Loveland JE, Martin FJ, Mudge JM, Morales J, Perry E, Ruffier M, Tate J, Thybert D, Trevanion SJ, Cunningham F, Yates AD, Zerbino DR, Flicek P. Ensembl 2021. Nucleic Acids Res. 2021 Jan 8;49(D1):D884-D891. doi: 10.1093/nar/gkaa942. PMID: 33137190; PMCID: PMC7778975.

 

 

QTL

 

Hu ZL, Park CA, Reecy JM. Building a livestock genetic and genomic information knowledgebase through integrative developments of Animal QTLdb and CorrDB. Nucleic Acids Res. 2019 Jan 8;47(D1):D701-D710. doi: 10.1093/nar/gky1084. PMID: 30407520; PMCID: PMC6323967.

 

 

PRJEB12891

 

Kuo RI, Tseng E, Eory L, Paton IR, Archibald AL, Burt DW. Normalized long read RNA sequencing in chicken reveals transcriptome complexity similar to human. BMC Genomics. 2017 Apr 24;18(1):323. doi: 10.1186/s12864-017-3691-9. PMID: 28438136; PMCID: PMC5404281.

 

 

PRJEB14330

 

Kern C, Wang Y, Chitwood J, Korf I, Delany M, Cheng H, Medrano JF, Van Eenennaam AL, Ernst C, Ross P, Zhou H. Genome-wide identification of tissue-specific long non-coding RNA in three farm animal species. BMC Genomics. 2018 Sep 18;19(1):684. doi: 10.1186/s12864-018-5037-7. PMID: 30227846; PMCID: PMC6145346.

 

 

PRJEB19199

 

Clark EL, Bush SJ, McCulloch MEB, Farquhar IL, Young R, Lefevre L, Pridans C, Tsang HG, Wu C, Afrasiabi C, Watson M, Whitelaw CB, Freeman TC, Summers KM, Archibald AL, Hume DA. A high resolution atlas of gene expression in the domestic sheep (Ovis aries). PLoS Genet. 2017 Sep 15;13(9):e1006997. doi: 10.1371/journal.pgen.1006997. PMID: 28915238; PMCID: PMC5626511.

 

Bush SJ, McCulloch MEB, Muriuki C, Salavati M, Davis GM, Farquhar IL, Lisowski ZM, Archibald AL, Hume DA, Clark EL. Comprehensive Transcriptional Profiling of the Gastrointestinal Tract of Ruminants from Birth to Adulthood Reveals Strong Developmental Stage Specific Gene Expression. G3 (Bethesda). 2019 Feb 7;9(2):359-373. doi: 10.1534/g3.118.200810. PMID: 30530642; PMCID: PMC6385975.

 

 

PRJEB19268

 

Derks MFL, Lopes MS, Bosse M, Madsen O, Dibbits B, Harlizius B, Groenen MAM, Megens HJ. Balancing selection on a recessive lethal deletion with pleiotropic effects on two neighboring genes in the porcine genome. PLoS Genet. 2018 Sep 19;14(9):e1007661. doi: 10.1371/journal.pgen.1007661. PMID: 30231021; PMCID: PMC6166978.

 

 

PRJEB19386

 

Warr A, Affara N, Aken B, Beiki H, Bickhart DM, Billis K, Chow W, Eory L, Finlayson HA, Flicek P, Girón CG, Griffin DK, Hall R, Hannum G, Hourlier T, Howe K, Hume DA, Izuogu O, Kim K, Koren S, Liu H, Manchanda N, Martin FJ, Nonneman DJ, O'Connor RE, Phillippy AM, Rohrer GA, Rosen BD, Rund LA, Sargent CA, Schook LB, Schroeder SG, Schwartz AS, Skinner BM, Talbot R, Tseng E, Tuggle CK, Watson M, Smith TPL, Archibald AL. An improved pig reference genome sequence to enable pig genetics and genomics research. Gigascience. 2020 Jun 1;9(6):giaa051. doi: 10.1093/gigascience/giaa051. PMID: 32543654; PMCID: PMC7448572.

 

 

PRJEB23196

 

Bush SJ, McCulloch MEB, Muriuki C, Salavati M, Davis GM, Farquhar IL, Lisowski ZM, Archibald AL, Hume DA, Clark EL. Comprehensive Transcriptional Profiling of the Gastrointestinal Tract of Ruminants from Birth to Adulthood Reveals Strong Developmental Stage Specific Gene Expression. G3 (Bethesda). 2019 Feb 7;9(2):359-373. doi: 10.1534/g3.118.200810. PMID: 30530642; PMCID: PMC6385975.

 

Muriuki C, Bush SJ, Salavati M, McCulloch MEB, Lisowski ZM, Agaba M, Djikeng A, Hume DA, Clark EL. A Mini-Atlas of Gene Expression for the Domestic Goat (Capra hircus). Front Genet. 2019 Nov 4;10:1080. doi: 10.3389/fgene.2019.01080. PMID: 31749840; PMCID: PMC6844187.

 

 

PRJEB25226

 

Young R, Lefevre L, Bush SJ, Joshi A, Singh SH, Jadhav SK, Dhanikachalam V, Lisowski ZM, Iamartino D, Summers KM, Williams JL, Archibald AL, Gokhale S, Kumar S, Hume DA. A Gene Expression Atlas of the Domestic Water Buffalo (Bubalus bubalis). Front Genet. 2019 Jul 24;10:668. doi: 10.3389/fgene.2019.00668. PMID: 31428126; PMCID: PMC6689995.

 

 

PRJEB26787

 

Gao S, Nanaei HA, Wei B, Wang Y, Wang X, Li Z, Dai X, Wang Z, Jiang Y, Shao J. Comparative Transcriptome Profiling Analysis Uncovers Novel Heterosis-Related Candidate Genes Associated with Muscular Endurance in Mules. Animals (Basel). 2020 Jun 4;10(6):980. doi: 10.3390/ani10060980. PMID: 32512843; PMCID: PMC7341310.

 

 

PRJEB27455

 

Foissac S, Djebali S, Munyard K, Vialaneix N, Rau A, Muret K, Esquerré D, Zytnicki M, Derrien T, Bardou P, Blanc F, Cabau C, Crisci E, Dhorne-Pollet S, Drouet F, Faraut T, Gonzalez I, Goubil A, Lacroix-Lamandé S, Laurent F, Marthey S, Marti-Marimon M, Momal-Leisenring R, Mompart F, Quéré P, Robelin D, Cristobal MS, Tosser-Klopp G, Vincent-Naulleau S, Fabre S, Pinard-Van der Laan MH, Klopp C, Tixier-Boichard M, Acloque H, Lagarrigue S, Giuffra E. Multi-species annotation of transcriptome and chromatin structure in domesticated animals. BMC Biol. 2019 Dec 30;17(1):108. doi: 10.1186/s12915-019-0726-5. PMID: 31884969; PMCID: PMC6936065.

 

 

PRJEB35307

 

Kingsley NB, Kern C, Creppe C, Hales EN, Zhou H, Kalbfleisch TS, MacLeod JN, Petersen JL, Finno CJ, Bellone RR. Functionally Annotating Regulatory Elements in the Equine Genome Using Histone Mark ChIP-Seq. Genes (Basel). 2019 Dec 18;11(1):3. doi: 10.3390/genes11010003. PMID: 31861495; PMCID: PMC7017286.

 

 

PRJEB4351

 

Low WY, Tearle R, Bickhart DM, Rosen BD, Kingan SB, Swale T, Thibaud-Nissen F, Murphy TD, Young R, Lefevre L, Hume DA, Collins A, Ajmone-Marsan P, Smith TPL, Williams JL. Chromosome-level assembly of the water buffalo genome surpasses human and goat genomes in sequence contiguity. Nat Commun. 2019 Jan 16;10(1):260. doi: 10.1038/s41467-018-08260-0. PMID: 30651564; PMCID: PMC6335429.

 

 

PRJEB6169

 

Clark EL, Bush SJ, McCulloch MEB, Farquhar IL, Young R, Lefevre L, Pridans C, Tsang HG, Wu C, Afrasiabi C, Watson M, Whitelaw CB, Freeman TC, Summers KM, Archibald AL, Hume DA. A high resolution atlas of gene expression in the domestic sheep (Ovis aries). PLoS Genet. 2017 Sep 15;13(9):e1006997. doi: 10.1371/journal.pgen.1006997. PMID: 28915238; PMCID: PMC5626511.

 

 

PRJNA204941

 

McCarthy FM, Pendarvis K, Cooksey AM, Gresham CR, Bomhoff M, Davey S, Lyons E, Sonstegard TS, Bridges SM, Burgess SC. Chickspress: a resource for chicken gene expression. Database (Oxford). 2019 Jan 1;2019:baz058. doi: 10.1093/database/baz058. PMID: 31210271; PMCID: PMC6556980.

 

 

PRJNA263600

 

Triant DA, Le Tourneau JJ, Diesh CM, Unni DR, Shamimuzzaman M, Walsh AT, Gardiner J, Goldkamp AK, Li Y, Nguyen HN, Roberts C, Zhao Z, Alexander LJ, Decker JE, Schnabel RD, Schroeder SG, Sonstegard TS, Taylor JF, Rivera RM, Hagen DE, Elsik CG. Using online tools at the Bovine Genome Database to manually annotate genes in the new reference genome. Anim Genet. 2020 Oct;51(5):675-682. doi: 10.1111/age.12962. Epub 2020 Jun 14. PMID: 32537769; PMCID: PMC7540445.

 

 

PRJNA294306

 

Triant DA, Le Tourneau JJ, Diesh CM, Unni DR, Shamimuzzaman M, Walsh AT, Gardiner J, Goldkamp AK, Li Y, Nguyen HN, Roberts C, Zhao Z, Alexander LJ, Decker JE, Schnabel RD, Schroeder SG, Sonstegard TS, Taylor JF, Rivera RM, Hagen DE, Elsik CG. Using online tools at the Bovine Genome Database to manually annotate genes in the new reference genome. Anim Genet. 2020 Oct;51(5):675-682. doi: 10.1111/age.12962. Epub 2020 Jun 14. PMID: 32537769; PMCID: PMC7540445.

 

 

PRJNA311523

 

Li M, Chen L, Tian S, Lin Y, Tang Q, Zhou X, Li D, Yeung CKL, Che T, Jin L, Fu Y, Ma J, Wang X, Jiang A, Lan J, Pan Q, Liu Y, Luo Z, Guo Z, Liu H, Zhu L, Shuai S, Tang G, Zhao J, Jiang Y, Bai L, Zhang S, Mai M, Li C, Wang D, Gu Y, Wang G, Lu H, Li Y, Zhu H, Li Z, Li M, Gladyshev VN, Jiang Z, Zhao S, Wang J, Li R, Li X. Comprehensive variation discovery and recovery of missing sequence in the pig genome using multiple de novo assemblies. Genome Res. 2017 May;27(5):865-874. doi: 10.1101/gr.207456.116. Epub 2016 Sep 19. PMID: 27646534; PMCID: PMC5411780.

 

 

PRJNA379574

 

Triant DA, Le Tourneau JJ, Diesh CM, Unni DR, Shamimuzzaman M, Walsh AT, Gardiner J, Goldkamp AK, Li Y, Nguyen HN, Roberts C, Zhao Z, Alexander LJ, Decker JE, Schnabel RD, Schroeder SG, Sonstegard TS, Taylor JF, Rivera RM, Hagen DE, Elsik CG. Using online tools at the Bovine Genome Database to manually annotate genes in the new reference genome. Anim Genet. 2020 Oct;51(5):675-682. doi: 10.1111/age.12962. Epub 2020 Jun 14. PMID: 32537769; PMCID: PMC7540445.