biostudies-literatureBlaxter MSwiss National Science FoundationWellcome Trustfsci.2025.1514835https://www.ebi.ac.uk/biostudies/studies/S-EPMC7618684biostudies-literatureUnknown3The Earth BioGenome Project (EBP) aims to "sequence life for the future of life" by generating high-quality reference genome sequences for all recognized eukaryotic species, thereby building a rich knowledge base to inform conservation, inspire bioindustry, ensure food security, advance medicine, and establish a deeper understanding of biodiversity. As the EBP works toward completing the original Phase I goal-a reference genome for each of the approximately 10,000 taxonomic families of eukaryotes-milestone publications have demonstrated the transformative potential of the project. The EBP has promoted global collaboration and established core methods and standards. By the end of 2024, EBP-affiliated projects had publicly released 2,000 high-quality genome assemblies, representing more thanFrontiers in scienceThe Earth BioGenome Project Phase II: illuminating the eukaryotic tree of life.PMC7618684207492206194222155202669226458218328Zhang GThibaud-Nissen FOLawniczak MKNSotero-Caio CWilliams JZhang HHoff KJHowe KHackett KLopez JVHarrison PWKatee SO'Neill ECRighi EDurbin RBalint MRubio JCCHall NMorin PPruitt KDKosch TUliano-Silva MSwarbreck DKocot KLewin HARyder OAMartin FJPaez SSantos BTiamiyu BBMulder NGilbert MTPMajewska RMcCarthy CMuigai AWMcKenna DDKersey PMapholi NLawniczak MMai MPettersson OVShikongo TTang BWei XRhie AThibaud-Nissen FAllende MWarnow TWaterhouse RMBista IHiller MDiPalma FWaterhouse RChaw SMWong LHesse UEBP Community of ScientistsFranz NMAstrin JMazzoni CJFranz NPhillippy AMarins LSSoltis PBertorelle GCook-Deegan RShirley LDi Palma FVernes SEziuzor SCrollius HRSaloma CHudson MCorominas MFlores MPLewin HGeorges AJakobsen KSDavey RHogg CO'Neill RJSahu SKRas VWang KFedrigo OGoldstein MLindblad-Toh KKuraku Sda Silva MBarker KMathews DJAleixo AJarvis EDBarnes IPoelchau MChilders AKGhansah AWeber CCJarvis EJue NKChen LWetzer RLi QChen HEvans JTsosie KSJohnson RNLi XKarlsson EKIsobe SKuja JLakshmikumaran MLu JBlaxter MKim JHRoquet CCorrigan SJones SMyers GRodriguez LIgiehon ONFormenti GHarrison PCai JCrandall KACrawford AJShimizu HGuigo RCaperello NLiu XBonet TMStauton CChallis RYracheta JMMathews DJHBraverman ITorrance ABelov KWideman JShunping HWright CJLeebens-Mack JGreely HTWegrzyn JKress WJDennis AVeale AMa JMcCartney AMBrown TShaffer HBRobinson GShank TMfalseThe Earth BioGenome Project Phase II: illuminating the eukaryotic tree of life.The Earth BioGenome Project (EBP) aims to "sequence life for the future of life" by generating high-quality reference genome sequences for all recognized eukaryotic species, thereby building a rich knowledge base to inform conservation, inspire bioindustry, ensure food security, advance medicine, and establish a deeper understanding of biodiversity. As the EBP works toward completing the original Phase I goal-a reference genome for each of the approximately 10,000 taxonomic families of eukaryotes-milestone publications have demonstrated the transformative potential of the project. The EBP has promoted global collaboration and established core methods and standards. By the end of 2024, EBP-affiliated projects had publicly released 2,000 high-quality genome assemblies, representing more than2025-01-01T00:00:00Z2025 Sep2026-06-20T03:19:17.554Z2026-06-20T03:09:40.52ZS-EPMC76186844162551910.3389/fsci.2025.1514835