{"entity": "researcher", "timestamp": "2026-08-20T20:49:24.054Z", "family": "Zhang", "given": "Guojie", "initials": "G", "orcid": "0000-0001-6860-1521", "affiliations": ["Section for Ecology and Evolution, Department of Biology, University of Copenhagen, Copenhagen, Denmark. guojie.zhang@bio.ku.dk.", "State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China. guojie.zhang@bio.ku.dk.", "Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China. guojie.zhang@bio.ku.dk.", "China National GeneBank, BGI-Shenzhen, Shenzhen, China. guojie.zhang@bio.ku.dk."], "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/researcher/9ec2e418a32c4161abc876171467f5ea.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/researcher/9ec2e418a32c4161abc876171467f5ea"}}, "publications": [{"entity": "publication", "iuid": "3841603fbf9e43e6a1460db8f686ef9e", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/3841603fbf9e43e6a1460db8f686ef9e.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/3841603fbf9e43e6a1460db8f686ef9e"}}, "title": "Why sequence all eukaryotes?", "authors": [{"family": "Blaxter", "given": "Mark", "initials": "M", "orcid": "0000-0003-2861-949X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9b785bc131a241c4815ab5ef1576709b.json"}}, {"family": "Archibald", "given": "John M", "initials": "JM", "orcid": "0000-0001-7255-780X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9381e61c33164dca82411b18b9fcc0d3.json"}}, {"family": "Childers", "given": "Anna K", "initials": "AK", "orcid": "0000-0002-0747-8539", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b04257eed5dd48a7b631d8c8e78c2df1.json"}}, {"family": "Coddington", "given": "Jonathan A", "initials": "JA", "orcid": "0000-0001-6004-7730", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/efae0bfdf0c64e86a175c8921b1af0b4.json"}}, {"family": "Crandall", "given": "Keith A", "initials": "KA", "orcid": "0000-0002-0836-3389", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/853c5da68a5a4c96bd2248b21bd15ba7.json"}}, {"family": "Di Palma", "given": "Federica", "initials": "F", "orcid": "0000-0002-4394-0102", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/3cf0785a103c45368f4e1cca6e5cb5f7.json"}}, {"family": "Durbin", "given": "Richard", "initials": "R", "orcid": "0000-0002-9130-1006", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4a8972546b724b0d9c6ed69a766cc41b.json"}}, {"family": "Edwards", "given": "Scott V", "initials": "SV", "orcid": "0000-0003-2535-6217", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/249a83cc8fb240609cd7bd76c6c79e2c.json"}}, {"family": "Graves", "given": "Jennifer A M", "initials": "JAM", "orcid": "0000-0001-6480-7856", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/48044e7f378c41e28b58ae92e1102efb.json"}}, {"family": "Hackett", "given": "Kevin J", "initials": "KJ", "orcid": "0000-0002-7459-7175", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/cc72dad2a31b443db715bf82966f44f4.json"}}, {"family": "Hall", "given": "Neil", "initials": "N", "orcid": "0000-0003-2808-0009", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/bc8087425525426994b690f1ae2637e0.json"}}, {"family": "Jarvis", "given": "Erich D", "initials": "ED"}, {"family": "Johnson", "given": "Rebecca N", "initials": "RN", "orcid": "0000-0003-3035-2827", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/5486418f837c4e9199e31f61b20887cd.json"}}, {"family": "Karlsson", "given": "Elinor K", "initials": "EK", "orcid": "0000-0002-4343-3776", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/81b5c82fcb904394b6a6b1d811863fa0.json"}}, {"family": "Kress", "given": "W John", "initials": "WJ", "orcid": "0000-0002-0140-5267", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/25477498e7dd41e7891088988a40713e.json"}}, {"family": "Kuraku", "given": "Shigehiro", "initials": "S", "orcid": "0000-0003-1464-8388", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/be2fb1e4a3e548498f5590365dedc81e.json"}}, {"family": "Lawniczak", "given": "Mara K N", "initials": "MKN"}, {"family": "Lindblad-Toh", "given": "Kerstin", "initials": "K", "orcid": "0000-0001-8338-0253", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/612a779b69494f1ca9b6c5f1d84fd711.json"}}, {"family": "Lopez", "given": "Jose V", "initials": "JV", "orcid": "0000-0002-1637-4125", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d60d31a72bb64d6894367a3ffc1785e7.json"}}, {"family": "Moran", "given": "Nancy A", "initials": "NA", "orcid": "0000-0003-2983-9769", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/74c685964435471096e5dbc580505cb8.json"}}, {"family": "Robinson", "given": "Gene E", "initials": "GE", "orcid": "0000-0003-4828-4068", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/86d1dc6e76694345ba735e5612bff820.json"}}, {"family": "Ryder", "given": "Oliver A", "initials": "OA", "orcid": "0000-0003-2427-763X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/3d18635ed6fa42d4bbcfddadae70e308.json"}}, {"family": "Shapiro", "given": "Beth", "initials": "B"}, {"family": "Soltis", "given": "Pamela S", "initials": "PS", "orcid": "0000-0001-9310-8659", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/7c4308f7e0e84bbfaad58eac840db765.json"}}, {"family": "Warnow", "given": "Tandy", "initials": "T", "orcid": "0000-0001-7717-3514", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/072c8f6823984406aedb974d6a97f7dc.json"}}, {"family": "Zhang", "given": "Guojie", "initials": "G", "orcid": "0000-0001-6860-1521", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9ec2e418a32c4161abc876171467f5ea.json"}}, {"family": "Lewin", "given": "Harris A", "initials": "HA", "orcid": "0000-0002-1043-7287", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/5059da24204049c696aec45b62526759.json"}}], "type": "journal article", "published": "2022-01-25", "journal": {"title": "Proc. Natl. Acad. Sci. U.S.A.", "issn": "1091-6490", "volume": "119", "issue": "4", "issn-l": "0027-8424"}, "abstract": "Life on Earth has evolved from initial simplicity to the astounding complexity we experience today. Bacteria and archaea have largely excelled in metabolic diversification, but eukaryotes additionally display abundant morphological innovation. How have these innovations come about and what constraints are there on the origins of novelty and the continuing maintenance of biodiversity on Earth? The history of life and the code for the working parts of cells and systems are written in the genome. The Earth BioGenome Project has proposed that the genomes of all extant, named eukaryotes-about 2 million species-should be sequenced to high quality to produce a digital library of life on Earth, beginning with strategic phylogenetic, ecological, and high-impact priorities. Here we discuss why we should sequence all eukaryotic species, not just a representative few scattered across the many branches of the tree of life. We suggest that many questions of evolutionary and ecological significance will only be addressable when whole-genome data representing divergences at all of the branchings in the tree of life or all species in natural ecosystems are available. We envisage that a genomic tree of life will foster understanding of the ongoing processes of speciation, adaptation, and organismal dependencies within entire ecosystems. These explorations will resolve long-standing problems in phylogenetics, evolution, ecology, conservation, agriculture, bioindustry, and medicine.", "doi": "10.1073/pnas.2115636118", "pmid": "35042801", "labels": [], "xrefs": [{"db": "pmc", "key": "PMC8795522"}, {"db": "pii", "key": "2115636118"}], "notes": [], "created": "2026-08-20T09:31:06.931Z", "modified": "2026-08-20T09:31:07.517Z"}, {"entity": "publication", "iuid": "626310cbddb14ff48c80c0f9372c585b", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/626310cbddb14ff48c80c0f9372c585b.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/626310cbddb14ff48c80c0f9372c585b"}}, "title": "The Earth BioGenome Project 2020: Starting the clock.", "authors": [{"family": "Lewin", "given": "Harris A", "initials": "HA", "orcid": "0000-0002-1043-7287", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/5059da24204049c696aec45b62526759.json"}}, {"family": "Richards", "given": "Stephen", "initials": "S", "orcid": "0000-0001-8959-5466", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c8005cf3b343461388e2b82a2c61c293.json"}}, {"family": "Lieberman Aiden", "given": "Erez", "initials": "E"}, {"family": "Allende", "given": "Miguel L", "initials": "ML", "orcid": "0000-0002-2783-2152", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/27d6fdda2e7b4487b651c852c3f3cd11.json"}}, {"family": "Archibald", "given": "John M", "initials": "JM"}, {"family": "B\u00e1lint", "given": "Mikl\u00f3s", "initials": "M"}, {"family": "Barker", "given": "Katharine B", "initials": "KB"}, {"family": "Baumgartner", "given": "Bridget", "initials": "B"}, {"family": "Belov", "given": "Katherine", "initials": "K"}, {"family": "Bertorelle", "given": "Giorgio", "initials": "G"}, {"family": "Blaxter", "given": "Mark L", "initials": "ML", "orcid": "0000-0003-2861-949X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9b785bc131a241c4815ab5ef1576709b.json"}}, {"family": "Cai", "given": "Jing", "initials": "J"}, {"family": "Caperello", "given": "Nicolette D", "initials": "ND"}, {"family": "Carlson", "given": "Keith", "initials": "K"}, {"family": "Castilla-Rubio", "given": "Juan Carlos", "initials": "JC"}, {"family": "Chaw", "given": "Shu-Miaw", "initials": "SM"}, {"family": "Chen", "given": "Lei", "initials": "L"}, {"family": "Childers", "given": "Anna K", "initials": "AK"}, {"family": "Coddington", "given": "Jonathan A", "initials": "JA", "orcid": "0000-0001-6004-7730", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/efae0bfdf0c64e86a175c8921b1af0b4.json"}}, {"family": "Conde", "given": "Dalia A", "initials": "DA", "orcid": "0000-0002-7923-8163", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/5b73243e2df04c5a8d771456b262a4bf.json"}}, {"family": "Corominas", "given": "Montserrat", "initials": "M", "orcid": "0000-0002-0724-8346", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/0805b84e0e824c93a51262f4fdc8f8e2.json"}}, {"family": "Crandall", "given": "Keith A", "initials": "KA", "orcid": "0000-0002-0836-3389", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/853c5da68a5a4c96bd2248b21bd15ba7.json"}}, {"family": "Crawford", "given": "Andrew J", "initials": "AJ"}, {"family": "DiPalma", "given": "Federica", "initials": "F"}, {"family": "Durbin", "given": "Richard", "initials": "R", "orcid": "0000-0002-9130-1006", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4a8972546b724b0d9c6ed69a766cc41b.json"}}, {"family": "Ebenezer", "given": "ThankGod E", "initials": "TE"}, {"family": "Edwards", "given": "Scott V", "initials": "SV", "orcid": "0000-0003-2535-6217", "researcher": {"href": 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"https://publications-affiliated.scilifelab.se/researcher/ea9e4bfb13764d13b4418be1ecc2d27d.json"}}, {"family": "Grigoriev", "given": "Igor V", "initials": "IV", "orcid": "0000-0002-3136-8903", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/5cb43708257842149fbbeed91293d400.json"}}, {"family": "Hackett", "given": "Kevin J", "initials": "KJ"}, {"family": "Hall", "given": "Neil", "initials": "N"}, {"family": "Haussler", "given": "David", "initials": "D"}, {"family": "Helgen", "given": "Kristofer M", "initials": "KM"}, {"family": "Hogg", "given": "Carolyn J", "initials": "CJ", "orcid": "0000-0002-6328-398X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/faf4b7a234c84bdbac97cf9b0e8f5531.json"}}, {"family": "Isobe", "given": "Sachiko", "initials": "S"}, {"family": "Jakobsen", "given": "Kjetill Sigurd", "initials": "KS", "orcid": "0000-0002-8861-5397", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f2fe02e097b342508301397260ef7cc3.json"}}, {"family": "Janke", "given": "Axel", "initials": "A", "orcid": "0000-0002-9394-1904", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/5ef0f0bab20e45cca4e726c84b8645f2.json"}}, {"family": "Jarvis", "given": "Erich D", "initials": "ED"}, {"family": "Johnson", "given": "Warren E", "initials": "WE", "orcid": "0000-0002-5954-186X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/aa69a0b1643541b0b490e0c1186c8307.json"}}, {"family": "Jones", "given": "Steven J M", "initials": "SJM"}, {"family": "Karlsson", "given": "Elinor K", "initials": "EK", "orcid": "0000-0002-4343-3776", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/81b5c82fcb904394b6a6b1d811863fa0.json"}}, {"family": "Kersey", "given": "Paul J", "initials": "PJ"}, {"family": "Kim", "given": "Jin-Hyoung", "initials": "JH"}, {"family": "Kress", "given": "W John", "initials": "WJ", "orcid": "0000-0002-0140-5267", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/25477498e7dd41e7891088988a40713e.json"}}, {"family": "Kuraku", "given": "Shigehiro", "initials": "S"}, {"family": "Lawniczak", "given": "Mara K N", "initials": "MKN"}, {"family": "Leebens-Mack", "given": "James H", "initials": "JH", "orcid": "0000-0003-4811-2231", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b52ac9ce6dba4bee8dae7b594242c49b.json"}}, {"family": "Li", "given": "Xueyan", "initials": "X"}, {"family": "Lindblad-Toh", "given": "Kerstin", "initials": "K", "orcid": "0000-0001-8338-0253", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/612a779b69494f1ca9b6c5f1d84fd711.json"}}, {"family": "Liu", "given": "Xin", "initials": "X"}, {"family": "Lopez", "given": "Jose V", "initials": "JV"}, {"family": "Marques-Bonet", "given": "Tomas", "initials": "T", "orcid": "0000-0002-5597-3075", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/1091cb5bfe394d459969d24bb1c22c66.json"}}, {"family": "Mazard", "given": "Sophie", "initials": "S"}, {"family": "Mazet", "given": "Jonna A K", "initials": "JAK", "orcid": "0000-0002-8712-5951", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9daa6d747c704145a06420aa76ce3426.json"}}, {"family": "Mazzoni", "given": "Camila J", "initials": "CJ"}, {"family": "Myers", "given": "Eugene W", "initials": "EW", "orcid": "0000-0002-6580-7839", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/bf74ba4bae3546eca812b29793341604.json"}}, {"family": "O'Neill", "given": "Rachel J", "initials": "RJ"}, {"family": "Paez", "given": "Sadye", "initials": "S"}, {"family": "Park", "given": "Hyun", "initials": "H"}, {"family": "Robinson", "given": "Gene E", "initials": "GE", "orcid": "0000-0003-4828-4068", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/86d1dc6e76694345ba735e5612bff820.json"}}, {"family": "Roquet", "given": "Cristina", "initials": "C", "orcid": "0000-0001-8748-3743", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/82e0bb00dab543318861f81cb3569541.json"}}, {"family": "Ryder", "given": "Oliver A", "initials": "OA", "orcid": "0000-0003-2427-763X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/3d18635ed6fa42d4bbcfddadae70e308.json"}}, {"family": "Sabir", "given": "Jamal S M", "initials": "JSM", "orcid": "0000-0003-4785-9894", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b644127a1d8740bba24dc2fef3c23c81.json"}}, {"family": "Shaffer", "given": "H Bradley", "initials": "HB", "orcid": "0000-0002-5795-9242", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/910008f9a77840e5ada4302460516dec.json"}}, {"family": "Shank", "given": "Timothy M", "initials": "TM"}, {"family": "Sherkow", "given": "Jacob S", "initials": "JS", "orcid": "0000-0002-9724-9261", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4ac5a78ced4f490499d8ea3358a73741.json"}}, {"family": "Soltis", "given": "Pamela S", "initials": "PS", "orcid": "0000-0001-9310-8659", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/7c4308f7e0e84bbfaad58eac840db765.json"}}, {"family": "Tang", "given": "Boping", "initials": "B", "orcid": "0000-0002-3241-7914", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ab99aedf62e948c5839d1912180fc2b9.json"}}, {"family": "Tedersoo", "given": "Leho", "initials": "L"}, {"family": "Uliano-Silva", "given": "Marcela", "initials": "M"}, {"family": "Wang", "given": "Kun", "initials": "K"}, {"family": "Wei", "given": "Xiaofeng", "initials": "X"}, {"family": "Wetzer", "given": "Regina", "initials": "R"}, {"family": "Wilson", "given": "Julia L", "initials": "JL"}, {"family": "Xu", "given": "Xun", "initials": "X"}, {"family": "Yang", "given": "Huanming", "initials": "H"}, {"family": "Yoder", "given": "Anne D", "initials": "AD", "orcid": "0000-0002-1781-9552", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/2f4e827f5db545de84e8ae91e7603fc1.json"}}, {"family": "Zhang", "given": "Guojie", "initials": "G", "orcid": "0000-0001-6860-1521", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9ec2e418a32c4161abc876171467f5ea.json"}}], "type": "introductory journal article", "published": "2022-01-25", "journal": {"title": "Proc. Natl. Acad. Sci. U.S.A.", "issn": "1091-6490", "volume": "119", "issue": "4", "issn-l": "0027-8424"}, "abstract": null, "doi": "10.1073/pnas.2115635118", "pmid": "35042800", "labels": [], "xrefs": [{"db": "pmc", "key": "PMC8795548"}, {"db": "pii", "key": "2115635118"}], "notes": [], "created": "2026-08-20T09:31:03.855Z", "modified": "2026-08-20T09:31:05.035Z"}, {"entity": "publication", "iuid": "1eefcae7314541e0a3860a83a1c16d84", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/1eefcae7314541e0a3860a83a1c16d84.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/1eefcae7314541e0a3860a83a1c16d84"}}, "title": "Progressive Cactus is a multiple-genome aligner for the thousand-genome era.", "authors": [{"family": "Armstrong", "given": "Joel", "initials": "J", "orcid": "0000-0003-2077-4671", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/e05c7c5e78e448cdb7d94bae26e7bcb1.json"}}, {"family": "Hickey", "given": "Glenn", "initials": "G"}, {"family": "Diekhans", "given": "Mark", "initials": "M", "orcid": "0000-0002-0430-0989", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/7999277bf08b4dbdbcc7d5e78cafcb00.json"}}, {"family": "Fiddes", "given": "Ian T", "initials": "IT"}, {"family": "Novak", "given": "Adam M", "initials": "AM", "orcid": "0000-0001-5828-047X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/0cc29a94bc2347e0a4d64bdb105b29c0.json"}}, {"family": "Deran", "given": "Alden", "initials": "A"}, {"family": "Fang", "given": "Qi", "initials": "Q", "orcid": "0000-0002-9181-8689", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a04a244840c248c4a7515c427ffdc5de.json"}}, {"family": "Xie", "given": "Duo", "initials": "D", "orcid": "0000-0001-7010-3601", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/0bee104c168a4a2994257ccca5a835ca.json"}}, {"family": "Feng", "given": "Shaohong", "initials": "S", "orcid": "0000-0002-2462-7348", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/458d41da2844484a82fb7b21231a567e.json"}}, {"family": "Stiller", "given": "Josefin", "initials": "J", "orcid": "0000-0001-6009-9581", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c58298dbc8ef46a086a0f74bdded4a6b.json"}}, {"family": "Genereux", "given": "Diane", "initials": "D"}, {"family": "Johnson", "given": "Jeremy", "initials": "J"}, {"family": "Marinescu", "given": "Voichita Dana", "initials": "VD"}, {"family": "Alf\u00f6ldi", "given": "Jessica", "initials": "J"}, {"family": "Harris", "given": "Robert S", "initials": "RS"}, {"family": "Lindblad-Toh", "given": "Kerstin", "initials": "K"}, {"family": "Haussler", "given": "David", "initials": "D", "orcid": "0000-0003-1533-4575", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c4b918ad2e1c4544a4a52dfd64f6ebba.json"}}, {"family": "Karlsson", "given": "Elinor", "initials": "E", "orcid": "0000-0002-4343-3776", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/81b5c82fcb904394b6a6b1d811863fa0.json"}}, {"family": "Jarvis", "given": "Erich D", "initials": "ED"}, {"family": "Zhang", "given": "Guojie", "initials": "G", "orcid": "0000-0001-6860-1521", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9ec2e418a32c4161abc876171467f5ea.json"}}, {"family": "Paten", "given": "Benedict", "initials": "B", "orcid": "0000-0001-8863-3539", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c916e24b35f2459480cf87e27bb21ee1.json"}}], "type": "comparative study", "published": "2020-11-00", "journal": {"title": "Nature", "issn": "1476-4687", "volume": "587", "issue": "7833", "pages": "246-251", "issn-l": "0028-0836"}, "abstract": "New genome assemblies have been arriving at a rapidly increasing pace, thanks to decreases in sequencing costs and improvements in third-generation sequencing technologies1-3. For example, the number of vertebrate genome assemblies currently in the NCBI (National Center for Biotechnology Information) database4 increased by more than 50% to 1,485 assemblies in the year from July 2018 to July 2019. In addition to this influx of assemblies from different species, new human de novo assemblies5 are being produced, which enable the analysis of not only small polymorphisms, but also complex, large-scale structural differences between human individuals and haplotypes. This coming era and its unprecedented amount of data offer the opportunity to uncover many insights into genome evolution but also present challenges in how to adapt current analysis methods to meet the increased scale. Cactus6, a reference-free multiple genome alignment program, has been shown to be highly accurate, but the existing implementation scales poorly with increasing numbers of genomes, and struggles in regions of highly duplicated sequences. Here we describe progressive extensions to Cactus to create Progressive Cactus, which enables the reference-free alignment of tens to thousands of large vertebrate genomes while maintaining high alignment quality. We describe results from an alignment of more than 600 amniote genomes, which is to our knowledge the largest multiple vertebrate genome alignment created so far.", "doi": "10.1038/s41586-020-2871-y", "pmid": "33177663", "labels": [], "xrefs": [{"db": "mid", "key": "NIHMS1615919"}, {"db": "pmc", "key": "PMC7673649"}, {"db": "pii", "key": "10.1038/s41586-020-2871-y"}], "notes": [], "created": "2026-08-20T08:56:20.261Z", "modified": "2026-08-20T08:56:56.935Z"}]}