The Ruminant Telomere-to-Telomere (RT2T) Consortium

Nurk, S. et al. The complete sequence of a human genome. Science 376, 44–53 (2022).Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Gershman, A. et al. Epigenetic patterns in a complete human genome. Science 376, eabj5089 (2022).Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Altemose, N. et al. Complete genomic and epigenetic maps of human centromeres. Science 376, eabl4178 (2022).Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Hoyt, S. J. et al. From telomere to telomere: the transcriptional and epigenetic state of human repeat elements. Science 376, eabk3112 (2022).Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Aganezov, S. et al. A complete reference genome improves analysis of human genetic variation. Science 376, eabl3533 (2022).Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Vollger, M. R. et al. Segmental duplications and their variation in a complete human genome. Science 376, eabj6965 (2022).Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Chen, J. et al. A complete telomere-to-telomere assembly of the maize genome. Nat. Genet. 55, 1221–1231 (2023).Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Zhang, C. et al. The T2T genome assembly of soybean cultivar ZH13 and its epigenetic landscapes. Mol. Plant 16, 1715–1718 (2023).Article 
CAS 
PubMed 

Google Scholar 
Deng, Y. et al. A telomere-to-telomere gap-free reference genome of watermelon and its mutation library provide important resources for gene discovery and breeding. Mol. Plant 15, 1268–1284 (2022).Article 
CAS 
PubMed 

Google Scholar 
Nakandala, U. et al. Haplotype resolved chromosome level genome assembly of Citrus australis reveals disease resistance and other citrus specific genes. Hortic. Res. 10, uhad058 (2023).Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Li, G. et al. The haplotype-resolved T2T reference genome highlights structural variation underlying agronomic traits of melon. Hortic. Res. 10, uhad182 (2023).Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Li, B. et al. A gap-free reference genome reveals structural variations associated with flowering time in rapeseed (Brassica napus). Hortic. Res. 10, uhad171 (2023).Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Alberto, F. J. et al. Convergent genomic signatures of domestication in sheep and goats. Nat. Commun. 9, 813 (2018).Article 
PubMed 
PubMed Central 

Google Scholar 
Hackmann, T. J. & Spain, J. N. Invited review: ruminant ecology and evolution: perspectives useful to ruminant livestock research and production. J. Dairy Sci. 93, 1320–1334 (2010).Article 
CAS 
PubMed 

Google Scholar 
Minervino, A. H. H., Zava, M., Vecchio, D. & Borghese, A. Bubalus bubalis: a short story. Front. Vet. Sci. 7, 570413 (2020).Article 
PubMed 
PubMed Central 

Google Scholar 
Gilbert, M. et al. Global distribution data for cattle, buffaloes, horses, sheep, goats, pigs, chickens and ducks in 2010. Sci. Data 5, 180227 (2018).
Google Scholar 
Graphodatsky, A., Perelman, P. & Obrien, S. J. in Atlas of Mammalian Chromosomes 706–857 (John Wiley & Sons, 2020).Chen, L. et al. Large-scale ruminant genome sequencing provides insights into their evolution and distinct traits. Science 364, eaav6202 (2019).Article 
CAS 
PubMed 

Google Scholar 
Ker, D. F. E. & Yang, Y. P. Ruminants: evolutionary past and future impact. Science 364, 1130–1131 (2019).Article 
CAS 
PubMed 

Google Scholar 
Wang, Y. et al. Genetic basis of ruminant headgear and rapid antler regeneration. Science 364, eaav6335 (2019).Article 
CAS 
PubMed 

Google Scholar 
Lin, Z. et al. Biological adaptations in the Arctic cervid, the reindeer (Rangifer tarandus). Science 364, eaav6312 (2019).Article 
CAS 
PubMed 

Google Scholar 
Rhie, A. et al. Towards complete and error-free genome assemblies of all vertebrate species. Nature 592, 737–746 (2021).Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Qiu, Q. et al. The yak genome and adaptation to life at high altitude. Nat. Genet. 44, 946–949 (2012).Article 
CAS 
PubMed 

Google Scholar 
Rice, E. S. et al. Continuous chromosome-scale haplotypes assembled from a single interspecies F1 hybrid of yak and cattle. Gigascience 9, giaa029 (2020).Article 
PubMed 
PubMed Central 

Google Scholar 
Lejeune, J. et al. A proposed standard system of nomenclature of human mitotic chromosomes. Lancet 275, 1063–1065 (1960).Cribiu, E. P. et al. International system for chromosome nomenclature of domestic bovids (ISCNDB 2000). Cytogenet. Cell Genet. 92, 283–299 (2001).Article 
CAS 
PubMed 

Google Scholar 
Brown, J. D. & O’Neill, R. J. Chromosomes, conflict, and epigenetics: chromosomal speciation revisited. Annu. Rev. Genomics Hum. Genet. 11, 291–316 (2010).CAS 

Google Scholar 
Potter, S. et al. Chromosomal speciation in the genomics era: disentangling phylogenetic evolution of rock-wallabies. Front. Genet. 8, 10 (2017).Article 
PubMed 
PubMed Central 

Google Scholar 
Wurster, D. H. & Benirschke, K. Indian muntjac, Muntiacus muntjak: a deer with a low diploid chromosome number. Science 168, 1364–1366 (1970).Article 
CAS 
PubMed 

Google Scholar 
Vujosevic, M., Rajicic, M. & Blagojevic, J. B chromosomes in populations of mammals revisited. Genes 9, 487 (2018).Article 
PubMed 
PubMed Central 

Google Scholar 
Bovine HapMap, C. et al. Genome-wide survey of SNP variation uncovers the genetic structure of cattle breeds. Science 324, 528–532 (2009).Article 

Google Scholar 
Rexroad, C. et al. Genome to phenome: improving animal health, production, and well-being — a new USDA blueprint for animal genome research 2018–2027. Front. Genet. 10, 327 (2019).Article 
PubMed 
PubMed Central 

Google Scholar 
Kalbfleisch, T. S. et al. A SNP resource for studying North American moose. F1000Res. 7, 40 (2018).Article 
PubMed 
PubMed Central 

Google Scholar 
Cherry, S. G., Merkle, J. A., Sigaud, M., Fortin, D. & Wilson, G. A. Managing genetic diversity and extinction risk for a rare plains bison (Bison bison bison) population. Environ. Manage. 64, 553–563 (2019).Article 
PubMed 

Google Scholar 
Theissinger, K. et al. How genomics can help biodiversity conservation. Trends Genet. 39, 545–559 (2023).Article 
CAS 
PubMed 

Google Scholar 
Paez, S. et al. Reference genomes for conservation. Science 377, 364–366 (2022).Article 
CAS 
PubMed 

Google Scholar 
Makova, K. D. et al. The complete sequence and comparative analysis of ape sex chromosomes. Nature 630, 401–411 (2024).Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Rautiainen, M. et al. Telomere-to-telomere assembly of diploid chromosomes with Verkko. Nat. Biotechnol. 41, 1474–1482 (2023).Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Cheng, H., Concepcion, G. T., Feng, X., Zhang, H. & Li, H. Haplotype-resolved de novo assembly using phased assembly graphs with hifiasm. Nat. Methods 18, 170–175 (2021).Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Corbo, M., Damas, J., Bursell, M. G. & Lewin, H. A. Conservation of chromatin conformation in carnivores. Proc. Natl Acad. Sci. USA 119, e2120555119 (2022).Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Foissac, S. et al. Multi-species annotation of transcriptome and chromatin structure in domesticated animals. BMC Biol. 17, 108 (2019).Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Spielmann, M., Lupianez, D. G. & Mundlos, S. Structural variation in the 3D genome. Nat. Rev. Genet. 19, 453–467 (2018).Article 
CAS 
PubMed 

Google Scholar 
Shanta, O., Noor, A., Human Genome Structural Variation Consortium & Sebat, J. The effects of common structural variants on 3D chromatin structure. BMC Genomics 21, 95 (2020).CAS 

Google Scholar 
Anania, C. & Lupianez, D. G. Order and disorder: abnormal 3D chromatin organization in human disease. Brief. Funct. Genomics 19, 128–138 (2020).Article 

Google Scholar 
Liao, Y., Zhang, X., Chakraborty, M. & Emerson, J. J. Topologically associating domains and their role in the evolution of genome structure and function in Drosophila. Genome Res. 31, 397–410 (2021).Article 
PubMed 
PubMed Central 

Google Scholar 
Mattick, J. S. et al. Long non-coding RNAs: definitions, functions, challenges and recommendations. Nat. Rev. Mol. Cell Biol. 24, 430–447 (2023).Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Tonegawa, S. Somatic generation of antibody diversity. Nature 302, 575–581 (1983).Article 
CAS 
PubMed 

Google Scholar 
Safonova, Y. et al. Variations in antibody repertoires correlate with vaccine responses. Genome Res. 32, 791–804 (2022).Article 
PubMed 
PubMed Central 

Google Scholar 
Sok, D. et al. Rapid elicitation of broadly neutralizing antibodies to HIV by immunization in cows. Nature 548, 108–111 (2017).Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Clark, T. A. et al. Characterization of DNA methyltransferase specificities using single-molecule, real-time DNA sequencing. Nucleic Acids Res. 40, e29 (2012).Article 
CAS 
PubMed 

Google Scholar 
Lee, W. C. et al. The complete methylome of Helicobacter pylori UM032. BMC Genomics 16, 424 (2015).
Google Scholar 
Payelleville, A. et al. The complete methylome of an entomopathogenic bacterium reveals the existence of loci with unmethylated adenines. Sci. Rep. 8, 12091 (2018).Article 
PubMed 
PubMed Central 

Google Scholar 
Rand, A. C. et al. Mapping DNA methylation with high-throughput nanopore sequencing. Nat. Methods 14, 411–413 (2017).Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Simpson, J. T. et al. Detecting DNA cytosine methylation using nanopore sequencing. Nat. Methods 14, 407–410 (2017).Article 
CAS 
PubMed 

Google Scholar 
Tvedte, E. S. et al. Comparison of long-read sequencing technologies in interrogating bacteria and fly genomes. G3 11, jkab083 (2017).Article 

Google Scholar 
Konstantinidis, I. et al. Major gene expression changes and epigenetic remodelling in Nile tilapia muscle after just one generation of domestication. Epigenetics 15, 1052–1067 (2020).Article 
PubMed 
PubMed Central 

Google Scholar 
Janowitz Koch, I. et al. The concerted impact of domestication and transposon insertions on methylation patterns between dogs and grey wolves. Mol. Ecol. 25, 1838–1855 (2016).Article 
CAS 
PubMed 

Google Scholar 
Hayes, B. J. & Daetwyler, H. D. 1000 Bull Genomes Project to map simple and complex genetic traits in cattle: applications and outcomes. Annu. Rev. Anim. Biosci. 7, 89–102 (2019).Article 
CAS 
PubMed 

Google Scholar 
Daetwyler, H. D. et al. Whole-genome sequencing of 234 bulls facilitates mapping of monogenic and complex traits in cattle. Nat. Genet. 46, 858–865 (2014).Article 
CAS 
PubMed 

Google Scholar 
Nguyen, T. V. et al. In it for the long run: perspectives on exploiting long-read sequencing in livestock for population scale studies of structural variants. Genet. Sel. Evol. 55, 9 (2023).Article 
PubMed 
PubMed Central 

Google Scholar 
Davenport, K. M. et al. An improved ovine reference genome assembly to facilitate in-depth functional annotation of the sheep genome. Gigascience 11, giab096 (2022).Article 
PubMed 
PubMed Central 

Google Scholar 
Guhlin, J. et al. Species-wide genomics of kākāpō provides tools to accelerate recovery. Nat. Ecol. Evol. 7, 1693–1705 (2023).Article 
PubMed 

Google Scholar 
Hogg, C. J. et al. Threatened Species Initiative: empowering conservation action using genomic resources. Proc. Natl Acad. Sci. USA 119, e2115643118 (2022).Article 
PubMed 
PubMed Central 

Google Scholar 
Lewin, H. A. et al. Earth BioGenome Project: sequencing life for the future of life. Proc. Natl Acad. Sci. USA 115, 4325–4333 (2018).Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Zurano, J. P. et al. Cetartiodactyla: updating a time-calibrated molecular phylogeny. Mol. Phylogenet. Evol. 133, 256–262 (2019).
Google Scholar 

Hot Topics

Related Articles