Meyer, A. et al. Giant lungfish genome elucidates the conquest of land by vertebrates. Nature 590, 284â289 (2021).
Wang, K. et al. African lungfish genome sheds light on the vertebrate water-to-land transition. Cell 184, 1362â1376.e1318 (2021).
Irisarri, I. et al. Phylotranscriptomic consolidation of the jawed vertebrate timetree. Nat. Ecol. Evol. 1, 1370â1378 (2017).
Krefft, J. L. G. Description of a gigantic amphibian allied to the genus Lepidosiren from the Wide-Bay district, Queensland. Proc. Zool. Soc. Lond. 1870, 221â224 (1870).
Meyer, A. & Dolven, S. I. Molecules, fossils, and the origin of tetrapods. J. Mol. Evol. 35, 102â113 (1992).
Kemp, A. The biology of the Australian lungfish, Neoceratodus forsteri (Krefft 1870). J. Morphol. 190, 181â198 (1986).
Nowoshilow, S. et al. The axolotl genome and the evolution of key tissue formation regulators. Nature 554, 50â55 (2018).
Shao, C. et al. The enormous repetitive Antarctic krill genome reveals environmental adaptations and population insights. Cell 186, 1279â1294.e1219 (2023).
Oliveira, C. et al. Chromosome formulae of neotropical freshwater fishes. Rev. Brasil. Genet. 11, 577â624 (1988).
Suzuki, A. & Yamanaka, K. Chromosomes of an African Lungfish, Protopterus annectens. Proc. Jpn Acad. B Phys. Biol. Sci. 64, 119â121 (1988).
Nurk, S. et al. The complete sequence of a human genome. Science 376, 44â53 (2022).
Irisarri, I. & Meyer, A. The identification of the closest living relative(s) of tetrapods: phylogenomic lessons for resolving short ancient internodes. Syst. Biol. 65, 1057â1075 (2016).
Brownstein, C. D., Harrington, R. C. & Near, T. J. The biogeography of extant lungfishes traces the breakup of Gondwana. J. Biogeogr. 50, 1191â1198 (2023).
Simakov, O. et al. Deeply conserved synteny resolves early events in vertebrate evolution. Nat. Ecol. Evol. 4, 820â830 (2020).
Simakov, O. et al. Deeply conserved synteny and the evolution of metazoan chromosomes. Sci. Adv. 8, eabi5884 (2022).
Muffato, M. et al. Reconstruction of hundreds of reference ancestral genomes across the eukaryotic kingdom. Nat. Ecol. Evol. 7, 355â366 (2023).
Bourque, G. et al. Ten things you should know about transposable elements. Genome Biol. 19, 199 (2018).
Meyer, A. & Schartl, M. Gene and genome duplications in vertebrates: the one-to-four (-to-eight in fish) rule and the evolution of novel gene functions. Curr. Opin. Cell Biol. 11, 699â704 (1999).
Thomson, K. S. An attempt to reconstruct evolutionary changes in the cellular DNA content of lungfish. J. Exp. Zool. 180, 363â371 (1972).
Gregory, T. R. The bigger the C-value, the larger the cell: genome size and red blood cell size in vertebrates. Blood Cells Mol. Dis. 27, 830â843 (2001).
Nystedt, B. et al. The Norway spruce genome sequence and conifer genome evolution. Nature 497, 579â584 (2013).
Falcon, F., Tanaka, E. M. & Rodriguez-Terrones, D. Transposon waves at the water-to-land transition. Curr. Opin. Genet. Dev. 81, 102059 (2023).
Brennecke, J. et al. Discrete small RNA-generating loci as master regulators of transposon activity in Drosophila. Cell 128, 1089â1103 (2007).
Yi, M. et al. Rapid evolution of piRNA pathway in the teleost fish: implication for an adaptation to transposon diversity. Genome Biol. Evol. 6, 1393â1407 (2014).
Wang, J. et al. Transposable element and host silencing activity in gigantic genomes. Front. Cell Dev. Biol. 11, 1124374 (2023).
Song, J. et al. Variation in piRNA and transposable element content in strains of Drosophila melanogaster. Genome Biol. Evol. 6, 2786â2798 (2014).
Aravin, A. A. et al. A piRNA pathway primed by individual transposons is linked to de novo DNA methylation in mice. Mol. Cell 31, 785â799 (2008).
Wang, W. et al. The initial uridine of primary piRNAs does not create the tenth adenine that is the hallmark of secondary piRNAs. Mol. Cell 56, 708â716 (2014).
Pasquesi, G. I. M. et al. Vertebrate lineages exhibit diverse patterns of transposable element regulation and expression across tissues. Genome Biol. Evol. 12, 506â521 (2020).
Kofler, R. piRNA clusters need a minimum size to control transposable element invasions. Genome Biol. Evol. 12, 736â749 (2020).
Liu, X. et al. Transposable element expansion and low-level piRNA silencing in grasshoppers may cause genome gigantism. BMC Biol. 20, 243 (2022).
Yang, P., Wang, Y. & Macfarlan, T. S. The role of KRAB-ZFPs in transposable element repression and mammalian evolution. Trends Genet. 33, 871â881 (2017).
Imbeault, M., Helleboid, P.-Y. & Trono, D. KRAB zinc-finger proteins contribute to the evolution of gene regulatory networks. Nature 543, 550â554 (2017).
Kaessmann, H., Vinckenbosch, N. & Long, M. RNA-based gene duplication: mechanistic and evolutionary insights. Nat. Rev. Genet. 10, 19â31 (2009).
Carelli, F. N. et al. The life history of retrocopies illuminates the evolution of new mammalian genes. Genome Res. 26, 301â314 (2016).
Chen, M. et al. Evolutionary patterns of RNA-based duplication in non-mammalian chordates. PLoS ONE 6, e21466 (2011).
Okabe, M. & Graham, A. The origin of the parathyroid gland. Proc. Natl Acad. Sci. USA 101, 17716â17719 (2004).
Li, C. et al. Genome sequences reveal global dispersal routes and suggest convergent genetic adaptations in seahorse evolution. Nat. Commun. 12, 1094 (2021).
Kerr, T. The scales of modern lungfish. Proc. Zool. Soc. Lond. 125, 335â345 (1955).
Lander, E. S. et al. Initial sequencing and analysis of the human genome. Nature 409, 860â921 (2001).
Di-Poï, N., Montoya-Burgos, J. I. & Duboule, D. Atypical relaxation of structural constraints in Hox gene clusters of the green anole lizard. Genome Res. 19, 602â610 (2009).
Feiner, N. Accumulation of transposable elements in Hox gene clusters during adaptive radiation of Anolis lizards. Proc. Biol. Sci. 283, 20161555 (2016).
Woltering, J. M., Noordermeer, D., Leleu, M. & Duboule, D. Conservation and divergence of regulatory strategies at Hox loci and the origin of tetrapod digits. PLoS Biol. 12, e1001773 (2014).
Berlivet, S. et al. Clustering of tissue-specific sub-TADs accompanies the regulation of HoxA genes in developing limbs. PLoS Genet. 9, e1004018 (2013).
Kemp, A., Cavin, L. & Guinot, G. Evolutionary history of lungfishes with a new phylogeny of post-Devonian genera. Palaeogeogr. Palaeoclimatol. Palaeoecol. 471, 209â219 (2017).
DÃaz-González, F. et al. Biallelic cGMP-dependent type II protein kinase gene (PRKG2) variants cause a novel acromesomelic dysplasia. J. Med. Genet. 59, 28â38 (2022).
Lewandowski, J. P. et al. Spatiotemporal regulation of GLI target genes in the mammalian limb bud. Dev. Biol. 406, 92â103 (2015).
Breslow, D. K. et al. A CRISPR-based screen for Hedgehog signaling provides insights into ciliary function and ciliopathies. Nat. Genet. 50, 460â471 (2018).
Yang, L. et al. Enlarged fins of Tibetan catfish provide new evidence of adaptation to high plateau. Sci. China Life Sci. 66, 1554â1568 (2023).
Letelier, J. et al. The Shh/Gli3 gene regulatory network precedes the origin of paired fins and reveals the deep homology between distal fins and digits. Proc. Natl Acad. Sci. USA 118, e2100575118 (2021).
Woltering, J. M. et al. Sarcopterygian fin ontogeny elucidates the origin of hands with digits. Sci. Adv. 6, eabc3510 (2020).
Kvon, E. Z. et al. Comprehensive in vivo interrogation reveals phenotypic impact of human enhancer variants. Cell 180, 1262â1271.e1215 (2020).
Roscito, J. G. et al. Convergent and lineage-specific genomic differences in limb regulatory elements in limbless reptile lineages. Cell Rep. 38, 110280 (2022).
Ovchinnikov, V. et al. Caecilian genomes reveal the molecular basis of adaptation and convergent evolution of limblessness in snakes and caecilians. Mol. Biol. Evol. 40, msad102 (2023).
Lopez-Rios, J. The many lives of SHH in limb development and evolution. Semin. Cell Dev. Biol. 49, 116â124 (2016).
Farrell, E. R. & Münsterberg, A. E. csal1 is controlled by a combination of FGF and Wnt signals in developing limb buds. Dev. Biol. 225, 447â458 (2000).
Carneiro, J. et al. Evidence of cryptic speciation in South American lungfish. J. Zool. Syst. Evol. Res. 59, 760â771 (2021).
Storer, J., Hubley, R., Rosen, J., Wheeler, T. J. & Smit, A. F. The Dfam community resource of transposable element families, sequence models, and genome annotations. Mob. DNA 12, 2 (2021); https://pubmed.ncbi.nlm.nih.gov/33436076/.
Flynn, J. M. et al. RepeatModeler2 for automated genomic discovery of transposable element families. Proc. Natl Acad. Sci USA 117, 9451â9457 (2020); https://pubmed.ncbi.nlm.nih.gov/32300014/.
Benson, G. Tandem repeats finder: a program to analyze DNA sequences. Nucleic Acids Res. 27, 573â580 (1999); https://pubmed.ncbi.nlm.nih.gov/9862982/.
Bao, Z., & Edyy, S. R. Automated de novo identification of repeat sequence families in sequenced genomes. Genome Res. 12, 1269â1276 (2002).
Price, A. L., Jones, N. C. & Pevzner, P. A. De novo identification of repeat families in large genomes. Bioinformatics 21, i351âi358 (2005).
Camacho, C. et al. BLAST+: architecture and applications. BMC Bioinform. 10, 421 (2009).
Chalopin, D., Naville, M., Plard, F., Galiana, D. & Volff, J.-N. Comparative analysis of transposable elements highlights mobilome diversity and evolution in vertebrates. Genome Biol. Evol. 7, 567â580 (2015).
Conte, M. A. et al. Chromosome-scale assemblies reveal the structural evolution of African cichlid genomes. Gigascience 8, giz030 (2019).
Brawand, D. et al. The genomic substrate for adaptive radiation in African cichlid fish. Nature 513, 375â381 (2014).
Kong, Y. et al. Transposable element expression in tumors is associated with immune infiltration and increased antigenicity. Nat. Commun. 10, 5228 (2019).
Yang, W. R., Ardeljan, D., Pacyna, C. N., Payer, L. M. & Burns, K. H. SQuIRE reveals locus-specific regulation of interspersed repeat expression. Nucleic Acids Res. 47, e27 (2019).
Peona, V. et al. The avian W chromosome is a refugium for endogenous retroviruses with likely effects on female-biased mutational load and genetic incompatibilities. Philos. Trans. R. Soc. Lond. B Biol. Sci. 376, 20200186 (2021).
Finn, R. D. et al. Pfam: the protein families database. Nucleic Acids Res. 42, D222âD230 (2014).
Ellinghaus, D., Kurtz, S. & Willhoeft, U. LTRharvest, an efficient and flexible software for de novo detection of LTR retrotransposons. BMC Bioinform. 9, 18 (2008).
Steinbiss, S., Willhoeft, U., Gremme, G. & Kurtz, S. Fine-grained annotation and classification of de novo predicted LTR retrotransposons. Nucleic Acids Res. 37, 7002â7013 (2009).
Llorens, C. et al. The Gypsy Database (GyDB) of mobile genetic elements: release 2.0. Nucleic Acids Res. 39, D70âD74 (2011).
Groza, C., Chen, X., Wheeler, T. J., Bourque, G. & Goubert, C. GraffiTE: a unified framework to analyzetransposable element insertion polymorphisms using genome-graphs. Preprint at bioRxiv https://doi.org/10.1101/2023.09.11.557209 (2023).
She, R., Chu, J. S., Wang, K., Pei, J. & Chen, N. GenBlastA: enabling BLAST to identify homologous gene sequences. Genome Res. 19, 143â149 (2009).
Pearson, W. R. Finding protein and nucleotide similarities with FASTA. Curr. Protoc. Bioinform. 53, 3.9.1â3.9.25 (2016).
Birney, E., Clamp, M. & Durbin, R. GeneWise and Genomewise. Genome Res. 14, 988â995 (2004).
Sellitto, A. et al. Molecular and functional characterization of the somatic PIWIL1/piRNA pathway in colorectal cancer cells. Cells 8, 1390 (2019).
Schmieder, R. & Edwards, R. Quality control and preprocessing of metagenomic datasets. Bioinformatics 27, 863â864 (2011).
Rosenkranz, D. & Zischler, H. proTRAC-a software for probabilistic piRNA cluster detection, visualization and analysis. BMC Bioinform. 13, 5 (2012).
Camacho, C. et al. BLAST+: architecture and applications. BMC Bioinform. 10, 421 (2009).
Emms, D. M. & Kelly, S. OrthoFinder: phylogenetic orthology inference for comparative genomics. Genome Biol. 20, 238 (2019).
Lartillot, N., Rodrigue, N., Stubbs, D. & Richer, J. PhyloBayes MPI: phylogenetic reconstruction with infinite mixtures of profiles in a parallel environment. Syst. Biol. 62, 611â615 (2013).
Delsuc, F., Brinkmann, H., Chourrout, D. & Philippe, H. Tunicates and not cephalochordates are the closest living relatives of vertebrates. Nature 439, 965â968 (2006).
Revell, L. J. phytools: an R package for phylogenetic comparative biology (and other things). Methods Ecol. Evol. 3, 217â223 (2012).
Thomson, K. S. & Muraszko, K. Estimation of cell size and DNA content in fossil fishes and amphibians. J. Exp. Zool. 205, 315â320 (1978).
Huang, Z. et al. Three amphioxus reference genomes reveal gene and chromosome evolution of chordates. Proc. Natl Acad. Sci. USA 120, e2201504120 (2023).
Kautt, A. F. et al. Contrasting signatures of genomic divergence during sympatric speciation. Nature 588, 106â111 (2020).
Suyama, M., Torrents, D. & Bork, P. PAL2NAL: robust conversion of protein sequence alignments into the corresponding codon alignments. Nucleic Acids Res. 34, W609âW612 (2006).
Edgar, R. C. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 32, 1792â1797 (2004).
Castresana, J. Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Mol. Biol. Evol. 17, 540â552 (2000).
Huerta-Cepas, J., Serra, F. & Bork, P. ETE 3: reconstruction, analysis, and visualization of phylogenomic data. Mol. Biol. Evol. 33, 1635â1638 (2016).
Emms, D. M. & Kelly, S. OrthoFinder: phylogenetic orthology inference for comparative genomics. Genome Biol. 20, 238 (2019).
Deng, W., Nickle, D. C., Learn, G. H., Maust, B. & Mullins, J. I. ViroBLAST: a stand-alone BLAST web server for flexible queries of multiple databases and userâs datasets. Bioinformatics 23, 2334â2336 (2007).
Montavon, T. et al. A regulatory archipelago controls Hox genes transcription in digits. Cell 147, 1132â1145 (2011).
Dixon, J. R. et al. Topological domains in mammalian genomes identified by analysis of chromatin interactions. Nature 485, 376â380 (2012).
Wang, Y. et al. The 3D Genome Browser: a web-based browser for visualizing 3D genome organization and long-range chromatin interactions. Genome Biol. 19, 151 (2018).
RamÃrez, F. et al. High-resolution TADs reveal DNA sequences underlying genome organization in flies. Nat. Commun. 9, 189 (2018).
Taylor, W. & Van Dyke, G. Revised procedures for staining and clearing small fishes and other vertebrates for bone and cartilage study. Cybium 9, 107â119 (1985).
Kvon, E. Z. et al. Progressive loss of function in a limb enhancer during snake evolution. Cell 167, 633â642.e611 (2016).
Osterwalder, M. et al. in Craniofacial Development Vol. 2403 (ed. Dworkin, S.) 147â186 (Humana, 2022).
Du, K. Lungfish genome annotation. figshare https://doi.org/10.6084/m9.figshare.24147732.v1 (2024).
