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Cited by 211Chromosomal and Genetic VariationsGenomics and Phylogenetic StudiesDevelopmental Biology and Gene Regulation

Giant lungfish genome elucidates the conquest of land by vertebrates

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Meyer, Axel, Schloissnig, Siegfried, Franchini, Paolo, Du, Kang, Woltering, Joost M., Irisarri, Iker, Wong, Wai Yee, Nowoshilow, Sergej +11 more·2021·Nature
DOI 10.1038/s41586-021-03198-8PMC PMC7875771
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Abstract

Lungfishes belong to lobe-fined fish (Sarcopterygii) that, in the Devonian period, ‘conquered’ the land and ultimately gave rise to all land vertebrates, including humans 1–3 . Here we determine the chromosome-quality genome of the Australian lungfish ( Neoceratodus forsteri ), which is known to have the largest genome of any animal. The vast size of this genome, which is about 14× larger than that of humans, is attributable mostly to huge intergenic regions and introns with high repeat content (around 90%), the components of which resemble those of tetrapods (comprising mainly long interspersed nuclear elements) more than they do those of ray-finned fish. The lungfish genome continues to expand independently (its transposable elements are still active), through mechanisms different to those of the enormous genomes of salamanders. The 17 fully assembled lungfish macrochromosomes maintain synteny to other vertebrate chromosomes, and all microchromosomes maintain conserved ancient homology with the ancestral vertebrate karyotype. Our phylogenomic analyses confirm previous reports that lungfish occupy a key evolutionary position as the closest living relatives to tetrapods 4,5 , underscoring the importance of lungfish for understanding innovations associated with terrestrialization. Lungfish preadaptations to living on land include the gain of limb-like expression in developmental genes such as hoxc13 and sall1 in their lobed fins. Increased rates of evolution and the duplication of genes associated with obligate air-breathing, such as lung surfactants and the expansion of odorant receptor gene families (which encode proteins involved in detecting airborne odours), contribute to the tetrapod-like biology of lungfishes. These findings advance our understanding of this major transition during vertebrate evolution.

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  • Particularly large or complex genomes, such as that of the lungfish, remain difficult to assemble to chromosomal completeness.

    “Particularly large or complex genomes, such as that of the lungfish, remain difficult to assemble to chromosomal completeness (94).”

    From Topological Approaches in Animal Comparative Genomics (2026) · cites this paper as [94]

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  1. [4]Irisarri I Meyer A The identification of the closest living relative(s) of tetrapods: phylogenomic lessons for resolving short ancient internodes Syst. Biol. 2016 65 1057 1075 27425642
  2. [6]Krefft G Description of a giant amphibian allied to the genus Lepidosiren from the Wide Bay district, Queensland Proc. Zool. Soc. Lond. 1870 1870 221 224
  3. [7]Gunther A XIX. Description of Ceratodus, a genus of ganoid fishes, recently discovered in rivers of Queensland, Australia Phil. Trans. R. Soc. B 1871 161 511 571
  4. [8]Nowoshilow S The axolotl genome and the evolution of key tissue formation regulators Nature 2018 554 50 55 29364872
  5. [9]Rock J Eldridge M Champion A Johnston P Joss J Karyotype and nuclear DNA content of the Australian lungfish, Neoceratodus forsteri (Ceratodidae: Dipnoi) Cytogenet. Cell Genet. 1996 73 187 189 8697805
  6. [10]Pedersen RA DNA content, ribosomal gene multiplicity, and cell size in fish J. Exp. Zool. 1971 177 65 78 5569239
  7. [11]Amemiya CT The African coelacanth genome provides insights into tetrapod evolution Nature 2013 496 311 316 23598338 PMC3633110
  8. [12]Fox DT Soltis DE Soltis PS Ashman T-L Van de Peer Y polyploidy: a biological force from cells to ecosystems Trends Cell Biol. 2020 30 688 694 32646579 PMC7484144
  9. [14]Putnam NH The amphioxus genome and the evolution of the chordate karyotype Nature 2008 453 1064 1071 18563158
  10. [15]Simakov O Deeply conserved synteny resolves early events in vertebrate evolution Nat. Ecol. Evol. 2020 4 820 830 32313176 PMC7269912
  11. [16]Braasch I The spotted gar genome illuminates vertebrate evolution and facilitates human–teleost comparisons Nat. Genet. 2016 48 427 437 26950095 PMC4817229
  12. [17]Jurka J Kapitonov VV Kohany O Jurka MV Repetitive sequences in complex genomes: structure and evolution Annu. Rev. Genomics Hum. Genet. 2007 8 241 259 17506661
  13. [18]Zhang Q Edwards SV The evolution of intron size in amniotes: a role for powered flight? Genome Biol. Evol. 2012 4 1033 1043 22930760 PMC3490418
  14. [20]Bradnam KR Korf I Longer first introns are a general property of eukaryotic gene structure PLoS ONE 2008 3 e3093 18769727 PMC2518113
  15. [21]Kugler MC Joyner AL Loomis CA Munger JS Sonic hedgehog signaling in the lung. From development to disease Am. J. Respir. Cell Mol. Biol. 2015 52 1 13 25068457 PMC4370254
  16. [22]Rankin SA A molecular atlas of Xenopus respiratory system development Dev. Dyn. 2015 244 69 85 25156440 PMC4276498
  17. [23]Døving KB Trotier D Structure and function of the vomeronasal organ J. Exp. Biol. 1998 201 2913 2925 9866877
  18. [24]Syed AS Sansone A Hassenklöver T Manzini I Korsching SI Coordinated shift of olfactory amino acid responses and V2R expression to an amphibian water nose during metamorphosis Cell. Mol. Life Sci. 2017 74 1711 1719 27990576 PMC11107701
  19. [25]Nakamuta S Nakamuta N Taniguchi K Taniguchi K Histological and ultrastructural characteristics of the primordial vomeronasal organ in lungfish Anat. Rec. (Hoboken) 2012 295 481 491 22271496
  20. [26]Visel A Minovitsky S Dubchak I Pennacchio LA VISTA enhancer browser—a database of tissue-specific human enhancers Nucleic Acids Res. 2007 35 D88 D92 17130149 PMC1716724
  21. [27]Pennacchio LA In vivo enhancer analysis of human conserved non-coding sequences Nature 2006 444 499 502 17086198
  22. [28]Dickel DE Visel A Pennacchio LA Functional anatomy of distant-acting mammalian enhancers Philos. Tras. R. Soc. Lond. B 2013 368 20120359 PMC3682724 23650633
  23. [29]Kawakami Y Sall genes regulate region-specific morphogenesis in the mouse limb by modulating Hox activities Development 2009 136 585 594 19168674 PMC3266482
  24. [30]Camp E Hope R Kortschak RD Cox TC Lardelli M Expression of three spalt (sal) gene homologues in zebrafish embryos Dev. Genes Evol. 2003 213 35 43 12590351
  25. [31]Fernandez-Guerrero M Mammalian-specific ectodermal enhancers control the expression of Hoxc genes in developing nails and hair follicles Proc. Natl Acad. Sci. USA 2020 117 30509 30519 33199643 PMC7720164
  26. [32]Spitz F Herkenne C Morris MA Duboule D Inversion-induced disruption of the Hoxd cluster leads to the partition of regulatory landscapes Nat. Genet. 2005 37 889 893 15995706
  27. [33]Andrey G A switch between topological domains underlies HoxD genes collinearity in mouse limbs Science 2013 340 1234167 23744951
  28. [34]Montavon T Duboule D Chromatin organization and global regulation of Hox gene clusters Philos. Trans. R. Soc. Lond. B. 2013 368 20120367 23650639 PMC3682730
  29. [35]Woltering JM Noordermeer D Leleu M Duboule D Conservation and divergence of regulatory strategies at Hox loci and the origin of tetrapod digits PLoS Biol. 2014 12 e1001773 24465181 PMC3897358
  30. [36]Woltering JM Sarcopterygian fin ontogeny elucidates the origin of hands with digits Sci. Adv. 2020 6 eabc3510 32875118 PMC7438105
  31. [37]Woltering JM Holzem M Meyer A Lissamphibian limbs and the origins of tetrapod hox domains Dev. Biol. 2019 456 138 144 31445923
  32. [40]Smith JJ A chromosome-scale assembly of the axolotl genome Genome Res. 2019 29 317 324 30679309 PMC6360810
  33. [41]Nowoshilow S Tanaka EM Introducing www.axolotl-omics.org – an integrated -omics data portal for the axolotl research community Exp. Cell Res. 2020 394 112143 32540400
  34. [43]Song L Florea L Rcorrector: efficient and accurate error correction for Illumina RNA-seq reads Gigascience 2015 4 48 26500767 PMC4615873
  35. [44]MacManes MD The Oyster River Protocol: a multi-assembler and kmer approach for de novo transcriptome assembly PeerJ 2018 6 e5428 30083482 PMC6078068
  36. [45]Chikhi R Medvedev P Informed and automated k-mer size selection for genome assembly Bioinformatics 2014 30 31 37 23732276
  37. [46]Robertson G De novo assembly and analysis of RNA-seq data Nat. Methods 2010 7 909 912 20935650
  38. [47]Emms DM Kelly S OrthoFinder: solving fundamental biases in whole genome comparisons dramatically improves orthogroup inference accuracy Genome Biol. 2015 16 157 26243257 PMC4531804
  39. [48]Li W Jaroszewski L Godzik A Clustering of highly homologous sequences to reduce the size of large protein databases Bioinformatics 2001 17 282 283 11294794
  40. [49]Simão FA Waterhouse RM Ioannidis P Kriventseva EV Zdobnov EM BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs Bioinformatics 2015 31 3210 3212 26059717
  41. [50]Nishimura O Hara Y Kuraku S gVolante for standardizing completeness assessment of genome and transcriptome assemblies Bioinformatics 2017 33 3635 3637 29036533 PMC5870689
  42. [51]Kim D Langmead B Salzberg SL HISAT: a fast spliced aligner with low memory requirements Nat. Methods 2015 12 357 360 25751142 PMC4655817
  43. [52]Pertea M Kim D Pertea GM Leek JT Salzberg SL Transcript-level expression analysis of RNA-seq experiments with HISAT, StringTie and Ballgown Nat. Protocols 2016 11 1650 1667 27560171 PMC5032908
  44. [53]Yan H Bombarely A Li S DeepTE: a computational method for de novo classification of transposons with convolutional neural network Bioinformatics 2020 36 4269 4275 32415954
  45. [54]Chalopin D Volff J-N Analysis of the spotted gar genome suggests absence of causative link between ancestral genome duplication and transposable element diversification in teleost fish J. Exp. Zoolog. B Mol. Dev. Evol. 2017 328 629 637 28921831
  46. [55]Lerat E Fablet M Modolo L Lopez-Maestre H Vieira C TEtools facilitates big data expression analysis of transposable elements and reveals an antagonism between their activity and that of piRNA genes Nucleic Acids Res. 2017 45 e17 28204592 PMC5389681
  47. [56]Wu TD Watanabe CK GMAP: a genomic mapping and alignment program for mRNA and EST sequences Bioinformatics 2005 21 1859 1875 15728110
  48. [57]Haas BJ Improving the Arabidopsis genome annotation using maximal transcript alignment assemblies Nucleic Acids Res. 2003 31 5654 5666 14500829 PMC206470
  49. [59]UniProt Consortium UniProt: a worldwide hub of protein knowledge Nucleic Acids Res. 2019 47 D506 D515 30395287 PMC6323992
  50. [60]Slater GSC Birney E Automated generation of heuristics for biological sequence comparison BMC Bioinformatics 2005 6 31 15713233 PMC553969
  51. [61]Pearson WR Finding protein and nucleotide similarities with FASTA Curr. Protoc. Bioinformatics 2016 53 3.9.1 3.9.25 27010337 PMC5072362
  52. [62]Chan PP Lowe TM tRNAscan-SE: searching for tRNA genes in genomic sequences Methods Mol. Biol. 2019 1962 1 14 31020551 PMC6768409
  53. [63]Nawrocki EP Eddy SR Infernal 1.1: 100-fold faster RNA homology searches Bioinformatics 2013 29 2933 2935 24008419 PMC3810854
  54. [64]Kozomara A Birgaoanu M Griffiths-Jones S miRBase: from microRNA sequences to function Nucleic Acids Res. 2019 47 D155 D162 30423142 PMC6323917
  55. [65]Enright AJ MicroRNA targets in Drosophila Genome Biol. 2003 5 R1 14709173 PMC395733
  56. [67]Kent WJ The human genome browser at UCSC Genome Res. 2002 12 996 1006 12045153 PMC186604
  57. [68]Blanchette M Aligning multiple genomic sequences with the threaded blockset aligner Genome Res. 2004 14 708 715 15060014 PMC383317
  58. [70]Cooper GM Distribution and intensity of constraint in mammalian genomic sequence Genome Res. 2005 15 901 913 15965027 PMC1172034
  59. [73]Whelan S Irisarri I Burki F PREQUAL: detecting non-homologous characters in sets of unaligned homologous sequences Bioinformatics 2018 34 3929 3930 29868763
  60. [75]Criscuolo A Gribaldo S BMGE (Block Mapping and Gathering with Entropy): a new software for selection of phylogenetic informative regions from multiple sequence alignments BMC Evol. Biol. 2010 10 210 20626897 PMC3017758
  61. [77]Dutheil JY Gaillard S Stukenbrock EH MafFilter: a highly flexible and extensible multiple genome alignment files processor BMC Genomics 2014 15 53 24447531 PMC3904536
  62. [79]Lartillot N Lepage T Blanquart S PhyloBayes 3: a Bayesian software package for phylogenetic reconstruction and molecular dating Bioinformatics 2009 25 2286 2288 19535536
  63. [81]Yang Z PAML 4: phylogenetic analysis by maximum likelihood Mol. Biol. Evol. 2007 24 1586 1591 17483113
  64. [82]Marjanović, D. The making of calibration sausage exemplified by recalibrating the transcriptomic timetree of jawed vertebrates Preprint at 10.1101/2019.12.19.882829 (2019). PMC8149952 34054911 · DOI
  65. [83]De Bie T Cristianini N Demuth JP Hahn MW CAFE: a computational tool for the study of gene family evolution Bioinformatics 2006 22 1269 1271 16543274
  66. [84]Buchfink B Xie C Huson DH Fast and sensitive protein alignment using DIAMOND Nat. Methods 2015 12 59 60 25402007
  67. [86]O’Brien KP Remm M Sonnhammer ELL Inparanoid: a comprehensive database of eukaryotic orthologs Nucleic Acids Res. 2005 33 D476 D480 15608241 PMC540061
  68. [87]Suyama M Torrents D Bork P PAL2NAL: robust conversion of protein sequence alignments into the corresponding codon alignments Nucleic Acids Res. 2006 34 W609 W612 16845082 PMC1538804
  69. [88]Edgar RC MUSCLE: multiple sequence alignment with high accuracy and high throughput Nucleic Acids Res. 2004 32 1792 1797 15034147 PMC390337
  70. [89]Castresana J Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis Mol. Biol. Evol. 2000 17 540 552 10742046
  71. [90]Huerta-Cepas J Serra F Bork P ETE 3: reconstruction, analysis, and visualization of phylogenomic data Mol. Biol. Evol. 2016 33 1635 1638 26921390 PMC4868116
  72. [91]Woltering JM Axial patterning in snakes and caecilians: evidence for an alternative interpretation of the Hox code Dev. Biol. 2009 332 82 89 19409887
  73. [92]Monti R Limb-Enhancer Genie: an accessible resource of accurate enhancer predictions in the developing limb PLoS Comput. Biol. 2017 13 e1005720 28827824 PMC5578682
  74. [93]Osterwalder M HAND2 targets define a network of transcriptional regulators that compartmentalize the early limb bud mesenchyme Dev. Cell 2014 31 345 357 25453830 PMC4357275
  75. [94]Osterwalder M Enhancer redundancy provides phenotypic robustness in mammalian development Nature 2018 554 239 243 29420474 PMC5808607
  76. [95]Bickelmann C Noncanonical Hox, Etv4, and Gli3 gene activities give insight into unique limb patterning in salamanders J. Exp. Zoolog. B Mol. Dev. Evol. 2018 330 138 147 29602205
  77. [96]Du K The sterlet sturgeon genome sequence and the mechanisms of segmental rediploidization Nat. Eco. Evol. 2020 4 841 852 PMC7269910 32231327

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Authors
Meyer, A., Schloissnig, S., Franchini, P., Du, K., Woltering, J. M., Irisarri, I., Wong, W. Y., Nowoshilow, S., Kneitz, S., Kawaguchi, A., Fabrizius, A., Xiong, P., Dechaud, C., Spaink, H. P., Volff, J.-N., Simakov, O., Burmester, T., Tanaka, E. M., & Schartl, M.
Affiliations
  • University of Konstanz (DE)
  • Research Institute of Molecular Pathology (AT)
  • Texas State University (US)
  • Museo Nacional de Ciencias Naturales (ES)
  • University of Vienna (AT)
  • University of Würzburg (DE)
  • Universität Hamburg (DE)
  • École Normale Supérieure de Lyon (FR)
  • Leiden University (NL)
Corresponding author
  • Meyer, Axel
  • Simakov, Oleg
  • Burmester, Thorsten
  • Tanaka, Elly M.
  • Schartl, Manfred
ORCID
Venue
Nature
Publisher
Springer Science and Business Media LLC
Published
2021-01-18
Volume
590
Issue
7845
Pages
284-289
ISSN
  • 0028-0836 (ISSN-L)
  • 1476-4687
DOI
10.1038/s41586-021-03198-8
PMC
PMC7875771
OpenAlex
W3125528398
Cited by
211
References
12
Citations by year
2026: 28 · 2025: 27 · 2024: 43 · 2023: 41 · 2022: 33 · 2021: 39
FWCI
23.03
Type
journal article
Language
en
Open access
Licence
Locations
  • Nature (publishedVersion, cc-by)
  • PubMed Central (publishedVersion, cc-by)
  • PubMed (publishedVersion)
  • IRIS Research product catalog (Sapienza University of Rome) (submittedVersion, cc-by)
  • RePEc: Research Papers in Economics (submittedVersion)
  • Leiden Repository (Leiden University) (submittedVersion, cc-by)
  • DIGITAL.CSIC (Spanish National Research Council (CSIC)) (submittedVersion, cc-by)
  • UnitusOpen (Tuscia University) (submittedVersion, public-domain)
  • UnitusOpen (Tuscia University) (submittedVersion, cc-by-nc-nd)
  • KOPS (University of Konstanz) (submittedVersion, cc-by)
  • Online Publication Service of Würzburg University (Würzburg University) (submittedVersion, cc-by)
  • GoeScholar The Publication Server of the Georg-August-Universität Göttingen (Georg-August-Universität Göttingen) (submittedVersion, cc-by)
Funders
  • Deutsche Forschungsgemeinschaft
  • Agence Nationale de la Recherche (ANR-16-CE92-0019)
  • Austrian Science Fund (P3219)
  • Ministerio de Economía y Competitividad
  • Georg-August-Universität Göttingen
  • Japan Society for the Promotion of Science
  • H2020 European Research Council (852725)
Topics
  • Life Sciences › Agricultural and Biological Sciences › Plant Science › Chromosomal and Genetic Variations
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Developmental Biology and Gene Regulation
Keywords
lungfish, Neoceratodus forsteri, genome size, land colonization, tetrapod evolution, Sarcopterygii, transposable elements, interspersed repeats, synteny, karyotype evolution, microchromosomes, phylogenomics, HOXC13, SALL1, olfactory receptor genes, gene duplication, Devonian
MeSH terms
Adaptation, Physiological, Air, Animals, Bayes Theorem, Chromosomes, Biological Evolution, Extremities, Female, Fishes, Gait, Genes, Homeobox, Humans, Lung, Phylogeny, Respiration, Smell, Vertebrates, Genome, Gene Expression Regulation, Developmental, Vomeronasal Organ, Long Interspersed Nucleotide Elements, Genomics, Synteny, Mice, Animal Fins, Molecular Sequence Annotation

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