Platypus and echidna genomes reveal mammalian biology and evolution.
Journal
Nature
ISSN: 1476-4687
Titre abrégé: Nature
Pays: England
ID NLM: 0410462
Informations de publication
Date de publication:
04 2021
04 2021
Historique:
received:
04
12
2019
accepted:
30
07
2020
pubmed:
8
1
2021
medline:
11
1
2022
entrez:
7
1
2021
Statut:
ppublish
Résumé
Egg-laying mammals (monotremes) are the only extant mammalian outgroup to therians (marsupial and eutherian animals) and provide key insights into mammalian evolution
Identifiants
pubmed: 33408411
doi: 10.1038/s41586-020-03039-0
pii: 10.1038/s41586-020-03039-0
pmc: PMC8081666
doi:
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
756-762Subventions
Organisme : Howard Hughes Medical Institute
Pays : United States
Références
Ashwell, K. Neurobiology of Monotremes: Brain Evolution in Our Distant Mammalian Cousins (CSIRO PUBLISHING, 2013).
Warren, W. C. et al. Genome analysis of the platypus reveals unique signatures of evolution. Nature 453, 175–183 (2008).
pubmed: 18464734
pmcid: 2803040
Grützner, F. et al. In the platypus a meiotic chain of ten sex chromosomes shares genes with the bird Z and mammal X chromosomes. Nature 432, 913–917 (2004).
pubmed: 15502814
Kortschak, R. D., Tsend-Ayush, E. & Grützner, F. Analysis of SINE and LINE repeat content of Y chromosomes in the platypus, Ornithorhynchus anatinus. Reprod. Fertil. Dev. 21, 964–975 (2009).
pubmed: 19874720
Boissinot, S. & Sookdeo, A. The evolution of LINE-1 in vertebrates. Genome Biol. Evol. 8, 3485–3507 (2016).
pubmed: 28175298
pmcid: 5381506
Phillips, M. J., Bennett, T. H. & Lee, M. S. Molecules, morphology, and ecology indicate a recent, amphibious ancestry for echidnas. Proc. Natl Acad. Sci. USA 106, 17089–17094 (2009).
pubmed: 19805098
pmcid: 2761324
Bellott, D. W. et al. Mammalian Y chromosomes retain widely expressed dosage-sensitive regulators. Nature 508, 494–499 (2014).
pubmed: 24759411
pmcid: 4139287
Whittington, C. M. et al. Defensins and the convergent evolution of platypus and reptile venom genes. Genome Res. 18, 986–994 (2008).
pubmed: 18463304
pmcid: 2413166
Julien, P. et al. Mechanisms and evolutionary patterns of mammalian and avian dosage compensation. PLoS Biol. 10, e1001328 (2012).
pubmed: 22615540
pmcid: 3352821
Rousselle, M., Laverré, A., Figuet, E., Nabholz, B. & Galtier, N. Influence of recombination and GC-biased gene conversion on the adaptive and nonadaptive substitution rate in mammals versus birds. Mol. Biol. Evol. 36, 458–471 (2019).
pubmed: 30590692
Hinch, A. G., Altemose, N., Noor, N., Donnelly, P. & Myers, S. R. Recombination in the human pseudoautosomal region PAR1. PLoS Genet. 10, e1004503 (2014).
pubmed: 25033397
pmcid: 4102438
Burt, D. W. Origin and evolution of avian microchromosomes. Cytogenet. Genome Res. 96, 97–112 (2002).
pubmed: 12438785
Dohm, J. C., Tsend-Ayush, E., Reinhardt, R., Grützner, F. & Himmelbauer, H. Disruption and pseudoautosomal localization of the major histocompatibility complex in monotremes. Genome Biol. 8, R175 (2007).
pubmed: 17727704
pmcid: 2375005
Cortez, D. et al. Origins and functional evolution of Y chromosomes across mammals. Nature 508, 488–493 (2014).
pubmed: 24759410
Zhou, Q. et al. Complex evolutionary trajectories of sex chromosomes across bird taxa. Science 346, 1246338 (2014).
pubmed: 25504727
pmcid: 6445272
Veyrunes, F. et al. Bird-like sex chromosomes of platypus imply recent origin of mammal sex chromosomes. Genome Res. 18, 965–973 (2008).
pubmed: 18463302
pmcid: 2413164
Braasch, I. et al. The spotted gar genome illuminates vertebrate evolution and facilitates human–teleost comparisons. Nat. Genet. 48, 427–437 (2016).
pubmed: 26950095
pmcid: 4817229
Gruetzner, F., Ashley, T., Rowell, D. M. & Marshall Graves, J. A. How did the platypus get its sex chromosome chain? A comparison of meiotic multiples and sex chromosomes in plants and animals. Chromosoma 115, 75–88 (2006).
pubmed: 16344965
Golczyk, H., Massouh, A. & Greiner, S. Translocations of chromosome end-segments and facultative heterochromatin promote meiotic ring formation in evening primroses. Plant Cell 26, 1280–1293 (2014).
pubmed: 24681616
pmcid: 4001384
de Waal Malefijt, M. & Charlesworth, B. A model for the evolution of translocation heterozygosity. Heredity 43, 315–331 (1979).
Casey, A. E., Daish, T. J., Barbero, J. L. & Grützner, F. Differential cohesin loading marks paired and unpaired regions of platypus sex chromosomes at prophase I. Sci. Rep. 7, 4217 (2017).
pubmed: 28652620
pmcid: 5484699
Dixon, J. R. et al. Topological domains in mammalian genomes identified by analysis of chromatin interactions. Nature 485, 376–380 (2012).
pubmed: 22495300
pmcid: 3356448
Griffiths, M. The Biology of Monotremes (Academic, 1978).
Meredith, R. W., Zhang, G., Gilbert, M. T., Jarvis, E. D. & Springer, M. S. Evidence for a single loss of mineralized teeth in the common avian ancestor. Science 346, 1254390 (2014).
pubmed: 25504730
Springer, M. S. et al. Odontogenic ameloblast-associated (ODAM) is inactivated in toothless/enamelless placental mammals and toothed whales. BMC Evol. Biol. 19, 31 (2019).
pubmed: 30674270
pmcid: 6343362
Ordoñez, G. R. et al. Loss of genes implicated in gastric function during platypus evolution. Genome Biol. 9, R81 (2008).
pubmed: 18482448
pmcid: 2441467
Hayakawa, T., Suzuki-Hashido, N., Matsui, A. & Go, Y. Frequent expansions of the bitter taste receptor gene repertoire during evolution of mammals in the Euarchontoglires clade. Mol. Biol. Evol. 31, 2018–2031 (2014).
pubmed: 24758778
Johnson, R. N. et al. Adaptation and conservation insights from the koala genome. Nat. Genet. 50, 1102–1111 (2018).
pubmed: 29967444
pmcid: 6197426
Liu, Z. et al. Dietary specialization drives multiple independent losses and gains in the bitter taste gene repertoire of Laurasiatherian mammals. Front. Zool. 13, 28 (2016).
pubmed: 27366197
pmcid: 4928315
Hunnicutt, K. E. et al. Comparative genomic analysis of the pheromone receptor class 1 family (V1R) reveals extreme complexity in mouse lemurs (genus, Microcebus) and a chromosomal hotspot across mammals. Genome Biol. Evol. 12, 3562–3579 (2020).
pubmed: 31555816
Johansen, K., Lenfant, C. & Grigg, G. C. Respiratory properties of blood and responses to diving of platypus Ornithorhynchus anatinus (Shaw). Comp. Biochem. Physiol. 18, 597–608 (1966).
pubmed: 5967684
Alayash, A. I. Haptoglobin: old protein with new functions. Clin. Chim. Acta 412, 493–498 (2011).
pubmed: 21159311
Wicher, K. B. & Fries, E. Haptoglobin, a hemoglobin-binding plasma protein, is present in bony fish and mammals but not in frog and chicken. Proc. Natl Acad. Sci. USA 103, 4168–4173 (2006).
pubmed: 16537503
pmcid: 1449665
Redmond, A. K. et al. Haptoglobin is a divergent masp family member that neofunctionalized to recycle hemoglobin via CD163 in mammals. J. Immunol. 201, 2483–2491 (2018).
pubmed: 30194112
Huttenlocker, A. K. & Farmer, C. G. Bone microvasculature tracks red blood cell size diminution in Triassic mammal and dinosaur forerunners. Curr. Biol. 27, 48–54 (2017).
pubmed: 28017610
Schaer, D. J. et al. CD163 is the macrophage scavenger receptor for native and chemically modified hemoglobins in the absence of haptoglobin. Blood 107, 373–380 (2006).
pubmed: 16189277
Griffiths, M. Echidnas (Pergamon, 1968).
Brawand, D., Wahli, W. & Kaessmann, H. Loss of egg yolk genes in mammals and the origin of lactation and placentation. PLoS Biol. 6, e63 (2008).
pubmed: 18351802
pmcid: 2267819
Pharo, E. A. et al. The mammary gland-specific marsupial ELP and eutherian CTI share a common ancestral gene. BMC Evol. Biol. 12, 80 (2012).
pubmed: 22681678
pmcid: 3426482
Lefèvre, C. M., Sharp, J. A. & Nicholas, K. R. Characterisation of monotreme caseins reveals lineage-specific expansion of an ancestral casein locus in mammals. Reprod. Fertil. Dev. 21, 1015–1027 (2009).
pubmed: 19874726
Holt, C., Carver, J. A., Ecroyd, H. & Thorn, D. C. Invited review: Caseins and the casein micelle: their biological functions, structures, and behavior in foods. J. Dairy Sci. 96, 6127–6146 (2013).
pubmed: 23958008
Kawasaki, K., Lafont, A. G. & Sire, J. Y. The evolution of milk casein genes from tooth genes before the origin of mammals. Mol. Biol. Evol. 28, 2053–2061 (2011).
pubmed: 21245413
Cardoso-Moreira, M. et al. Gene expression across mammalian organ development. Nature 571, 505–509 (2019).
pubmed: 31243369
pmcid: 6658352
Kajitani, R. et al. Efficient de novo assembly of highly heterozygous genomes from whole-genome shotgun short reads. Genome Res. 24, 1384–1395 (2014).
pubmed: 24755901
pmcid: 4120091
Li, H. & Durbin, R. Fast and accurate short read alignment with Burrows–Wheeler transform. Bioinformatics 25, 1754–1760 (2009).
pubmed: 19451168
pmcid: 2705234
Birney, E., Clamp, M. & Durbin, R. Genewise and genomewise. Genome Res. 14, 988–995 (2004).
pubmed: 15123596
pmcid: 479130
Li, H. & Durbin, R. Fast and accurate long-read alignment with Burrows–Wheeler transform. Bioinformatics 26, 589–595 (2010).
pubmed: 20080505
pmcid: 2828108
Li, H. Minimap2: pairwise alignment for nucleotide sequences. Bioinformatics 34, 3094–3100 (2018).
pubmed: 29750242
pmcid: 6137996
Jain, C., Koren, S., Dilthey, A., Phillippy, A. M. & Aluru, S. A fast adaptive algorithm for computing whole-genome homology maps. Bioinformatics 34, i748–i756 (2018).
pubmed: 30423094
pmcid: 6129286
Rens, W. et al. The multiple sex chromosomes of platypus and echidna are not completely identical and several share homology with the avian Z. Genome Biol. 8, R243 (2007).
pubmed: 18021405
pmcid: 2258203
Bao, W., Kojima, K. K. & Kohany, O. Repbase update, a database of repetitive elements in eukaryotic genomes. Mob. DNA 6, 11 (2015).
pubmed: 26045719
pmcid: 4455052
Chen, N. Using RepeatMasker to identify repetitive elements in genomic sequences. Curr. Protoc. Bioinformatics 5, 4.10.1–4.10.14 (2004).
Benson, G. Tandem repeats finder: a program to analyze DNA sequences. Nucleic Acids Res. 27, 573–580 (1999).
pubmed: 9862982
pmcid: 148217
Yates, A. et al. Ensembl 2016. Nucleic Acids Res. 44, D710–D716 (2016).
pubmed: 26687719
Altschul, S. F., Gish, W., Miller, W., Myers, E. W. & Lipman, D. J. Basic local alignment search tool. J. Mol. Biol. 215, 403–410 (1990).
pubmed: 2231712
Stanke, M., Schöffmann, O., Morgenstern, B. & Waack, S. Gene prediction in eukaryotes with a generalized hidden Markov model that uses hints from external sources. BMC Bioinformatics 7, 62 (2006).
pubmed: 16469098
pmcid: 1409804
Brawand, D. et al. The evolution of gene expression levels in mammalian organs. Nature 478, 343–348 (2011).
pubmed: 22012392
Kim, D., Langmead, B. & Salzberg, S. L. HISAT: a fast spliced aligner with low memory requirements. Nat. Methods 12, 357–360 (2015).
pubmed: 25751142
pmcid: 4655817
Pertea, M. et al. StringTie enables improved reconstruction of a transcriptome from RNA-seq reads. Nat. Biotechnol. 33, 290–295 (2015).
pubmed: 25690850
pmcid: 4643835
UniProt Consortium. UniProt: a worldwide hub of protein knowledge. Nucleic Acids Res. 47, D506–D515 (2019).
Jones, P. et al. InterProScan 5: genome-scale protein function classification. Bioinformatics 30, 1236–1240 (2014).
pubmed: 24451626
pmcid: 3998142
Bickhart, D. M. et al. Single-molecule sequencing and chromatin conformation capture enable de novo reference assembly of the domestic goat genome. Nat. Genet. 49, 643–650 (2017).
pubmed: 28263316
pmcid: 5909822
Harris, R. S. Improved Pairwise Alignment of Genomic DNA. PhD thesis, Pennsylvania State Univ. (2007).
Zhang, G. et al. Comparative genomics reveals insights into avian genome evolution and adaptation. Science 346, 1311–1320 (2014).
pubmed: 25504712
pmcid: 4390078
Stamatakis, A. RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics 30, 1312–1313 (2014).
pubmed: 24451623
pmcid: 3998144
Yang, Z. PAML 4: phylogenetic analysis by maximum likelihood. Mol. Biol. Evol. 24, 1586–1591 (2007).
pubmed: 17483113
Benton, M. J. et al. Constraints on the timescale of animal evolutionary history. Palaeontol. Electronica 18, 1–106 (2015).
Blanchette, M. et al. Aligning multiple genomic sequences with the threaded blockset aligner. Genome Res. 14, 708–715 (2004).
pubmed: 15060014
pmcid: 383317
Hubisz, M. J., Pollard, K. S. & Siepel, A. PHAST and RPHAST: phylogenetic analysis with space/time models. Brief. Bioinform. 12, 41–51 (2011).
pubmed: 21278375
Li, L., Stoeckert, C. J., Jr & Roos, D. S. OrthoMCL: identification of ortholog groups for eukaryotic genomes. Genome Res. 13, 2178–2189 (2003).
pubmed: 12952885
pmcid: 403725
Han, M. V., Thomas, G. W., Lugo-Martinez, J. & Hahn, M. W. Estimating gene gain and loss rates in the presence of error in genome assembly and annotation using CAFE 3. Mol. Biol. Evol. 30, 1987–1997 (2013).
pubmed: 23709260
Seki, R. et al. Functional roles of Aves class-specific cis-regulatory elements on macroevolution of bird-specific features. Nat. Commun. 8, 14229 (2017).
pubmed: 28165450
pmcid: 5473641
Supek, F., Bošnjak, M., Škunca, N. & Šmuc, T. REVIGO summarizes and visualizes long lists of gene ontology terms. PLoS ONE 6, e21800 (2011).
pubmed: 21789182
pmcid: 3138752
Ma, J. et al. Reconstructing contiguous regions of an ancestral genome. Genome Res. 16, 1557–1565 (2006).
pubmed: 16983148
pmcid: 1665639
Jones, B. R., Rajaraman, A., Tannier, E. & Chauve, C. ANGES: reconstructing ANcestral GEnomeS maps. Bioinformatics 28, 2388–2390 (2012).
pubmed: 22820205
Deakin, J. E. et al. Reconstruction of the ancestral marsupial karyotype from comparative gene maps. BMC Evol. Biol. 13, 258 (2013).
pubmed: 24261750
pmcid: 4222502
Wang, Y. et al. MCScanX: a toolkit for detection and evolutionary analysis of gene synteny and collinearity. Nucleic Acids Res. 40, e49 (2012).
pubmed: 22217600
pmcid: 3326336
Tesler, G. GRIMM: genome rearrangements web server. Bioinformatics 18, 492–493 (2002).
pubmed: 11934753
Kim, J. et al. Reconstruction and evolutionary history of eutherian chromosomes. Proc. Natl Acad. Sci. USA 114, E5379–E5388 (2017).
pubmed: 28630326
pmcid: 5502614
Löytynoja, A. Phylogeny-aware alignment with PRANK. Methods Mol. Biol. 1079, 155–170 (2014).
pubmed: 24170401
Talavera, G. & Castresana, J. Improvement of phylogenies after removing divergent and ambiguously aligned blocks from protein sequence alignments. Syst. Biol. 56, 564–577 (2007).
pubmed: 17654362
Anders, S. & Huber, W. Differential expression analysis for sequence count data. Genome Biol. 11, R106 (2010).
pubmed: 20979621
pmcid: 3218662
Yanai, I. et al. Genome-wide midrange transcription profiles reveal expression level relationships in human tissue specification. Bioinformatics 21, 650–659 (2005).
pubmed: 15388519
Servant, N. et al. HiC-Pro: an optimized and flexible pipeline for Hi-C data processing. Genome Biol. 16, 259 (2015).
pubmed: 26619908
pmcid: 4665391
Ramírez, F. et al. High-resolution TADs reveal DNA sequences underlying genome organization in flies. Nat. Commun. 9, 189 (2018).
pubmed: 29335486
pmcid: 5768762
Jolma, A. et al. DNA-binding specificities of human transcription factors. Cell 152, 327–339 (2013).
pubmed: 23332764
Bailey, T. L. & Elkan, C. Fitting a mixture model by expectation maximization to discover motifs in biopolymers. Proc. Int. Conf. Intell. Syst. Mol. Biol. 2, 28–36 (1994).
pubmed: 7584402
Tsend-Ayush, E. et al. Higher-order genome organization in platypus and chicken sperm and repositioning of sex chromosomes during mammalian evolution. Chromosoma 118, 53–69 (2009).
pubmed: 18726609
Ling, J. Q. et al. CTCF mediates interchromosomal colocalization between Igf2/H19 and Wsb1/Nf1. Science 312, 269–272 (2006).
pubmed: 16614224
Parra, Z. E. et al. Comparative genomic analysis and evolution of the T cell receptor loci in the opossum Monodelphis domestica. BMC Genomics 9, 111 (2008).
pubmed: 18312668
pmcid: 2275272
Van Laere, A. S., Coppieters, W. & Georges, M. Characterization of the bovine pseudoautosomal boundary: documenting the evolutionary history of mammalian sex chromosomes. Genome Res. 18, 1884–1895 (2008).
pubmed: 18981267
pmcid: 2593575