Journal article
Platypus and echidna genomes reveal mammalian biology and evolution
Y Zhou, L Shearwin-Whyatt, J Li, Z Song, T Hayakawa, D Stevens, JC Fenelon, E Peel, Y Cheng, F Pajpach, N Bradley, H Suzuki, M Nikaido, J Damas, T Daish, T Perry, Z Zhu, Y Geng, A Rhie, Y Sims Show all
Nature | Published : 2021
Open access
Abstract
Egg-laying mammals (monotremes) are the only extant mammalian outgroup to therians (marsupial and eutherian animals) and provide key insights into mammalian evolution1,2. Here we generate and analyse reference genomes of the platypus (Ornithorhynchus anatinus) and echidna (Tachyglossus aculeatus), which represent the only two extant monotreme lineages. The nearly complete platypus genome assembly has anchored almost the entire genome onto chromosomes, markedly improving the genome continuity and gene annotation. Together with our echidna sequence, the genomes of the two species allow us to detect the ancestral and lineage-specific genomic changes that shape both monotreme and mammalian evolu..
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Grants
Awarded by National Key Research and Development Program of China
Funding Acknowledgements
We thank members of BGI-Shenzhen, China National GeneBank and VGP, and P. Baybayan, R. Hall and J. Howard for help carrying out the sequencing of the platypus and echidna genomes, M. Asahara for discussion, and D. Charlesworth for comments. Work was supported by the Strategic Priority Research Program of the Chinese Academy of Sciences (XDB31020000), the National Key R&D Program of China (MOST) grant 2018YFC1406901, International Partnership Program of Chinese Academy of Sciences (152453KYSB20170002), Carlsberg foundation (CF16-0663) and Villum Foundation (25900) to G.Z. Q.Z. is supported by the National Natural Science Foundation of China (31722050, 31671319 and 32061130208), Natural Science Foundation of Zhejiang Province (LD19C190001), European Research Council Starting Grant (grant agreement 677696) and start-up funds from Zhejiang University. F.G., L.S.-W. and T.D. are supported by Australian Research Council (FT160100267, DP170104907 and DP110105396). M.B.R., J.C.F. and S.D.J. are supported by the Australian Research Council (LP160101728). We acknowledge the Kyoto University Research Administration Office for support and Human Genome Center, the Institute of Medical Science, the University of Tokyo for the super-computing resource for supporting T.H.'s research facilities. T.H. was financed by JSPS KAKENHI grant numbers 16K18630 and 19K16241 and the Sasakawa Scientific Research Grant from the Japan Science Society. The echidna RNA-sequencing analysis was supported by H.K.'s grant from the European Research Council (615253, OntoTransEvol). This work was supported by Guangdong Provincial Academician Workstation of BGI Synthetic Genomics No. 2017B090904014 (H.Y.), Robert and Rosabel Osborne Endowment, Howard Hughes Medical Institute (E.D.J.), Rockefeller University start-up funds (E.D.J.), Intramural Research Program of the National Human Genome Research Institute, National Institutes of Health (A.R. and A.M.P.), Korea Health Technology R&D Project through the Korea Health Industry Development Institute HI17C2098 (A.R.). This work used the computational resources of BGI-Shenzhen and the NIH HPC Biowulf cluster (https://hpc.nih.gov).Animal icons are from https://www.flaticon.com/(made by Freepik) and http://phylopic.org/.