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Nature ecology & evolution
07, 2021;5 (7): 927-938.

The genome of Nautilus pompilius illuminates eye evolution and biomineralization.

Yang Zhang, Fan Mao, Huawei Mu, Minwei Huang, Yongbo Bao, Lili Wang, Nai-Kei Wong, Shu Xiao, He Dai, Zhiming Xiang, Mingli Ma, Yuanyan Xiong, Ziwei Zhang, Lvping Zhang, Xiaoyuan Song, Fan Wang, Xiyu Mu, Jun Li, Haitao Ma, Yuehuan Zhang, Hongkun Zheng, Oleg Simakov, Ziniu Yu
Author Information
  1. Yang Zhang: Key Laboratory of Tropical Marine Bio-resources and Ecology and Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China. ORCID
  2. Fan Mao: Key Laboratory of Tropical Marine Bio-resources and Ecology and Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China.
  3. Huawei Mu: MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, Hefei National Laboratory for Physical Sciences at the Microscale, CAS Key Laboratory of Brain Function and Disease, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China.
  4. Minwei Huang: Key Laboratory of Tropical Marine Bio-resources and Ecology and Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China. ORCID
  5. Yongbo Bao: Zhejiang Key Laboratory of Aquatic Germplasm Resources, College of Biological and Environmental Sciences, Zhejiang Wanli University, Ningbo, China.
  6. Lili Wang: Biomarker Technologies Corporation, Beijing, China.
  7. Nai-Kei Wong: Key Laboratory of Tropical Marine Bio-resources and Ecology and Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China.
  8. Shu Xiao: Key Laboratory of Tropical Marine Bio-resources and Ecology and Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China. ORCID
  9. He Dai: Biomarker Technologies Corporation, Beijing, China.
  10. Zhiming Xiang: Key Laboratory of Tropical Marine Bio-resources and Ecology and Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China.
  11. Mingli Ma: Biomarker Technologies Corporation, Beijing, China.
  12. Yuanyan Xiong: State Key Laboratory of Biocontrol, College of Life Sciences, Sun Yat-sen University, Guangzhou, China.
  13. Ziwei Zhang: State Key Laboratory of Biocontrol, College of Life Sciences, Sun Yat-sen University, Guangzhou, China. ORCID
  14. Lvping Zhang: Key Laboratory of Tropical Marine Bio-resources and Ecology and Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China.
  15. Xiaoyuan Song: MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, Hefei National Laboratory for Physical Sciences at the Microscale, CAS Key Laboratory of Brain Function and Disease, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China.
  16. Fan Wang: Biomarker Technologies Corporation, Beijing, China.
  17. Xiyu Mu: Biomarker Technologies Corporation, Beijing, China.
  18. Jun Li: Key Laboratory of Tropical Marine Bio-resources and Ecology and Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China.
  19. Haitao Ma: Key Laboratory of Tropical Marine Bio-resources and Ecology and Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China.
  20. Yuehuan Zhang: Key Laboratory of Tropical Marine Bio-resources and Ecology and Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China.
  21. Hongkun Zheng: Biomarker Technologies Corporation, Beijing, China. ORCID
  22. Oleg Simakov: Department of Neuroscience and Developmental Biology, University of Vienna, Vienna, Austria. ORCID
  23. Ziniu Yu: Key Laboratory of Tropical Marine Bio-resources and Ecology and Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China. carlzyu@scsio.ac.cn. ORCID
PMID: 33972735 DOI: 10.1038/s41559-021-01448-6

Abstract

Nautilus is the sole surviving externally shelled cephalopod from the Palaeozoic. It is unique within cephalopod genealogy and critical to understanding the evolutionary novelties of cephalopods. Here, we present a complete Nautilus pompilius genome as a fundamental genomic reference on cephalopod innovations, such as the pinhole eye and biomineralization. Nautilus shows a compact, minimalist genome with few encoding genes and slow evolutionary rates in both non-coding and coding regions among known cephalopods. Importantly, multiple genomic innovations including gene losses, independent contraction and expansion of specific gene families and their associated regulatory networks likely moulded the evolution of the nautilus pinhole eye. The conserved molluscan biomineralization toolkit and lineage-specific repetitive low-complexity domains are essential to the construction of the nautilus shell. The nautilus genome constitutes a valuable resource for reconstructing the evolutionary scenarios and genomic innovations that shape the extant cephalopods.

References

Nat Rev Genet. 2005 Dec;6(12):881-92 [PMID: 16341069]
Proc Natl Acad Sci U S A. 2020 Jan 7;117(1):503-512 [PMID: 31871200]
J Mol Evol. 2006 Mar;62(3):362-74 [PMID: 16501879]
Mol Biol Evol. 2007 Aug;24(8):1586-91 [PMID: 17483113]
Nucleic Acids Res. 2003 Oct 1;31(19):5654-66 [PMID: 14500829]
Ecol Evol. 2016 Jun 21;6(14):4924-35 [PMID: 27547323]
Nature. 2011 Sep 04;477(7365):452-6 [PMID: 21892190]
J Comp Psychol. 2009 Aug;123(3):264-74 [PMID: 19685967]
Mol Biol Evol. 2017 Apr 1;34(4):779-792 [PMID: 28053006]
Dev Cell. 2015 May 4;33(3):314-27 [PMID: 25942623]
Bioessays. 2011 Aug;33(8):602-13 [PMID: 21681989]
Curr Top Dev Biol. 2008;80:209-76 [PMID: 17950376]
Bioinformatics. 2009 Jul 15;25(14):1754-60 [PMID: 19451168]
Mob DNA. 2015 Jun 02;6:11 [PMID: 26045719]
Cell. 2017 Apr 6;169(2):191-202.e11 [PMID: 28388405]
Nature. 2015 Aug 13;524(7564):220-4 [PMID: 26268193]
PLoS One. 2012;7(12):e52249 [PMID: 23284954]
Bioinformatics. 2009 Jul 1;25(13):1609-16 [PMID: 19389736]
BMC Bioinformatics. 2003 Sep 11;4:41 [PMID: 12969510]
Sci Data. 2019 Apr 1;6(1):13 [PMID: 30931949]
Gigascience. 2018 Nov 1;7(11): [PMID: 30256935]
FEBS J. 2009 Jun;276(11):3020-30 [PMID: 19490105]
Nucleic Acids Res. 2016 May 19;44(9):e89 [PMID: 26893356]
Nature. 2012 Oct 4;490(7418):49-54 [PMID: 22992520]
Nat Biotechnol. 2011 May 15;29(7):644-52 [PMID: 21572440]
Nature. 2014 Jan 9;505(7482):174-9 [PMID: 24402279]
PeerJ. 2016 Jun 08;4:e2016 [PMID: 27330851]
Nat Rev Immunol. 2007 May;7(5):353-64 [PMID: 17457343]
Bioinformatics. 2005 Jun;21 Suppl 1:i152-8 [PMID: 15961452]
Nucleic Acids Res. 2010 Dec;38(22):e199 [PMID: 20880995]
Proc Natl Acad Sci U S A. 2019 Feb 19;116(8):3030-3035 [PMID: 30635418]
Brain Behav Evol. 2009;74(3):231-45 [PMID: 20029186]
Nature. 2016 Dec 14;540(7633):395-399 [PMID: 27974754]
Trends Immunol. 2004 Nov;25(11):601-9 [PMID: 15489189]
Curr Biol. 2008 Dec 9;18(23):R1096-8 [PMID: 19081043]
Bioinformatics. 2014 Dec 15;30(24):3506-14 [PMID: 25165095]
Curr Protoc Bioinformatics. 2007 Jun;Chapter 4:Unit 4.3 [PMID: 18428791]
Bioinformatics. 2014 May 1;30(9):1312-3 [PMID: 24451623]
Science. 2002 May 31;296(5573):1634-5 [PMID: 12040173]
Nat Protoc. 2012 Mar 01;7(3):562-78 [PMID: 22383036]
Bioinformatics. 2005 Jun;21 Suppl 1:i351-8 [PMID: 15961478]
Cell. 2005 Aug 12;122(3):449-59 [PMID: 16096063]
Nucleic Acids Res. 2016 Nov 2;44(19):e147 [PMID: 27458204]
Curr Biol. 2019 Aug 5;29(15):R726-R732 [PMID: 31386844]
Bioessays. 2019 Dec;41(12):e1900073 [PMID: 31664724]
Nature. 2012 Oct 18;490(7420):393-6 [PMID: 23034648]
Mol Biol Evol. 2010 Mar;27(3):591-608 [PMID: 19915030]
FEBS J. 2013 Jan;280(1):214-32 [PMID: 23145877]
Methods Mol Biol. 2019;1962:161-177 [PMID: 31020559]
Bioinformatics. 2003 Oct;19 Suppl 2:ii215-25 [PMID: 14534192]
Bioinformatics. 2015 Oct 1;31(19):3210-2 [PMID: 26059717]
Nat Ecol Evol. 2017 Apr 03;1(5):120 [PMID: 28812685]
Nature. 2018 Oct;562(7727):361-366 [PMID: 30333578]
Dev Dyn. 2004 Mar;229(3):440-8 [PMID: 14991699]
Genome Res. 2017 May;27(5):722-736 [PMID: 28298431]
Mol Biol Evol. 2018 Nov 1;35(11):2751-2761 [PMID: 30169718]
Bioinformatics. 2009 May 1;25(9):1105-11 [PMID: 19289445]
Nat Rev Genet. 2005 Dec;6(12):893-904 [PMID: 16341070]
Genome Res. 2003 Sep;13(9):2178-89 [PMID: 12952885]
Nucleic Acids Res. 2003 Jan 1;31(1):365-70 [PMID: 12520024]
Nat Ecol Evol. 2019 Mar;3(3):469-478 [PMID: 30804520]
Bioinformatics. 2005 Sep 15;21(18):3674-6 [PMID: 16081474]
Science. 2012 Feb 17;335(6070):848-51 [PMID: 22223739]
Curr Protoc Bioinformatics. 2009 Mar;Chapter 4:4.10.1-4.10.14 [PMID: 19274634]
Sci Rep. 2013;3:1432 [PMID: 23478590]
Science. 2012 Nov 9;338(6108):758-67 [PMID: 23145453]
Science. 1998 Apr 3;280(5360):115-8 [PMID: 9525857]
J Exp Biol. 2008 Jun;211(Pt 12):1992-8 [PMID: 18515730]
Nature. 2013 Jan 24;493(7433):526-31 [PMID: 23254933]
Nat Rev Genet. 2008 Nov;9(11):868-82 [PMID: 18927580]
Integr Comp Biol. 2015 Dec;55(6):1070-83 [PMID: 26002349]
Proc Natl Acad Sci U S A. 2011 Jan 25;108(4):1513-8 [PMID: 21187386]
Cell. 2009 Oct 16;139(2):246-64 [PMID: 19837030]
Proc Natl Acad Sci U S A. 2005 Aug 30;102(35):12413-8 [PMID: 16116091]
J Mol Biol. 1997 Apr 25;268(1):78-94 [PMID: 9149143]
Cell Host Microbe. 2012 Oct 18;12(4):432-44 [PMID: 23084913]
Mol Ecol. 2015 Jul;24(13):3316-28 [PMID: 26033519]
Science. 1972 Sep 15;177(4053):949-59 [PMID: 5055944]
Science. 1986 May 2;232(4750):619-22 [PMID: 17781412]
Nat Ecol Evol. 2019 Apr;3(4):528-538 [PMID: 30858589]
Nature. 2011 Jun 29;474(7353):631-4 [PMID: 21720369]
Proc Natl Acad Sci U S A. 2005 Apr 26;102(17):6177-82 [PMID: 15837919]
Bioinformatics. 2006 May 15;22(10):1269-71 [PMID: 16543274]
Nature. 1997 Jun 5;387(6633):563-4 [PMID: 9177341]
Nucleic Acids Res. 2007 Jul;35(Web Server issue):W265-8 [PMID: 17485477]
Nucleic Acids Res. 2000 Jan 1;28(1):27-30 [PMID: 10592173]
Philos Trans R Soc Lond B Biol Sci. 2009 Oct 12;364(1531):2833-47 [PMID: 19720648]
Prog Biophys Mol Biol. 2019 Sep;146:98-103 [PMID: 30557534]
Proc Biol Sci. 2017 Mar 15;284(1850): [PMID: 28250188]
Mol Biol Evol. 2016 Jul;33(7):1870-4 [PMID: 27004904]
J Hered. 2006 Jan-Feb;97(1):1-12 [PMID: 16394255]
Proc Natl Acad Sci U S A. 2019 Oct 8;116(41):20388-20397 [PMID: 31551265]
J Morphol. 2008 Jan;269(1):1-17 [PMID: 17654542]
Sci Rep. 2015 Mar 03;5:8693 [PMID: 25732911]
Proc Biol Sci. 2012 Jan 7;279(1726):3-14 [PMID: 22012981]
Mol Cell Biol. 1998 Apr;18(4):2067-76 [PMID: 9528779]
Nat Rev Genet. 2016 Dec;17(12):744-757 [PMID: 27818507]
Annu Rev Physiol. 2002;64:153-87 [PMID: 11826267]
FEBS J. 2011 Jun;278(12):2117-30 [PMID: 21585656]
J Proteomics. 2017 Feb 23;155:22-30 [PMID: 28095328]
Mol Biol Evol. 2013 Sep;30(9):2209-23 [PMID: 23842528]
Mol Biol Evol. 2018 Jul 1;35(7):1638-1652 [PMID: 29672732]
Nat Rev Genet. 2007 Dec;8(12):973-82 [PMID: 17984973]
Bioinformatics. 2004 Nov 1;20(16):2878-9 [PMID: 15145805]
Genome Biol Evol. 2016 Dec 1;8(12):3640-3652 [PMID: 28172965]
Nature. 2008 Jan 24;451(7177):431-6 [PMID: 18094683]
Nucleic Acids Res. 2004 Mar 19;32(5):1792-7 [PMID: 15034147]
BMC Bioinformatics. 2004 May 14;5:59 [PMID: 15144565]
Science. 2012 Aug 10;337(6095):704-9 [PMID: 22879512]

Grants

  1. P 30686/Austrian Science Fund FWF

MeSH Term

Animals
Biomineralization
Genome
Humans
Nautilus
Journal Article Research Support, Non-U.S. Gov't

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