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Title: Genome evolution in the allotetraploid frog Xenopus laevis

Journal Article · · Nature (London)
DOI:https://doi.org/10.1038/nature19840· OSTI ID:1615264
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  1. Univ. of California, Berkeley, CA (United States); USDOE Joint Genome Inst. (JGI), Walnut Creek, CA (United States)
  2. Nagoya Univ. (Japan)
  3. Univ. of Texas, Austin, TX (United States); Ulsan National Inst. of Science and Technology, Ulsan (Republic of Korea)
  4. USDOE Joint Genome Inst. (JGI), Walnut Creek, CA (United States)
  5. National Inst. of Genetics, Shizuoka (Japan)
  6. Hiroshima Univ. (Japan)
  7. Hokkaido Univ., Sapporo (Japan)
  8. Univ. of Tokyo (Japan)
  9. Radboud Univ., Nijmegen (The Netherlands)
  10. Salk Inst., La Jolla, San Diego, CA (United States). Molecular Neurobiology Lab.
  11. Salk Inst. for Biological Studies, La Jolla, San Diego, CA (United States)
  12. Nagahama Inst. of Bio-Science and Technology (Japan)
  13. Yamagata Univ. (Japan)
  14. Univ. of California, Berkeley, CA (United States)
  15. Okinawa Inst. of Science and Technology Graduate Univ., Onna (Japan)
  16. Dovetail Genomics LLC, Santa Cruz, CA (United States)
  17. National Research Inst. for Child Health and Development, Tokyo (Japan)
  18. Tokyo Inst. of Technology, Yokohama (Japan)
  19. Tokushima Univ. (Japan)
  20. Univ. of Western Australia, Perth, WA (Australia)
  21. Rikkyo Univ., Tokyo (Japan)
  22. Univ. of Maryland, Baltimore, MD (United States)
  23. Kitasato Univ., Tokyo (Japan)
  24. USDOE Joint Genome Inst. (JGI), Walnut Creek, CA (United States); HudsonAlpha Inst. of Biotechnology, Huntsville, AL (United States)
  25. Univ. of Chicago, IL (United States)
  26. National Inst. of Advanced Industrial Science and Technology (AIST) (Japan)
  27. National Inst. for Basic Biology, Okazaki (Japan)
  28. Illumina Inc., Hayward, CA (United States)
  29. Univ. of Washington, Seattle, WA (United States)
  30. Univ. of Virginia, Charlottesville, VA (United States)
  31. Niigata Univ. (Japan)
  32. Univ. of Rochester, NY (United States)
  33. Cincinnati Children's Research Foundation, OH (United States)
  34. Univ. of Calgary, AB (Canada)
  35. Okinawa Inst. of Science and Technology Graduate Univ. (Japan)
  36. Univ. of Iowa, Iowa City, IA (United States)
  37. Univ. of Basel (Switzerland)
  38. Kitasato Univ., Kanagawa (Japan)
  39. Univ. of Texas, Austin, TX (United States)
  40. National Inst. for Basic Biology, Okazaki (Japan); The Graduate Univ. for Advanced Studies (SOKENDAI), Okazaki (Japan)
  41. National Inst. of Genetics, Shizuoka (Japan); National Inst. of Informatics, Tokyo (Japan); The Graduate Univ. for Advanced Studies (SOKENDAI), Shizoka (Japan)
  42. Univ. of California, Berkeley, CA (United States); USDOE Joint Genome Inst. (JGI), Walnut Creek, CA (United States); Okinawa Inst. of Science and Technology Graduate Univ., Onna (Japan)
+ Show Author Affiliations

To explore the origins and consequences of tetraploidy in the African clawed frog, we sequenced the Xenopus laevis genome and compared it to the related diploid X. tropicalis genome. We characterize the allotetraploid origin of X. laevis by partitioning its genome into two homoeologous subgenomes, marked by distinct families of 'fossil' transposable elements. On the basis of the activity of these elements and the age of hundreds of unitary pseudogenes, we estimate that the two diploid progenitor species diverged around 34 million years ago (Ma) and combined to form an allotetraploid around 17-18 Ma. More than 56% of all genes were retained in two homoeologous copies. Protein function, gene expression, and the amount of conserved flanking sequence all correlate with retention rates. The subgenomes have evolved asymmetrically, with one chromosome set more often preserving the ancestral state and the other experiencing more gene loss, deletion, rearrangement, and reduced gene expression.

Research Organization:
Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States); USDOE Joint Genome Institute (JGI), Berkeley, CA (United States)
Sponsoring Organization:
USDOE Office of Science (SC), Biological and Environmental Research (BER); Eunice Kennedy Shriver National Institute for Child Health & Human Development (NICHD); Japan Society for the Promotion of Science (JSPS); UNIST Research Fund; National Human Genome Research Institute (NHGRI); Hiroshima University Phoenix Leader Education Program; Ministry of Education, Culture, Sports, Science and Technology (MEXT); National Institutes of Health (NIH); National Institute of Allergy and Infectious Diseases (NIAID); National Institute of General Medical Sciences (NIGMS); National Science Foundation (NSF); Cancer Prevention and Research Institute of Texas (CPRIT); Welch Foundation; National Heart, Lung and Blood Institute (NHLBI); Okinawa Institute for Science and Technology Graduate University; SURF Foundation; Netherlands Organization for Scientific Research (NWO); Australian Research Council (ARC)
Grant/Contract Number:
AC02-05CH11231; HD065705; HD080708; P41 HD064556; GM086321; 221S0002; 24590232; 25440180; 15K14521; 15K07082; 22570137; 25460245; 23370059; 23113004; 25251026; 22127007; 1.150094.01; 1.150043.01; 1.160060.01; F1515; R01HD069344; 863.12.002; DE140101962; 1S10OD018174
OSTI ID:
1615264
Journal Information:
Nature (London), Vol. 538, Issue 7625; ISSN 0028-0836
Publisher:
Nature Publishing GroupCopyright Statement
Country of Publication:
United States
Language:
English
Citation Metrics:
Cited by: 577 works
Citation information provided by
Web of Science

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Functional Characterization of Xenopus Thyroid Hormone Transporters mct8 and oatp1c1 journal June 2017
A comprehensive reference transcriptome resource for the Iberian ribbed newt Pleurodeles waltl , an emerging model for developmental and regeneration biology journal September 2018
Xenopus fraseri: Mr. Fraser, where did your frog come from? journal September 2019
Embryonic regeneration by relocalization of the Spemann organizer during twinning in Xenopus journal April 2018
The Consequences of Chromosome Segregation Errors in Mitosis and Meiosis journal February 2017
Cells from subcutaneous tissues contribute to scarless skin regeneration in Xenopus laevis froglets: Hypodermis Contributes To Skin Regeneration journal June 2017
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Regulatory remodeling in the allo-tetraploid frog Xenopus laevis journal March 2017
Developmental Systems Drift and the Drivers of Sex Chromosome Evolution journal November 2019
Extreme nuclear branching in healthy epidermal cells of the Xenopus tail fin journal January 2018
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The fast block to polyspermy: New insight into a century-old problem journal August 2018
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Figures / Tables (15)

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59 BASIC BIOLOGICAL SCIENCES
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