Genome evolution in the allotetraploid frog Xenopus laevis

被引：678

作者：

Session, Adam M. ^{[1
,2
,3
]}

Uno, Yoshinobu ^{[4
]}

Kwon, Taejoon ^{[5
,6
]}

Hapman, Jarrod A. C. ^{[3
]}

Toyoda, Atsushi ^{[7
,8
]}

Takahashi, Shuji ^{[9
]}

Fukui, Akimasa ^{[10
]}

Hikosaka, Akira ^{[11
]}

Suzuki, Atsushi ^{[9
]}

Kondo, Mariko ^{[12
]}

van Heeringen, Simon J. ^{[13
]}

Quigley, Ian ^{[14
]}

Heinz, Sven ^{[15
]}

Ogino, Hajime ^{[16
]}

Ochi, Haruki ^{[17
]}

Hellsten, Uffe ^{[3
]}

Lyons, Jessica B. . ^{[1
,2
]}

Simakov, Oleg ^{[18
]}

Putnam, Nicholas ^{[19
]}

Stites, Jonathan ^{[19
]}

Kuroki, Yoko ^{[20
]}

Tanaka, Toshiaki ^{[21
]}

Michiue, Tatsuo ^{[22
]}

Watanabe, Minoru ^{[23
]}

Ogdanovic, Ozren B. ^{[24
,25
]}

Lister, Ryan ^{[24
,25
]}

Georgiou, Georgios ^{[13
]}

Paranjpe, Sarita S. ^{[13
]}

Van Kruijsbergen, Ila ^{[13
]}

Shu, Shengquiang ^{[3
]}

Carlson, Joseph ^{[3
]}

Kinoshita, Tsutomu ^{[26
]}

Ohta, Yuko ^{[27
]}

Mawaribuchi, Shuuji ^{[28
]}

Jenkins, Jerry ^{[3
,29
]}

Grimwood, Jane ^{[3
,29
]}

Schmutz, Jeremy ^{[3
,29
]}

Mitros, Therese ^{[1
,2
]}

Mozaffari, Sahar V. ^{[30
]}

Suzuki, Yutaka ^{[31
]}

Haramoto, Yoshikazu ^{[32
]}

Yamamoto, Takamasa S. ^{[33
]}

Takagi, Chiyo ^{[33
]}

Heald, Rebecca ^{[34
]}

Miller, Kelly ^{[34
]}

Haudenschild, Christian ^{[35
,50
]}

Kitzman, Jacob ^{[36
]}

Nakayama, Takuya ^{[37
]}

Zutsu, Yumi I. ^{[38
]}

Robert, Jacques ^{[39
]}

机构：

[1] Univ Calif Berkeley, Dept Mol & Cell Biol, Life Sci Addit 3200, Berkeley, CA 94720 USA

[2] Univ Calif Berkeley, Ctr Integrat Genom, Life Sci Addit 3200, Berkeley, CA 94720 USA

[3] US DOE, Joint Genome Inst, Walnut Creek, CA 94598 USA

[4] Nagoya Univ, Grad Sch Bioagr Sci, Dept Appl Mol Biosci, Chikusa Ku, Furo Cho, Nagoya, Aichi 4648601, Japan

[5] Univ Texas Austin, Ctr Syst & Synthet Biol, Dept Mol Biosci, Austin, TX 78712 USA

[6] Ulsan Natl Inst Sci & Technol, Sch Life Sci, Dept Biomed Engn, Ulsan 689798, South Korea

[7] Natl Inst Genet, Ctr Informat Biol, 1111 Yata, Mishima, Shizuoka 4118540, Japan

[8] Natl Inst Genet, Adv Genom Ctr, 1111 Yata, Mishima, Shizuoka 4118540, Japan

[9] Hiroshima Univ, Grad Sch Sci, Amphibian Res Ctr, 1-3-1 Kagamiyama, Hiroshima 7398526, Japan

[10] Hokkaido Univ, Fac Adv Life Sci, Lab Tissue & Polymer Sci, Kita Ku, N10W8, Sapporo, Hokkaido 0600810, Japan

[11] Hiroshima Univ, Grad Sch Integrated Arts & Sci, Div Human Sci, 1-7-1 Kagamiyama, Hiroshima 7398521, Japan

[12] Univ Tokyo, Grad Sch Sci, MMBS, 1024 Koajiro, Miura, Kanagawa 2380225, Japan

[13] Radboud Univ Nijmegen, Fac Sci, Dept Mol Dev Biol, 259 RIMLS,M850-2-97,Geert Grootepl 28, NL-6525 GA Nijmegen, Netherlands

[14] Salk Inst Biol Studies, Mol Neurobiol Lab, La Jolla, CA 92037 USA

[15] Salk Inst Biol Studies, 10010 North Torrey Pines Rd, La Jolla, CA 92037 USA

[16] Nagahama Inst Biosci & Technol, Dept Anim Biosci, 1266 Tamura, Nagahama, Shiga 5260829, Japan

[17] Yamagata Univ, Fac Med, Inst Promot Med Sci Res, 2-2-2 Iida Nishi, Yamagata, Yamagata 9909585, Japan

[18] Okinawa Inst Sci & Technol Grad Univ, Mol Genet Unit, Onna, Okinawa 9040495, Japan

[19] Dovetail Genom LLC, Santa Cruz, CA 95060 USA

[20] NCCHD, Natl Res Inst Child Hlth & Dev, Dept Genome Med, Setagaya Ku, 2-10-1 Okura, Tokyo 1578535, Japan

[21] Tokyo Inst Technol, Dept Life Sci & Technol, Midori Ku, 4259 Nagatsuta, Yokohama, Kanagawa 2268501, Japan

[22] Univ Tokyo, Grad Sch Arts & Sci, Dept Life Sci, Meguro Ku, 3-8-1 Komaba, Tokyo 1538902, Japan

[23] Univ Tokushima, Inst Inst Liberal Arts & Fundamental Educ, 1-1 Minamijosanjima Cho, Tokushima 7708502, Japan

[24] Univ Western Australia, Harry Perkins Inst Med Res, Perth, WA 6009, Australia

[25] Univ Western Australia, ARC Ctr Excellence Plant Energy Biol, Perth, WA 6009, Australia

[26] Rikkyo Univ, Fac Sci, Dept Life Sci, Toshima Ku, 3-34-1 Nishi Ikebukuro, Tokyo 1718501, Japan

[27] Univ Maryland, Dept Microbiol & Immunol, 655 W Baltimore St, Baltimore, MD 21201 USA

[28] Kitasato Univ, Kitasato Inst Life Sci, Minato Ku, 5-9-1 Shirokane, Tokyo 1088641, Japan

[29] HudsonAlpha Inst Biotechnol, Huntsville, AL 35806 USA

[30] Univ Chicago, Dept Human Genet, 920 E 58th St,CLSC 431F, Chicago, IL 60637 USA

[31] Univ Tokyo, Dept Computat Biol & Med Sci, 5-1-5 Kashiwanoha, Kashiwa, Chiba 2778568, Japan

[32] Natl Inst Adv Ind Sci & Technol, Biotechnol Res Inst Drug Discovery, Cent 5,1-1-1 Higashi, Tsukuba, Ibaraki 3058565, Japan

[33] Natl Inst Basic Biol, Dept Dev Biol, Div Morphogenesis, 38 Nishigonaka, Okazaki, Aichi 4448585, Japan

[34] Univ Calif Berkeley, Dept Mol & Cell Biol, Life Sci Addit 3200, Berkeley, CA 94701 USA

[35] Illumina Inc, 25861 Ind Blvd, Hayward, CA 94545 USA

[36] Univ Washington, Dept Genome Sci, Foege Bldg S-250,Box 355065,3720 15th Ave NE, Seattle, WA 98195 USA

[37] Univ Virginia, Dept Biol, Charlottesville, VA 22904 USA

[38] Niigata Univ, Fac Sci, Dept Biol, Nishi Ku, 8050,Ikarashi 2 No Cho, Niigata 9502181, Japan

[39] Univ Rochester, Med Ctr, Dept Microbiol & Immunol, Rochester, NY 14642 USA

[40] Cincinnati Childrens Res Fdn, Div Dev Biol, Cincinnati, OH 45229 USA

[41] Univ Calgary, Dept Biol Sci, 2500 Univ Dr 1 NW, Calgary, AB T2N 1N4, Canada

[42] Okinawa Inst Sci & Technol Grad Univ, Marine Genom Unit, 1919-1 Tancha, Onna, Okinawa 9040495, Japan

[43] Univ Iowa, Dept Biol, 257 Biol Bldg, Iowa City, IA 52242 USA

[44] Univ Basel, Dept Zool & Evolutionary Biol, CH-4051 Basel, Switzerland

[45] Kitasato Univ, Sch Sci, Dept Biol Sci, 1-15-1 Minamiku, Sagamihara, Kanagawa 2520373, Japan

[46] SOKENDAI, Dept Basic Biol, 38 Nishigonaka, Okazaki, Aichi 4448585, Japan

[47] Natl Inst Informat, Principles Informat, Chiyoda Ku, 2-1-2 Hitotsubashi, Tokyo 1018430, Japan

[48] SOKENDAI, Dept Genet, 1111 Yata, Mishima, Shizuoka 4118540, Japan

[49] Univ Tokyo, Grad Sch Sci, Dept Biol Sci, Bunkyo Ku, 7-3-1 Hongo, Tokyo 1130033, Japan

[50] Personalis Inc, 1330 OBrien Dr, Menlo Pk, CA 94025 USA

来源：

NATURE | 2016年 / 538卷 / 7625期

关键词：

GENE DUPLICATIONS; CHROMOSOMES; POLYPLOIDY; TROPICALIS; ORIGIN; SUBFUNCTIONALIZATION; DIFFERENTIATION; FRACTIONATION; TRANSCRIPTOME; CONSEQUENCES;

D O I：

10.1038/nature19840

中图分类号：

O [数理科学和化学]; P [天文学、地球科学]; Q [生物科学]; N [自然科学总论];

学科分类号：

07 ; 0710 ; 09 ;

摘要：

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.

引用

页码：336 / +

页数：26

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