Phylogenomics reveals multiple losses of nitrogen-fixing root nodule symbiosis

被引：301

作者：

Griesmann, Maximilian ^{[1
,2
]}

Chang, Yue ^{[3
,4
]}

Liu, Xin ^{[3
,4
]}

Song, Yue ^{[3
,4
]}

Haberer, Georg ^{[2
]}

Crook, Matthew B. ^{[5
]}

Billault-Penneteau, Benjamin ^{[1
]}

Lauressergues, Dominique ^{[6
]}

Keller, Jean ^{[6
]}

Imanishi, Leandro ^{[7
]}

Roswanjaya, Yuda Purwana ^{[8
]}

Kohlen, Wouter ^{[8
]}

Pujic, Petar ^{[9
]}

Battenberg, Kai ^{[10
]}

Alloisio, Nicole ^{[9
]}

Liang, Yuhu ^{[3
,4
]}

Hilhorst, Henk ^{[11
]}

Salgado, Marco G. ^{[12
]}

Hocher, Valerie ^{[13
]}

Gherbi, Hassen ^{[13
]}

Svistoonoff, Sergio ^{[13
]}

Doyle, Jeff J. ^{[14
]}

He, Shixu ^{[3
,4
]}

Xu, Yan ^{[3
,4
]}

Xu, Shanyun ^{[3
,4
]}

Qu, Jing ^{[3
,4
]}

Gao, Qiang ^{[3
,15
]}

Fang, Xiaodong ^{[3
,15
]}

Fu, Yuan ^{[3
,4
]}

Normand, Philippe ^{[9
]}

Berry, Alison M. ^{[10
]}

Wall, Luis G. ^{[7
]}

Ane, Jean-Michel ^{[16
,17
]}

Pawlowski, Katharina ^{[12
]}

Xu, Xun ^{[3
,4
]}

Yang, Huanming ^{[3
,18
]}

Spannagl, Manuel ^{[2
]}

Mayer, Klaus F. X. ^{[2
,19
]}

Wong, Gane Ka-Shu ^{[3
,20
,21
]}

Parniske, Martin ^{[1
]}

Delaux, Pierre-Marc ^{[6
]}

Cheng, Shifeng ^{[3
,4
]}

机构：

[1] Ludwig Maximilians Univ Munchen, Fac Biol, Genet, Grosshaderner Str 2-4, D-82152 Martinsried, Germany

[2] Helmholtz Ctr Munich, German Res Ctr Environm Hlth, PGSB, D-85764 Neuherberg, Germany

[3] BGI Shenzhen, Shenzhen 518083, Peoples R China

[4] BGI Shenzhen, China Natl GeneBank, Shenzhen 518120, Peoples R China

[5] Weber State Univ, Dept Microbiol, Ogden, UT 84408 USA

[6] Univ Toulouse, LRSV, CNRS, UPS, 24 Chemin Borde Rouge,BP42617, F-31326 Castanet Tolosan, France

[7] Univ Nacl Quilmes, CONICET, Dept Ciencia & Tecnol, LBMIBS, R Saenz Pena 352,B1876BXD, Bernal, Argentina

[8] Wageningen Univ, Mol Biol Lab, Droevendaalsesteeg 1, NL-6708 PB Wageningen, Netherlands

[9] Univ Lyon 1, Univ Lyon, CNRS, UMR 5557,Ecol Microbienne, F-69622 Villeurbanne, France

[10] Univ Calif Davis, Dept Plant Sci, Davis, CA 95616 USA

[11] Wageningen Univ, Lab Plant Physiol, Droevendaalsesteeg 1, NL-6708 PB Wageningen, Netherlands

[12] Stockholm Univ, Dept Ecol Environm & Plant Sci, S-10691 Stockholm, Sweden

[13] Univ Montpellier, French Natl Res Inst Sustainable Dev IRD, UMR LSTM, IRD,INRA,CIRAD,Supagro, Campus Int Baillarguet,TA A-82-J, F-34398 Montpellier 5, France

[14] Cornell Univ, Sch Integrated Plant Sci, Sect Plant Breeding & Genet, Ithaca, NY 14853 USA

[15] BGI Shenzhen, BGI Genom, Shenzhen 518083, Peoples R China

[16] Univ Wisconsin, Dept Agron, 1575 Linden Dr, Madison, WI 53706 USA

[17] Univ Wisconsin, Dept Bacteriol, Madison, WI 53706 USA

[18] James D Watson Inst Genome Sci, Hangzhou 310058, Zhejiang, Peoples R China

[19] Tech Univ Munich, TUM Sch Life Sci Weihenstephan, D-85354 Freising Weihenstephan, Germany

[20] Univ Alberta, Dept Biol Sci, Edmonton, AB T6G 2E9, Canada

[21] Univ Alberta, Dept Med, Edmonton, AB T6G 2E, Canada

来源：

SCIENCE | 2018年 / 361卷 / 6398期

基金：

美国国家科学基金会; 欧洲研究理事会; 瑞典研究理事会;

关键词：

ARBUSCULAR MYCORRHIZA; PHYLOGENETIC ANALYSIS; SEQUENCE ALIGNMENT; GENOME; EVOLUTION; GENE; INFERENCE; FIXATION; ORIGINS; NIN;

D O I：

10.1126/science.aat1743

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：

The root nodule symbiosis of plants with nitrogen-fixing bacteria affects global nitrogen cycles and food production but is restricted to a subset of genera within a single clade of flowering plants. To explore the genetic basis for this scattered occurrence, we sequenced the genomes of 10 plant species covering the diversity of nodule morphotypes, bacterial symbionts, and infection strategies. In a genome-wide comparative analysis of a total of 37 plant species, we discovered signatures of multiple independent loss-of-function events in the indispensable symbiotic regulator NODULE INCEPTION in 10 of 13 genomes of nonnodulating species within this clade. The discovery that multiple independent losses shaped the present-day distribution of nitrogen-fixing root nodule symbiosis in plants reveals a phylogenetically wider distribution in evolutionary history and a so-far-underestimated selection pressure against this symbiosis. © The Authors, some rights reserved.

引用

页数：11

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