Comparative phylogenomics and phylotranscriptomics provide insights into the genetic complexity of nitrogen-fixing root-nodule symbiosis  

作　　者：Yu Zhang Yuan Fu Wenfei Xian Xiuli Li Yong Feng Fengjiao Bu Yan Shi Shiyu Chen Robin van Velzen Kai Battenberg Alison M.Berry Marco G.Salgado Hui Liu Tingshuang Yi Pascale Fournier Nicole Alloisio Petar Pujic Hasna Boubakri M.Eric Schranz Pierre-Marc Delaux Gane Ka-Shu Wong Valerie Hocher Sergio Svistoonoff Hassen Gherbi Ertao Wang Wouter Kohlen Luis G.Wall Martin Parniske Katharina Pawlowski Philippe Normand Jeffrey J.Doyle Shifeng Cheng 

机构地区：[1]Shenzhen Branch,Guangdong Laboratory for Lingnan Modern Agriculture,Genome Analysis Laboratory of the Ministry of Agriculture,Agricultural Genomics Institute at Shenzhen,Chinese Academy of Agricultural Sciences,Shenzhen 518124,China [2]Biosystematics Group,Department of Plant Sciences,Wageningen University,6708PB Wageningen,the Netherlands [3]Department of Plant Sciences,University of California,Davis,Davis,CA 95616,USA [4]Department of Ecology,Environment and Plant Sciences,Stockholm University,10691 Stockholm,Sweden [5]Germplasm Bank of Wild Species,Kunming Institute of Botany,Chinese Academy of Sciences,Lanhei Road,Kunming 650201,China [6]Universite´de Lyon,Universite´Lyon 1,CNRS,UMR5557,Ecologie Microbienne,INRA,UMR 1418,43 bd du 11 novembre 1918,69622 Villeurbanne,France [7]Laboratoire de Recherche en Sciences Ve´ge´tales(LRSV),Universite´de Toulouse,CNRS,UPS,24 chemin de Borde Rouge,Auzeville,BP42617,31326 Castanet Tolosan,France [8]Department of Biological Sciences,University of Alberta,Edmonton,AB T6G 2E9,Canada [9]French National Research Institute for Sustainable Development(IRD),UMR LSTM(IRD/CIRAD/INRAe/Montpellier University/Supagro)-Campus International Baillarguet,TA A-82/J,34398 Montpellier Cedex 5,France [10]National Key Laboratory of Plant Molecular Genetics,CAS Center for Excellence in Molecular Plant Sciences,Institute of Plant Physiology and Ecology,SIBS,Chinese Academy of Sciences,Shanghai,China [11]Laboratory of Molecular Biology,Department of Plant Sciences,Wageningen University,6708PB Wageningen,the Netherlands [12]Laboratory of Biochemistry,Microbiology and Soil Biological Interactions,Department of Science and Technology,National University of Quilmes,CONICET,Bernal,Argentina [13]Faculty of Biology,Genetics,LMU Munich,Großhaderner Strasse 2-4,82152 Martinsried,Germany [14]School of Integrative Plant Science,Sections of Plant Biology and Plant Breeding&Genetics,Cornell University,Ithaca,NY 14853,USA [15]State Key Laboratory of Systematic and Evolutionary Botany,Institute of Botan

出　　处：《Plant Communications》2024年第1期130-147,共18页植物通讯（英文）

基　　金：supported by the National Natural Science Foundation of China (32022006);the Program for Guangdong"ZhuJiang"Innovation Teams (2019ZT08N628);the Agricultural Science and Technology Innovation Program (ASTIP) (CAAS-XTCX2016001);the special funds for science technology innovation and industrial development of Shenzhen Dapeng New District (PT202101-01);supported by the National Natural Science Foundation of China (32070250);the Natural Science Foundation of Guangdong Province (2020A1515011030);the open research project of"Cross-Cooperative Team"of the Germplasm Bank of Wild Species,Kunming Institute of Botany,Chinese Academy of Sciences;supported by the Natural Science Foundation of Guangdong Province (2022A1515110240);support was provided by IRD and the Agence Nationale de la Recherche (Project SESAM,2010 BLAN 170801).

摘　　要：Plant root-nodule symbiosis(RNS)with mutualistic nitrogen-fixing bacteria is restricted to a single clade of angiosperms,the Nitrogen-Fixing Nodulation Clade(NFNC),and is best understood in the legume family.Nodulating species share many commonalities,explained either by divergence from a common ancestor over 100 million years ago or by convergence following independent origins over that same time period.Regardless,comparative analyses of diverse nodulation syndromes can provide insights into constraints on nodulation—what must be acquired or cannot be lost for a functional symbiosis—and the latitude for Plant Communications Genomic landscape of nodulation variation in the symbiosis.However,much remains to be learned about nodulation,especially outside of legumes.Here,we employed a large-scale phylogenomic analysis across 88 species,complemented by 151 RNA-seq libraries,to elucidate the evolution of RNS.Our phylogenomic analyses further emphasize the uniqueness of the transcription factor NIN as a master regulator of nodulation and identify key muta-tions that affect its function across the NFNC.Comparative transcriptomic assessment revealed nodule-specific upregulated genes across diverse nodulating plants,while also identifying nodule-specific and nitrogen-response genes.Approximately 70%of symbiosis-related genes are highly conserved in the four representative species,whereas defense-related and host-range restriction genes tend to be lineage specific.Our study also identified over 900000 conserved non-coding elements(CNEs),over 300000 of which are unique to sampled NFNC species.NFNC-specific CNEs are enriched with the active H3K9ac mark and are correlated with accessible chromatin regions,thus representing a pool of candidate regula-tory elements for genes involved in RNS.Collectively,our results provide novel insights into the evolution of nodulation and lay a foundation for engineering of RNS traits in agriculturally important crops.

关 键 词：nitrogen-fixing root-nodule symbiosis two competing hypotheses PHYLOGENOMICS phylotranscrip-tomics conserved non-coding elements convergence deep homology 

分 类 号：Q94[生物学—植物学]