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Pathway Discovery in Deep Convergence “Repeated convergent evolution in Big Data in Phylogenomics for Nitrogen- phenotypic traits can be traced back to Fixing Root Nodule Symbiosis convergence at the genome level”

Shifeng CHENG Agricultural Genomics Institute, CAAS; (BGI-Shenzhen) Do new anatomical structures arise de novo, or do [email protected]，January 15, PAG XVVII they evolve from pre-existing structures?

Host-microbe symbiosis is a crucial trait for life growth and development

Parasitic ? or Symbiotic?

Homology means common ancestor !

Each Plant or Animal has its “second genome” !! Deep Homology --- mutualisms !! and the origins of evolutionary novelty

Animals: Plants: For Plants, ① Bats/Dolphins echolocation ① Flowering/leaves ② Electric organs in diverse fishes ② Photosynthesis One of the symbioses Legume-rhizobia is ③ Animal eyes/photoreceptors ③ AM-fungi symbiosis is…. one of the important ④ Tetrapod limbs/fish fins ⑤ Giant beetle horns symbioses for plants

Hox-gene

$100 billion economic & environmental cost, globally

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Families (order) # genus # genus # Species/in Chiina ① typical legume nodule World China ② Evolutionary symbiosis 远志科Polygalaceae (豆目Fabales) 17 4 950/47 19 families: between land plants and 皂皮树科Quillajaceae (豆目Fabales) 4 0 44/0 Microbes:Arbuscular 海人树科Surianaceae (豆目Fabales) 5 1 7/1 close-related Mycorrhizal (AM) & 胡桃科Juglandaceae (壳斗目Fagales) 9 7 59/21 Root Nodule Symbiosis 核果木科Ticodendraceae (壳斗目Fagales) 1 0 1/0 non-nodulators (RNS) 壳斗科Fagaceae (壳斗目Fagales) 7 7 700/294 马尾树科Rhoipteleaceae (壳斗目Fagales) 1 1 1/1 Conserved: 南青冈科Nothofagaceae (壳斗目Fagales) 1 0 35/0 RNS symbiosis shares a 钩毛树科Barbeyaceae (蔷薇目Rosales) 1 0 1/0 lot of conserved genetic 桑科Moraceae (蔷薇目Rosales) 37 9 1100/126 荨麻科Urticaceae (蔷薇目Rosales) 45 25 1000/339 toolkit with AM-fungi 朴科Celtidaceae (蔷薇目Rosales) 1 1 70/11 symbiosis 大麻科Cannabaceae (蔷薇目Rosales) 3 3 3/3 伞树科Cecropiaceae (蔷薇目Rosales) 6 1 180/2 八瓣果科Dirachmaceae (蔷薇目Rosales) 1 0 1/0 葫芦科Cucurbitaceae (葫芦目Cucurbitales) 110 30 775/149 秋海棠科Begoniaceae (葫芦目Cucurbitales) 3 1 900/124 棒果木科Corynocarpaceae (葫芦目 1 0 4/0 Wu et. al, 2006 Cucurbitales) 异叶木科Anisophyllaceae (葫芦目 4 0 29/0 Martin et al., 2015 Cucurbitales) 总计： 259 90 4872/1109

(豆科) 10 families: nodulators 19 families: close relatives

(蔷薇科)

N

- fixing fixing clade

(桦木科) “2016, Multiple Gains Hypothesis”

(壳斗科)

(i) Independent gains with parallel evolution (葫芦科) (ii) a single gain of nodulation followed by massive losses (Doyle,1998; Sprent, 2007) The later is much more reasonable?

Family (order) # Genus/N- Distribution in #species/in China fixing genus China In the past 20+ years: Evolutionary trajectory, genomic evidence… Symbiosis with Rhizobium 10 families: 1995, Predisposition hypothesis (PNAS) 2014, Predisposition/precursor Event revisit (Nature Communication) 豆科Fabaceae (豆目Fabales) 634/most 152 17275/1432 N-fixing 榆科Ulmaceae (蔷薇目Rosales) 14/1 7 100/33 nodulators Summary： 648 159 17375/1465 Symbiosis with Frankia

桦木科Betulaceae (壳斗目Fagales) 6/1 6 110/89 木麻黄科Casuarinaceae (壳斗目Fagales) 4/4 1（intr.） 96/3 杨梅科Myricaceae (壳斗目Fagales) 3/2 1 59/4 胡颓子科Elaeagnaceae (蔷薇目Rosales) 3/3 2 60/58 鼠李科Rhamnaceae (蔷薇目Rosales) 49/7 15 875/127 What are the 蔷薇科Rosaceae (蔷薇目Rosales) 95/5 62 2825/886 Genetic Innovations & 四数木科Datiscaceae (葫芦目Cucurbitales) 3/1 1 4/1 Genomic Modification 马桑科Coriariaceae (葫芦目Cucurbitales) 1/1 1 5/5 that drives nodulatino? Summary： 164/24 89 4033/1172 Wu et. al, 2006 Jeff et al., 2011 In total： 812 248 21408/2637

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The “Evolution of Nodulation” Project, 2015 May --- What we found: NIN and NPG are both present in all Nodulators, but absence in all Non-nodulators Shifeng Cheng, Pierre-marc Deulax, Martin Parniske, Gane Ka-shu wong, et al., --- Co-elimination evolution for the Non-nodulators?

To uunderstand genome evolution and diversification of plant-microbe symbioses that are responsible for N- fixing Root Nodule Symbiosis

Question: What cause the present-day

phylogenetic distribution of plant- (Rosid I) Rhizobia/Frankia Root Nodule symbiosis ? -- a global-scale phylogenomics study Supported by: synteny and PCR Independent NIN mutation events: Deletions monophyletic group, nitrogen-fixing clade: Truncations Fabales, Fagales, Cucurbitales, Rosales NIN: NODULE INCEPTION transcription factor that is essential for nodule formation in legumes. Indel mutation RPG: RHIZOBIUM-DIRECTED POLAR GROWTH, a long coiled-coil protein that is essential for rhizobial infection in No gene erosion legumes. Different to loss of AM

37 Genomes: Fagales: 3 Cucurbitales: 4 Rosales: 8 Fabales: 13 Outgroups: 9

A Novel Evolutionary Scenario for the evolution of NFN clade: what cause the present-day phylogenetic distribution of plant-Rhizobia/Frankia Root Nodule symbiosis ?

“Multiple Losses Hypothesis”

7 losses in Fagales, 5 in Cucurbitales, 17 in Rosales, and 36 in Fabales

“Drop it is a relieve”

Ortholog inference Why lost? The root nodule symbiosis is under negative selection ! Genome-wide approach Phylogenomics Possible drivers: Orthofinder ① energetic balance Target approach ② Cheaters: ‘cheating’ bacteria 21-symbiosis gene families (phylogeny) ③ Environmental factors: Climate changes with decreased CO2

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“Pathway Discovery”? Big Omics: 97% of the genome “dark more details, matter”, non-coding sequences through more questions await… multi-omics research, Chip-seq, Methylation, Y2H Novelty and Homology Big Evolution: 28 sequenced genomes vs. 40,000 species in genetic regulatory cascade/circuits NFN clade . Co-option/rewiring and deployment

Interactomics: complementary metabolic pathway, soil microbtiota It is not possible to identify what is new in evolution without understanding the old “Man still bears in his bodily frame the indelible stamp of his lowly origin.”  PACEs to be found? (Matin Parniske) PACE in the NIN promoter(Predisposition Associated Cis-Element)  More missing genes/elements in non-nodulating plants?  What happened in non-coding RNAs, promoters, regulators, and genetic network  Genetic mechanism underlying the generality and specification of plant-microbiome Symbiotic Host Range;

• Jeff: “Understanding predisposition towards nodulation is something of such a ‘holy grail’ ” Laboratoire de Recherche en Acknowledgement • Chasing Unicorns: Engineering Nodulation in Non-nodulators Sciences Végétales (LRSV), CNRS Pierre-marc Delaux

NFN clade LMU Munich: “EvoNod Team” Martin Parniske Maximilian Griesmann Cucurbitale: melon, vegetable Rosales: fruits Fabales: beans, medicinal plants Big Evolution: Trait Revisit with Phylogenomics Fagales: trees, shrubs of forest University of Alberta: Big Omics: Pathway Discovery Gane Ka-shu Wong Big Engineering: Pathway recruitment & invention Cereals BGI-Shenzhen: Huanming Yang, Xun Xu Evolution: Deep homology Xin Liu Omics: DNA central dogma Yue Chang Yue Song, et al. Engineering: Genome-aided CRISPR/synthetic biology Grasses: >70% of foods consumed

Phylogeny tree mind Genome mind

Phylogenomics

From Darwin, 1859 We need a Deep Map (of Genomes) Thanks

map genes/pathways to the tree

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