@article{fdi:010089548,
  title = {{C}omparative phylogenomics and phylotranscriptomics provide insights into the genetic complexity of nitrogen-fixing root-nodule symbiosis},
  author = {{Z}hang, {Y}. and {F}u, {Y}. and {X}ian, {W}. {F}. and {L}i, {X}. {L}. and {F}eng, {Y}. and {B}u, {F}. {J}. and {S}hi, {Y}. and {C}hen, {S}. {Y}. and van {V}elzen, {R}. and {B}attenberg, {K}. and {B}erry, {A}. {M}. and {S}algado, {M}. {G}. and {L}iu, {H}. and {Y}i, {T}. {S}. and {F}ournier, {P}. and {A}lloisio, {N}. and {P}ujic, {P}. and {B}oubakri, {H}. and {S}chranz, {M}. {E}. and {D}elaux, {P}. {M}. and {W}ong, {G}. {K}. {S}. and {H}ocher, {V}al{\'e}rie and {S}vistoonoff, {S}ergio and {G}herbi, {H}assen and {W}ang, {E}. and {K}ohlen, {W}. and {W}all, {L}. {G}. and {P}arniske, {M}. and {P}awlowski, {K}. and {N}ormand, {P}. and {D}oyle, {J}. {J}. and {C}heng, {S}. {F}.},
  editor = {},
  language = {{ENG}},
  abstract = {{P}lant root-nodule symbiosis ({RNS}) with mutualistic nitrogen-fixing bacteria is restricted to a single clade of angiosperms, the {N}itrogen-{F}ixing {N}odulation {C}lade ({NFNC}), and is best understood in the legume family. {N}odulating 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. {R}egardless, 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 variation in the symbiosis. {H}owever, much remains to be learned about nodulation, especially outside of legumes. {H}ere, we employed a large-scale phylogenomic analysis across 88 species, complemented by 151 {RNA}-seq libraries, to elucidate the evolution of {RNS}. {O}ur phylogenomic analyses further emphasize the uniqueness of the transcription factor {NIN} as a master regulator of nodulation and identify key mutations that affect its function across the {NFNC}. {C}omparative transcriptomic assessment revealed nodulespecific upregulated genes across diverse nodulating plants, while also identifying nodule-specific and nitrogen-response genes. {A}pproximately 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. {O}ur study also identified over 900 000 conserved non-coding elements ({CNE}s), over 300 000 of which are unique to sampled {NFNC} species. {NFNC}-specific {CNE}s are enriched with the active {H}3{K}9ac mark and are correlated with accessible chromatin regions, thus representing a pool of candidate regulatory elements for genes involved in {RNS}. {C}ollectively, our results provide novel insights into the evolution of nodulation and lay a foundation for engineering of {RNS} traits in agriculturally important crops.},
  keywords = {nitrogen-fixing root-nodule symbiosis ; two competing hypotheses ; phylogenomics ; phylotranscriptomics ; conserved non-coding elements ; convergence ; deep homology},
  booktitle = {},
  journal = {{P}lant {C}ommunications},
  volume = {[{E}arly access]},
  numero = {1},
  pages = {100671 [18 p.]},
  ISSN = {2590-3462},
  year = {2024},
  DOI = {10.1016/j.xplc.2023.100671},
  URL = {https://www.documentation.ird.fr/hor/fdi:010089548},
}