@article{fdi:010086934,
  title = {{G}lobal transcriptome profiling reveals differential regulatory, metabolic and hormonal networks during somatic embryogenesis in {C}offea arabica},
  author = {{A}wada, {R}. and {L}epelley, {M}. and {B}reton, {D}. and {C}harpagne, {A}. and {C}ampa, {C}laudine and {B}erry, {V}. and {G}eorget, {F}. and {B}reitler, {J}. {C}. and {L}eran, {S}. and {D}jerrab, {D}. and {M}artinez-{S}eidel, {F}. and {D}escombes, {P}. and {C}rouzillat, {D}. and {B}ertrand, {B}. and {E}tienne, {H}.},
  editor = {},
  language = {{ENG}},
  abstract = {{B}ackground{S}omatic embryogenesis ({SE}) is one of the most promising processes for large-scale dissemination of elite varieties. {H}owever, for many plant species, optimizing {SE} protocols still relies on a trial and error approach. {W}e report the first global scale transcriptome profiling performed at all developmental stages of {SE} in coffee to unravel the mechanisms that regulate cell fate and totipotency.{R}esults{RNA}-seq of 48 samples (12 developmental stages x 4 biological replicates) generated 90 million high quality reads per sample, approximately 74% of which were uniquely mapped to the {A}rabica genome. {F}irst, the statistical analysis of transcript data clearly grouped {SE} developmental stages into seven important phases ({L}eaf, {D}edifferentiation, {P}rimary callus, {E}mbryogenic callus, {E}mbryogenic cell clusters, {R}edifferentiation and {E}mbryo) enabling the identification of six key developmental phase switches, which are strategic for the overall biological efficiency of embryo regeneration. {D}ifferential gene expression and functional analysis showed that genes encoding transcription factors, stress-related genes, metabolism-related genes and hormone signaling-related genes were significantly enriched. {S}econd, the standard environmental drivers used to control {SE}, i.e. light, growth regulators and cell density, were clearly perceived at the molecular level at different developmental stages. {T}hird, expression profiles of auxin-related genes, transcription factor-related genes and secondary metabolism-related genes were analyzed during {SE}. {G}ene co-expression networks were also inferred. {A}uxin-related genes were upregulated during dedifferentiation and redifferentiation while transcription factor-related genes were switched on from the embryogenic callus and onward. {S}econdary metabolism-related genes were switched off during dedifferentiation and switched back on at the onset of redifferentiation. {S}econdary metabolites and endogenous {IAA} content were tightly linked with their respective gene expression. {L}astly, comparing {A}rabica embryogenic and non-embryogenic cell transcriptomes enabled the identification of biological processes involved in the acquisition of embryogenic capacity.{C}onclusions{T}he present analysis showed that transcript fingerprints are discriminating signatures of cell fate and are under the direct influence of environmental drivers. {A} total of 23 molecular candidates were successfully identified overall the 12 developmental stages and can be tested in many plant species to optimize {SE} protocols in a rational way.},
  keywords = {{C}ell fate ; {C}offee ; {M}olecular markers ; {M}olecular networks ; {S}omatic embryogenesis ; {T}otipotency ; {T}ranscriptomics},
  booktitle = {},
  journal = {{BMC} {G}enomics},
  volume = {24},
  numero = {1},
  pages = {41 [19 p.]},
  ISSN = {1471-2164},
  year = {2023},
  DOI = {10.1186/s12864-022-09098-z},
  URL = {https://www.documentation.ird.fr/hor/fdi:010086934},
}