@article{fdi:010084735,
  title = {{N}ew cup out of old coffee : contribution of parental gene expression legacy to phenotypic novelty in coffee beans of the allopolyploid {C}offea arabica {L}},
  author = {{C}ombes, {M}arie-{C}hristine and {J}o{\¨e}t, {T}hierry and {S}tavrinides, {A}. {K}. and {L}ashermes, {P}hilippe},
  editor = {},
  language = {{ENG}},
  abstract = {{B}ackground and {A}ims {A}llopolyploidization is a widespread phenomenon known to generate novel phenotypes by merging evolutionarily distinct parental genomes and regulatory networks in a single nucleus. {T}he objective of this study was to investigate the transcriptional regulation associated with phenotypic novelty in coffee beans of the allotetraploid {C}offea arabica. {M}ethods {A} genome-wide comparative transcriptomic analysis was performed in {C}. arabica and its two diploid progenitors, {C}. canephora and {C}. eugenioides. {G}ene expression patterns and homeologue expression were studied on seeds at five different maturation stages. {T}he involvement of homeologue expression bias ({HEB}) in specific traits was addressed both by functional enrichment analyses and by the study of gene expression in the caffeine and chlorogenic acid biosynthesis pathways. {K}ey {R}esults {E}xpression-level dominance in {C}. arabica seed was observed for most of the genes differentially expressed between the species. {A}pproximately a third of the genes analysed showed {HEB}. {T}his proportion increased during seed maturation but the biases remained equally distributed between the sub-genomes. {T}he relative expression levels of homeologues remained relatively constant during maturation and were correlated with those estimated in leaves of {C}. arabica and interspecific hybrids between {C}. canephora and {C}. eugenioides. {F}unctional enrichment analyses performed on genes exhibiting {HEB} enabled the identification of processes potentially associated with physiological traits. {T}he expression profiles of the genes involved in caffeine biosynthesis mirror the differences observed in the caffeine content of mature seeds of {C}. arabica and its parental species. {C}onclusions {N}either of the two sub-genomes is globally preferentially expressed in {C}. arabica seeds, and homeologues appear to be co-regulated by shared trans-regulatory mechanisms. {T}he observed {HEB}s are thought to be a legacy of gene expression differences inherited from diploid progenitor species. {P}re-existing functional divergences between parental species appear to play an important role in controlling the phenotype of {C}. arabica seeds.},
  keywords = {{A}llopolyploidy ; {C}offea arabica ; gene expression ; homeologue expression ; bias ; caffeine ; additivity ; expression-level dominance ; phenotype ; desiccation tolerance ; seed},
  booktitle = {},
  journal = {{A}nnals of {B}otany},
  volume = {[{E}arly access]},
  numero = {},
  pages = {[14 p.]},
  ISSN = {0305-7364},
  year = {2022},
  DOI = {10.1093/aob/mcac041},
  URL = {https://www.documentation.ird.fr/hor/fdi:010084735},
}