Organisation and evolution of gene families involved in the ripening of banana fruits
Cyril Jourda
Abstract:
Whole genome duplications (WGD) are widespread in plants and the analysis of the banana (Musa acuminata ssp. malaccensis, accession DH-Pahang) genome has identified three whole genome duplication events in this species. To study the impact of these WGDs on the evolution of banana gene families, we have focused on genes involved in the ethylene biosynthesis and signalling pathway and in starch metabolism which are of particular importance for fruit ripening in banana.
The impact of ethylene on banana ripening was studied by fruit transcriptome analysis using RNA-Seq, at five days after treatment with acetylene (an ethylene analog). The results have shown a global transcriptional reprogramming involving up to more than 4000 differentially expressed genes including 597 transcription factors, genes encoding enzymes of cell wall degradation and genes of the starch and soluble carbohydrate metabolisms.
In parallel, all members of 14 gene families involved in ethylene biosynthesis and signalling and in starch metabolism have been identified through a comparative genomics approach. Gene family evolution was studied by phylogenetic analyses and the identification of gene duplication modes. In banana, seven out of ten ethylene pathway gene families have evolved through WGD and four of them (ACS, EIL, EBF, ERF) have expanded through preferential retention after WGD. Banana orthologs to AtEIN3 and AtEIL1, two major genes for ethylene signalling in Arabidopsis were found particularly expanded and a co-expansion of EBF genes that are responsible for control of EIL proteins levels was also observed. Gene expression profiles in banana pulp and peel tissues suggested functional redundancy for several MaEBF and MaEIL gene duplicates resulting from WGD and subfunctionalisation for some of them.
In addition, four gene families from the starch metabolism have evolved in an independent way in banana and in the grasses, through specific duplications including WGDs for the AGPases and for subfamilies of the starch synthases and β-amylases, and through gene scale duplications for α-amylases.
Finally, these comparative genomics and phylogenetic approaches combined to expression data in banana fruits allowed the identification of gene members from these gene families that are potentially involved in the fruit ripening process.
The results obtained here illustrate the impact of WGDs on the evolution of banana gene families throughout biological pathways and represent a basis for future work on the characterisation of the genetic bases of an important and complex trait, banana fruit quality.
Journal:
Thesis of the University of Montpellier
Link:
publications.cirad.fr/en/une_notice.php?dk=572010