Comparative transcriptome analysis to identify fruit coloration-related genes of late-ripening litchi mutants and their wild type

•Two continuous generations of mutants matured later than their original cultivar. They are useful experimental system for studying the mechanism of litchi fruit development.•Genes related to anthocyanin synthesis and chlorophyll degradation were significantly differentially expressed in HL and its mutants during the color transition period.•We identified some novel candidate genes which may be involved in regulating litchi fruits pigmentation by WGCNA analysis. Litchi (Litchi chinensis Sonn.) is an important subtropical fruit crop with high economic and nutritional values. Fruit coloration is a sign of litchi fruit ripening and an important external quality traits. Two continuous generations of mutants, named MS1 and MS2, originally derived from cultivar ‘Heli’, exhibited the distinctive characteristic of late maturation of 20 d, with observable delays in coloration. The present study aimed to understand the mechanism underlying maturation difference between ‘Heli’ and its two mutants. An RNA-seq analysis revealed 6,145 differentially expressed genes, mostly identified at the color-breaking stage. The maximum expression levels of some genes involved in anthocyanin biosynthesis and chlorophyll degradation were delayed in the pericarp of the mutants compared with in the original cultivar. Generally, they peaked at earlier stages (S2/S3) in ‘Heli’, compared with later stages (S4/S5) in mutants. Moreover, some hormonal signal receptors, especially those involved in abscisic and ethylene signaling pathways, were also differentially expressed between the original cultivar and the mutant. Transcription factors, including MYB, bHLH, bZIP, and WRKY, correlated with anthocyanin biosynthesis, chlorophyll degradation and abscisic acid signal pathways were identified. The late pigmentation in mutants was related to the fruit ripening program, a complex and comprehensive process. Additionally, we identified novel candidate genes that are involved in the regulation of litchi fruit pigmentation of and gained significant insights into the process of litchi fruit ripening.