A chromosome-level genome assembly for Chinese plum‘Wushancuili'reveals the molecular basis of its fruit color and susceptibility to rain-cracking

Chinese plum(Prunus salicina Lindl.)originates from China and makes a large contribution to the global production of plums.The P.salicina‘Wushancuili'has a green coloration and high fruit quality and is economically important in eliminating poverty and protecting ecology in the Yangtze River Three Gorges Reservoir.However,rain-induced cracking(rain-cracking,literally skin cracking caused by rain)is a limitation to‘Wushancuili'fruit production and causes severe losses.This study reported a high-quality‘Wushancuili'genome assembly consisting of a 302.17-Mb sequence with eight pseudo-chromosomes and a contig N50 of 23.59 Mb through the combination of Illumina sequencing,Pacific Biosciences HiFiⅢsequencing,and high-throughput chromosome conformation capture technology.A total of 25109 protein-coding genes are predicted and 54.17%of the genome is composed of repetitive sequences.‘Wushancuili'underwent a remarkable orthoselection during evolution.Gene identification revealed that loss-of-function in four core MYB10 genes results in the anthocyanin deficiency and absence of red color,revealing the green coloration due to the residual high chlorophyll in fruit skin.Besides,the occurrence of cracking is assumed to be closely associated with cell wall modification and frequently rain-induced pathogen enrichment through transcriptomic analysis.The loss of MYB10 genes might render fruit more susceptible to pathogen-mediated cracking by weakening the epidermal strength and reactive oxygen species(ROS)scavenging.Our findings provided fundamental knowledge regarding fruit coloration and rain-cracking and will facilitate genetic improvement and cultivation management in Chinese plums.

SlMYB75,an MYB-type transcription factor,promotes anthocyanin accumulation and enhances volatile aroma production in tomato fruits

Genetic manipulation of genes to upregulate specific branches of metabolic pathways is a method that is commonly used to improve fruit quality.However,the use of a single gene to impact several metabolic pathways is difficult.Here,we show that overexpression of the single gene SlMYB75(SlMYB75-OE)is effective at improving multiple fruit quality traits.In these engineered fruits,the anthocyanin content reached 1.86mg g−1 fresh weight at the red-ripe stage,and these SlMYB75-OE tomatoes displayed a series of physiological changes,including delayed ripening and increased ethylene production.In addition to anthocyanin,the total contents of phenolics,flavonoids and soluble solids in SlMYB75-OE fruits were enhanced by 2.6,4,and 1.2 times,respectively,compared to those of wild-type(WT)fruits.Interestingly,a number of aroma volatiles,such as aldehyde,phenylpropanoid-derived and terpene volatiles,were significantly increased in SlMYB75-OE fruits,with some terpene volatiles showing more than 10 times higher levels than those in WT fruits.Consistent with the metabolic assessment,transcriptomic profiling indicated that the genes involved in the ethylene signaling,phenylpropanoid and isoprenoid pathways were greatly upregulated in SlMYB75-OE fruits.Yeast one-hybrid and transactivation assays revealed that SlMYB75 is able to directly bind to the MYBPLANT and MYBPZM cis-regulatory elements and to activate the promoters of the LOXC,AADC2 and TPS genes.The identification of SlMYB75 as a key regulator of fruit quality attributes through the transcriptional regulation of downstream genes involved in several metabolic pathways opens new avenues towards engineering fruits with a higher sensory and nutritional quality.

PaPYL9 is involved in the regulation of apricot fruit ripening through ABA signaling pathway

Abscisic acid(ABA)is a major regulator of non-climacteric fruit ripening;however,the role of ABA in the ripening of climacteric fruit is not clear.Here,as a typical climacteric fruit,apricots were used to investigate the role of ABA in fruit ripening.Based on weighted gene coexpression network analysis(WGCNA)of our previous transcriptome data,we treated‘Danxing’fruit with exogenous ABA and obtained ABA receptor genes,genes related to ABA biosynthesis and signal transduction,and analyzed the response of these candidate genes to exogenous ABA during fruit ripening.Subsequently,the full length of candidate PYLs genes were cloned,and their putative function were analyzed by phylogenetic analysis and protein structure domain analysis.And then the function of one candidate gene PaPYL9 was verified by using transgenic tomato.Furthermore,the response genes in transgenic tomato were screened by transcriptome sequencing,and ultimately the related regulatory network was proposed.The results showed that the injection of exogenous 1.89 mmol·L^(-1) ABA remarkably promoted fruit coloration,and increased the color index for red grapes(CIRG)and the total soluble solids(TSS)content,but significantly decreased the firmness and titratable acid(TA)content(p<0.01).Nordihydroguaiaretic acid(NDGA),the inhibitor of ABA,appeared to have the converse role in TA,TSS,CIRG and firmness,during the ripening process.One NCED(9-cis-epoxycarotenoiddioxygenase)and five ABA receptor genes related to signal transduction were mined from the transcriptome data of apricot fruit through WGCNA.Compared with the control,the expression levels of NCED1,PYL9(PYR/PYL/RCAR),SnRK2(SUCROSE NON-FERMENTING1(SNF1)-RELATED PROTEIN KINASE 2S),and ABF2(ABRE-binding bZIP transcription)were induced dramatically by ABA treatment(p<0.01),while NDGA treatment significantly inhibited their expression.Based on gene expression and protein domain analysis,we inferred that PaPYL9 is putatively involved in apricot fruit ripening.Overexpression of PaPYL9 in Micro-TOM tomatoes resulted in the promotion of early ripening.Simultaneously,the expression levels of genes related ethylene biosynthesis,chlorophyll degradation,fruit softening,flavor formation,pigment synthesis,and metabolism were all significantly induced in overexpression of PaPYL9 tomatoes.This indicates the central role of ABA in climacteric fruit ripening.A regulatory network was tentatively proposed,laying the foundation to unveil the molecular mechanism of the regulatory role of PaPYL9 in fruit ripening.