Transcriptomics and metabolomics analyses provide insights into postharvest ripening and senescence of tomato fruit under low temperature

Tomato is one of the most important vegetable crops in the world and is a model plant used to study the ripening of climacteric fleshy fruit.During the ripening process of tomato fruit,flavor and aroma metabolites,color,texture and plant hormones undergo significant changes.However,low temperatures delayed the ripening process of tomato fruit,inhibiting flavor compounds and ethylene production.Metabolomics and transcriptomics analyses of tomato fruit stored under low temperature(LT,5°C)and room temperature(RT,25°C)were carried out to investigate the effects of storage temperature on the physiological changes in tomato fruit after harvest.The results of transcriptomics changes revealed that the differentially expressed genes(DEGs)involved in tomato fruit ripening,including several kinds of transcription factors(TFs)(TCP,WRKY,MYB and bZIP),enzymes involved in cell wall metabolism[beta-galactosidase(β-GAL),pectinesterase(PE)and pectate lyase(PL),cellulose and cellulose synthase(CESA)],enzymes associated with fruit flavor and aroma[acetyltransferase(AT),malic enzyme(ME),lipoxygenase(LOX),aldehyde dehydrogenase(ALDH),alcohol dehydrogenase(ADH)and hexokinase(HK)],genes associated with heat stress protein 70 and genes involved in the production of plant hormones such as Ethylene responsive factor 1(ERF1),Auxin/indoleacetic acids protein(AUX/IAA),gibberellin regulated protein.Based on the above results,we constructed a regulatory network model of the effects of different temperatures during the fruit ripening process.According to the analysis of the metabolomics results,it was found that the contents of many metabolites in tomato fruit were greatly affected by storage temperature,including,organic acids(L-tartaric acid,a-hydroxyisobutyric acid and 4-acetamidobutyric acid),sugars(melezitose,beta-Dlactose,D-sedoheptulose 7-phosphate,2-deoxyribose 1-phosphate and raffinose)and phenols(coniferin,curcumin and feruloylputrescine).This study revealed the effects of storage temperature on postharvest tomato fruit and provided a basis for further understanding of the molecular biology and biochemistry of fruit ripening.

Combined genomic, transcriptomic, and metabolomic an alyses provide in sights into chayote (Sechium edule) evolution and fruit development

Chayote(Sechium edule)is an agricultural crop in the Cucurbitaceae family that is rich in bioactive components.To enhance genetic research on chayote,we used Nanopore third-generation sequencing combined with Hi-C data to assemble a draft chayote genome.A chromosome-level assembly anchored on 14 chromosomes(N50 contig and scaffold sizes of 8.40 and 46.56 Mb,respectively)estimated the genome size as 606.42 Mb,which is large for the Cucurbitaceae,with 65.94%(401.08 Mb)ofthe genome comprising repetitive sequences;28,237 protein-coding genes were predicted.Comparative genome analysis indicated that chayote and snake gourd diverged from sponge gourd and that a whole-genome duplication(WGD)event occurred in chayote at 25±4 Mya.Transcriptional and metabolic analysis revealed genes involved in fruit texture,pigment,fl avor,fl avonoids,antioxidants,and plant hormones during chayote fruit development.The analysis of the genome,transcriptome,and metabolome provides insights into chayote evolution and lays the groundwork for future research on fruit and tuber development and genetic improvements in chayote.

Regulations of m^(6)A methylation on tomato fruit chilling injury

Tomato fruit are sensitive to chilling injury(CI)during cold storage.Several factors have been discovered to be involved in chilling injury of tomato fruit.Plant hormones play an important regulatory role,however,the relationship between chilling injury and N6-methyladenosine(m^(6)A)methylation of transcripts in plant hormone pathways has not been reported yet.In order to clarify the complex regulatory mechanism of m^(6)A methylation on chilling injury in tomato fruit,Nanopore direct RNA sequencing was employed.A large number of enzymes and transcription factors were found to be involved in the regulation process of fruit chilling injury,which were associated with plant hormone,such as 1-aminocyclopropane 1-carboxylate synthase(ACS),aspartate aminotransferase(AST),auxin response factor(ARF2),ethylene response factor 2(ERF2),gibberellin 20-oxidase-3(GA20ox)and jasmonic acid(JA).By conjoint analysis of the differential expression transcripts related to chilling injury andm^(6)Amethylation differential expression transcripts 41 differential expression transcripts were identified involved in chilling injury including 1-aminocyclopropane-1-carboxylate oxidase(ACO)and pectinesterase(PE)were down-regulated and heat shock cognate 70 kD protein 2(cpHSC70),HSP70-binding protein(HspBP)and salicylic acid-binding protein 2(SABP2)were up-regulated.Our results will provide a deeper understanding for chilling injury regulatory mechanism and post-harvest cold storage of tomato fruit.

The genome and transcriptome analysis of snake gourd provide insights into its evolution and fruit development and ripening

Snake gourd(Trichosanthes anguina L.),which belongs to the Cucurbitaceae family,is a popular ornamental and food crop species with medicinal value and is grown in many parts of the world.Although progress has been made in its genetic improvement,the organization,composition,and evolution of the snake gourd genome remain largely unknown.Here,we report a high-quality genome assembly for snake gourd,comprising 202 contigs,with a total size of 919.8 Mb and an N50 size of 20.1 Mb.These findings indicate that snake gourd has one of the largest genomes of Cucurbitaceae species sequenced to date.The snake gourd genome assembly harbors 22,874 protein-coding genes and 80.0%of the genome consists of repetitive sequences.Phylogenetic analysis reveals that snake gourd is closely related to sponge gourd but diverged from their common ancestor~33–47 million years ago.The genome sequence reported here serves as a valuable resource for snake gourd genetic research and comparative genomic studies in Cucurbitaceae and other plant species.In addition,fruit transcriptome analysis reveals the candidate genes related to quality traits during snake gourd fruit development and provides a basis for future research on snake gourd fruit development and ripening at the transcript level.

Novel Tuning Buttons in Tomato Fruit Ripening:miRNAs and siRNAs

Tomato has emerged as an emblematic model plants for fleshy fruit research and tomato fruit ripening is a complex and highly coordinated developmental process.The many physiology and biochemical processes associated with tomato fruit ripening require changes in the expression of hundreds to thousands of genes.Gene expression is regulated by transcriptional and post-transcriptional pathways,one of the recently discovered mechanisms in plants was small RNAs mediated gene silencing at post-transcriptional(PTGS) level.Intriguingly,several mi RNAs and endogenous si RNAs were revealed to be involved in the fruit ripening process which opened a new avenue in the field of fleshy fruit biology.This review compiled the most recent advances made in deciphering the regulation functions of mi RNAs and si RNAs in tomato fruit ripening.It also emphasized the new perspectives now possible in the small RNAs regulation research in tomato fruit ripening and senescence.