Integrative analysis of the transcriptome and metabolome reveals the response mechanism to tomato spotted wilt virus

Tomato spotted wilt virus(TSWV)is an important virus that has rapidly spread throughout the world.TSWV seriously hinders the production of tomato(Solanum lycopersicum)and other plants.In order to discover more new genes and metabolites related to TSWV resistance in tomato plants,the genes and metabolites related to the resistance of tomato plants inoculated with TSWV were identified and studied herein.The tomato TSWV-resistance line YNAU335(335)and TSWV-susceptible lines NO5 and 96172I(961)were used as the transcriptome and metabolome research materials.Transcriptomic and metabolomic techniques were used to analyze the gene and metabolite response mechanisms to TSWV inoculation.A total of 3566,2951,and 2674 differentially expressed genes(DEGs)were identified in lines 335,NO5,and961,respectively.Meanwhile,208,228,and 273 differentially accumulated metabolites(DAMs)were identified in lines 335,NO5,and 961,respectively.In line 335,the number of DEGs was the highest,but the number of DAMs was lowest.Furthermore,903 DEGs and 94 DAMs were common to the response to TSWV in the three inbred lines.The 903 DEGs and 94 DAMs were mainly enriched in the plant hormone signal transduction and flavonoid synthesis pathways.In addition,many nucleotide-binding site-leucine-rich repeat genes and transcription factors were found that might be involved in the TSWV response.These results provide new insights into TSWV resistance mechanisms.

Transcriptome Analysis of Molecular Mechanisms Underlying Phenotypic Variation in Phaseolus vulgaris Mutant‘nts’

The phenotype of a common bean plant is often closely related to its yield,and the yield of plants with reduced height or poor stem development during growth is low.Mutants serve as an essential gene resource for common bean breeding genetic research.Although model plants and crops are studied to comprehend the molecular mechanisms and genetic basis of plant phenotypes,the molecular mechanism of phenotypic variation in common beans remains underexplored.We here used the mutant‘nts’as material for transcriptome sequencing analysis.This mutant was obtained through 60Co-γirradiation from the common bean variety‘A18’.Differentially expressed genes were mainly enriched in GO functional entries such as cell wall organization,auxin response and transcription factor activity.Metabolic pathways significantly enriched in KEGG analysis included plant hormone signal transduction pathways,phenylpropanoid biosynthesis pathways,and fructose and mannose metabolic pathways.AUX1(Phvul.001G241500),the gene responsible for auxin transport,may be the key gene for auxin content inhibition.In the plant hormone signal transduction pathway,AUX1 expression was downregulated and auxin transport across the membrane was blocked,resulting in stunted growth of the mutant‘nts’.The results provide important clues for revealing the molecular mechanism of‘nts’phenotype regulation in bean mutants and offer basic materials for breeding beneficial phenotypes of bean varieties.

Transcriptome Profiling Reveals Candidate Genes Involved in Stem Swelling of Tumorous Stem Mustard

Tumorous stem mustard is well known for its swollen stem from which pickled“Fuling Mustard”is made.The molecular mechanisms governing the formation of the modified swollen stems are still poorly understood.This paper aims to identify candidate genes involved in the developmental regulation of the swollen stems.We sought to map previously published transcriptome datasets for Brassica juncea,including those derived from swollen stems at four different developmental stages and a mutant variety without swollen stems.Using pairwise comparisons of the five datasets,we identified 31368 differentially expressed genes(DEGs).A total of 55 DEGs related to plant hormone signal transduction and 259 continuously up-or downregulated transcription factors were identified during stem development using Gene Ontology(GO)analysis.Quantitative real-time PCR(qRT-PCR)results showed that the expressions of 12 important candidate DEGs were consistent with RNA-seq results.Our study provided digital gene expression profiling and a dynamic view of the swollen stem development process.Furthermore,we identified candidate genes for further studies on mechanisms of modified stem development in non-model species.