Comparative transcriptome analysis uncovers the regulatory functions of long noncoding RNAs in fruit development and color changes of Fragaria pentaphylla

To investigate the molecular mechanism underlying fruit development and color change,comparative transcriptome analysis was employed to generate transcriptome profiles of two typical wild varieties of Fragaria pentaphylla at three fruit developmental stages(green fruit stage,turning stage,and ripe fruit stage).We identified 25,699 long noncoding RNAs(lncRNAs)derived from 25,107 loci in the F.pentaphylla fruit transcriptome,which showed distinct stage-and genotype-specific expression patterns.Time course analysis detected a large number of differentially expressed protein-coding genes and lncRNAs associated with fruit development and ripening in both of the F.pentaphylla varieties.The target genes downregulated in the late stages were enriched in terms of photosynthesis and cell wall organization or biogenesis,suggesting that lncRNAs may act as negative regulators to suppress photosynthesis and cell wall organization or biogenesis during fruit development and ripening of F.pentaphylla.Pairwise comparisons of two varieties at three developmental stages identified 365 differentially expressed lncRNAs in total.Functional annotation of target genes suggested that lncRNAs in F.pentaphylla may play roles in fruit color formation by regulating the expression of structural genes or regulatory factors.Construction of the regulatory network further revealed that the low expression of Fra a and CHS may be the main cause of colorless fruit in F.pentaphylla.

Comparative metabolomics provides novel insights into the basis of petiole color differences in celery(Apium graveolens L.)

Plant metabolites are important for plant development and human health.Plants of celery(Apium graveolens L.)with different-colored petioles have been formed in the course of long-term evolution.However,the composition,content distribution,and mechanisms of accumulation of metabolites in different-colored petioles remain elusive.Using ultra-high performance liquid chromatography-tandem mass spectrometry(UHPLC-MS/MS),1159 metabolites,including 100 lipids,72 organic acids and derivatives,83 phenylpropanoids and polyketides,and several alkaloids and terpenoids,were quantified in four celery cultivars,each with a different petiole color.There were significant differences in the types and contents of metabolites in celery with different-colored petioles,with the most striking difference between green celery and purple celery,followed by white celery and green celery.Annotated analysis of metabolic pathways showed that the metabolites of the different-colored petioles were significantly enriched in biosynthetic pathways such as anthocyanin,flavonoid,and chlorophyll pathways,suggesting that these metabolic pathways may play a key role in determining petiole color in celery.The content of chlorophyll in green celery was significantly higher than that in other celery cultivars,yellow celery was rich in carotenoids,and the content of anthocyanin in purple celery was significantly higher than that in the other celery cultivars.The color of the celery petioles was significantly correlated with the content of related metabolites.Among the four celery cultivars,the metabolites of the anthocyanin biosynthesis pathway were enriched in purple celery.The results of quantitative real-time polymerase chain reaction(q RT-PCR)suggested that the differential expression of the chalcone synthase(CHS)gene in the anthocyanin biosynthesis pathway might affect the biosynthesis of anthocyanin in celery.In addition,HPLC analysis revealed that cyanidin is the main pigment in purple celery.This study explored the differences in the types and contents of metabolites in celery cultivars with different-colored petioles and identified key substances for color formation.The results provide a theoretical basis and technical support for genetic improvement of celery petiole color.