RNA-Seq profiling reveals the plant hormones and molecular mechanisms stimulating the early ripening in apple.

Fruit development and ripening are essential components of human and animal diets. Fruit ripening is also a vital plant trait for plant shelf life at the commercial level. In the present study, two apple cultivars, Hanfu wild (HC) and Hanfu mutant (HM), were employed for RNA-Sequencing (RNA-Seq) to explore the genes involved in fruit ripening. We retrieved 2642 genes, differentially expressed in HC and HM apple cultivars. Gene ontology (GO) analysis revealed the 569 categories, significantly enriched in biological process, cellular component, and molecular function. KEGG analysis exhibited the plant hormone transduction and flavonoid-anthocyanin biosynthesis pathways, might be involved in the fruit ripening and anthocyanin biosynthesis mechanism. A cluster of 13 and 26 DEGs was retrieved, representing the plant hormones and transcription factors, respectively, that may be important for early ripening in HM genotype. This transcriptome study would be useful for researchers to functionally characterize the DEGs responsible for early ripening.

A high-quality apple genome assembly reveals the association of a retrotransposon and red fruit colour.

A complete and accurate genome sequence provides a fundamental tool for functional genomics and DNA-informed breeding. Here, we assemble a high-quality genome (contig N50 of 6.99 Mb) of the apple anther-derived homozygous line HFTH1, including 22 telomere sequences, using a combination of PacBio single-molecule real-time (SMRT) sequencing, chromosome conformation capture (Hi-C) sequencing, and optical mapping. In comparison to the Golden Delicious reference genome, we identify 18,047 deletions, 12,101 insertions and 14 large inversions. We reveal that these extensive genomic variations are largely attributable to activity of transposable elements. Interestingly, we find that a long terminal repeat (LTR) retrotransposon insertion upstream of MdMYB1, a core transcriptional activator of anthocyanin biosynthesis, is associated with red-skinned phenotype. This finding provides insights into the molecular mechanisms underlying red fruit coloration, and highlights the utility of this high-quality genome assembly in deciphering agriculturally important trait in apple.