‘Vanilla’ (XQC, brassica variety chinensis) is an important vegetable crop in the Brassica family, named for its strong volatile fragrance. In this study, we report the high-quality chromosome-level genome sequence of XQC. The assembled genome length was determined as 466.11 Mb, with an N50 scaffold of 46.20 Mb. A total of 59.50% repetitive sequences were detected in the XQC genome, including 47 570 genes. Among all examined Brassicaceae species, XQC had the closest relationship with B. rapa QGC (‘QingGengCai’) and B. rapa Pakchoi. Two whole-genome duplication (WGD) events and one recent whole-genome triplication (WGT) event occurred in the XQC genome in addition to an ancient WGT event. The recent WGT was observed to occur during 21.59–24.40 Mya (after evolution rate corrections). Our findings indicate that XQC experienced gene losses and chromosome rearrangements during the genome evolution of XQC. The results of the integrated genomic and transcriptomic analyses revealed critical genes involved in the terpenoid biosynthesis pathway and terpene synthase (TPS) family genes. In summary, we determined a chromosome-level genome of B. rapa XQC and identified the key candidate genes involved in volatile fragrance synthesis. This work can act as a basis for the comparative and functional genomic analysis and molecular breeding of B. rapa in the future.

Background: Fruit expansion stage is crucial to fruit yield and quality formation, and auxin plays a significant role by mediating multi-hormone signals during fruit expansion. However, till now, it is still unclear of the molecular regulatory network during auxin-mediated peach fruit expansion. Results: Here, exogenous NAA application markedly increased IAA content and drastically decreased ABA content at the fruit expansion stage. Correspondingly, NAA mainly induced the auxin biosynthesis gene (1 PpYUCCA) and early auxin-responsive genes (7PpIAA, 3 PpGH3, and 14 PpSAUR); while NAA down-regulated ABA biosynthesis genes (2 PpNCED, 1 PpABA3, and 1 PpAAO3). In addition, many DEGs involved in other plant hormone biosynthesis and signal transduction were significantly enriched after NAA treatment, including 7 JA, 7 CTK, 6 ETH, and 3 GA. Furthermore, we also found that NAA treatment down-regulated most of genes involved in the growth and development of peach fruit, including the cell wall metabolism-related genes (PpEG), sucrose metabolism-related genes (PpSPS), phenylalanine metabolism-related genes (PpPAL, Pp4CL, and PpHCT), and transcription factors (PpNAC, PpMADS-box, PpDof, PpSBP, and PpHB). Conclusion: Overall, NAA treatment at the fruit expansion stage could inhibit some metabolism processes involved in the related genes in the growth and development of peach fruit by regulating multiple-hormone signaling networks. These results help reveal the short-term regulatory mechanism of auxin at the fruit expansion stage and provide new insights into the multi-hormone cascade regulatory network of fruit growth and development.

Peach (Prunus persica L.) is a key drupe fruit crop characterized by a double-sigmoid growth pattern during fruit development. MicroRNAs (miRNAs) play pivotal regulatory roles in this process; however, their functions in early peach fruit development remain poorly understood. To address this, we conducted high-throughput small RNA (sRNA) sequencing at three critical developmental stages: 20, 50, and 75 d post-anthesis (DPA20, DPA50, DPA75), representing exponential growth, lag phase, and rapid regrowth, respectively. We identified 124 known miRNAs from 70 families and 86 novel miRNAs, with 97 and 79 miRNAs differentially expressed between DPA50 vs DPA20 and DPA75 vs DPA50, respectively. Degradome sequencing revealed 216 target genes for 74 known and eight novel miRNAs, with targets of ppe-miR160a and ppe-miR393b validated using RNA ligase-mediated rapid amplification of 5' cDNA ends (RLM-5'RACE). Quantitative reverse transcriptase polymerase chain reaction (qRT-PCR) confirmed the expression patterns of five miRNAs and their target genes, consistent with sequencing data. Network analysis revealed the involvement of the auxin signaling pathway and a complex miRNA regulatory network in fruit enlargement. Key miRNA-target interactions, such as ppe-miR160a-ARFs, ppe-miR172a/c/d-AP2s, ppe-miR166a -ATHBs, and ppe-miR319c/e-TCPs were implicated in cell proliferation and differentiation, with novel findings including ppe-miR171b/f/h-SCL6s in cell division. In summary, peach miRNAs primarily regulate early fruit growth and development by modulating auxin signaling and mediating cell division and differentiation. These findings provide critical insights into miRNA-mediated mechanisms underlying peach fruit development and establish a foundation for future research on drupe fruit crops.

Ethylene is one crucial phytohormone modulating plants’ organ development and ripening process, especially in fruits, but its action modes and discrepancies in non-climacteric grape and climacteric peach in these processes remain elusive. This work is focused on the action mode divergences of ethylene during the modulation of the organ development and ripening process in climacteric/non-climacteric plants. We characterized the key enzyme genes in the ethylene synthesis pathway, VvACO1 and PpACO1, and uncovered that their sequence structures are highly conserved, although their promoters exhibit important divergences in the numbers and types of the cis-elements responsive to hormones, implying various responses to hormone signals. Subsequently, we found the two have similar expression modes in vegetative organ development but inverse patterns in reproductive ones, especially in fruits. Then, VvACO1 and PpACO1 were further validated in promoting fruit ripening functions through their transient over-expression/RNAi-expression in tomatoes, of which the former possesses a weaker role than the latter in the fruit ripening process. Our findings illuminated the divergence in the action patterns and function traits of the key VvACO1/PpACO1 genes in the tissue development of climacteric/non-climacteric plants, and they have implications for further gaining insight into the interaction mechanism of ethylene signaling during the modulation of the organ development and ripening process in climacteric/non-climacteric plants.