Olive (Olea europaea L.) is internationally renowned for its high-end product, extra virgin olive oil. An incomplete genome of O. europaea was previously obtained using shotgun sequencing in 2016. To further explore the genetic and breeding utilization of olive, an updated draft genome of olive was obtained using Oxford Nanopore third-generation sequencing and Hi-C technology. Seven different assembly strategies were used to assemble the final genome of 1.30 Gb, with contig and scaffold N50 sizes of 4.67 Mb and 42.60 Mb, respectively. This greatly increased the quality of the olive genome. We assembled 1.1 Gb of sequences of the total olive genome to 23 pseudochromosomes by Hi-C, and 53,518 protein-coding genes were predicted in the current assembly. Comparative genomics analyses, including gene family expansion and contraction, whole-genome replication, phylogenetic analysis, and positive selection, were performed. Based on the obtained high-quality olive genome, a total of nine gene families with 202 genes were identified in the oleuropein biosynthesis pathway, which is twice the number of genes identified from the previous data. This new accession of the olive genome is of sufficient quality for genome-wide studies on gene function in olive and has provided a foundation for the molecular breeding of olive species.

Polyploids generally show vegetative growth superiority, higher biological yield, and enhanced resistance compared with diploids, which is already an important strategy in plant breeding; however, the mechanism by which these polyploid characteristics are formed remains unclear. Here, we developed a poplar polyploidy system to compare the phenotype and gene expression differences among newly synthesized Populus allotriploids and allotetraploids and their full-sib diploids. Analysis of gene expression revealed 156 genes that were significantly differentially expressed between diploids and triploids, among which 87 and 69 were up- and downregulated, respectively. Meanwhile, 384 genes were differentially expressed between diploids and tetraploids, and there were 259 upregulated and 125 downregulated genes, respectively. Polyploids showed a bigger stomatal, and stomatal length and width increased with ploidy level, whereas relative stomatal density decreased, which may mainly attribute to the differently expression of mitogen-activated protein kinase gene, YODA, and five plant hormone-related genes (SAUR, MES17, IAR3, BAS1, ABCG25). Plant height, leaf area, and petiole length were also observed to be significantly superior in polyploids than diploids, and E3 ligase BIG BROTHER (BB) and growth-regulating factor (GRF10) were selected as candidate genes responsible for variations in organ size and leaf growth. These results provided a robust resource for investigating the function of genes associated with polyploid genotype differences. Meanwhile, our study suggests that the poplar polyploidy system with clear and complete genetic backgrounds may be used as a good model for studies in polyploidization advantage.

Olea europaea L. is an important oil crop with excellent nutritional properties. In this study, a full-length transcriptome combined with fatty acid composition was used to investigate the molecular mechanism of fatty acid (FA) metabolism of olive fruits at various stages of development (S1–S5). A total of 34 fatty acids (FAs) were measured using gas chromatography-mass spectrometry (GC-MS). All transcripts of FA metabolism during olive fruit development were studied, including glycolysis, fatty acid synthesis, triacylglycerol synthesis, and FA degradation. A total of 100 transcripts of 11 gene families, 68 transcripts of 12 gene families, 55 transcripts of 7 gene families, and 28 transcripts of 7 gene families were identified as encoding for enzymes involved in FA metabolism. Furthermore, one of the critical reactions in TAG metabolism is the activation of fatty acyl chains to fatty acyl CoA, which is catalyzed by long-chain acyl CoA synthetases (LACS). Phylogenetic analysis showed that 13 putative LACS-encoding genes clustered into five groups, of which two putative transcripts encoding LACS6/7 may participate in FA degradation. The aim of this study was to evaluate the fatty acid from synthesis to degradation pathways during olive fruit development to provide a better understanding of the molecular mechanism of FA metabolism during olive fruit maturation and provide information to improve the synthesis of oil components that are beneficial to human health.

Browning of olive (Olea europaea L.) fruit reduces the sensory and nutritional qualities of olive oil, thereby increasing production costs. Polyphenol oxidases (PPOs) are the key enzymes that catalyze phenolic substance oxidation and mediate enzymatic browning in olive fruit, but the exact regulatory mechanism remains unclear. The main challenge is the lack of comprehensive information on OePPOs at the genome-wide level. In this study, 18 OePPO genes were identified. Subsequently, we performed a bioinformatic analysis on them. We also analyzed the expression patterns and determined the relationship among browning degree, PPO activity, and expression of OePPOs in the fruits of three olive varieties. Based on our analysis, we identified the four most conserved motifs. OePPOs were classified into two groups, with OePPOs from Group 1 showing only diphenolase activity and OePPOs from Group 2 exhibiting both mono-/diphenolase activities. Seven pairs of gene duplication events were identified, and purifying selection was found to have played a critical role in the evolution of the OePPO gene family. A positive correlation was observed between the browning degree of olive fruit and PPO activity across different olive varieties. Moreover, two important genes were found: OePPO-5 the main effector gene responsible for fruit browning, and OePPO-8, a key gene associated with specialized metabolite synthesis in the olive fruit. In short, our discoveries provide a basis for additional functional studies on OePPO genes and can help elucidate the mechanism of enzymatic browning in olive fruit in the future.

Olive oil has been favored as high-quality edible oil because it contains balanced fatty acids (FAs) and high levels of minor components. The contents of FAs and minor components are variable in olive fruits of different color at harvest time, which render it difficult to determine the optimal harvest strategy for olive oil producing. Here, we combined metabolome, Pacbio Iso-seq, and Illumina RNA-seq transcriptome to investigate the association between metabolites and gene expression of olive fruits at harvest time. A total of 34 FAs, 12 minor components, and 181 other metabolites (including organic acids, polyols, amino acids, and sugars) were identified in this study. Moreover, we proposed optimal olive harvesting strategy models based on different production purposes. In addition, we used the combined Pacbio Iso-seq and Illumina RNA-seq gene expression data to identify genes related to the biosynthetic pathways of hydroxytyrosol and oleuropein. These data lay the foundation for future investigations of olive fruit metabolism and gene expression patterns, and provide a method to obtain olive harvesting strategies for different production purposes.