Pitaya (Hylocereus polyrhizus) has attracted much interest from consumers as it is a novelty fruit with high nutrient content and a tolerance to drought stress. As a group of attractive pigment- and health-promoting natural compounds, betalains represent a visual feature for pitaya fruit quality. However, little information on the correlation between betalains and relevant metabolites exists so far. Currently, color (Commission International del’Eclairage, CIE) parameters, betalain contents, and untargeted metabolic profiling (gas chromatography-time-of-flight-mass spectrometry, GC–MS and liquid chromatography tandem mass spectrometry, LC–MS) have been examined on ‘Zihonglong’ fruits at nine different developmental stages, and the variation character of the metabolite contents was simultaneously investigated between peel and pulp. Furthermore, principal component analysis (PCA) and partial least-squares discriminant analysis (PLS-DA) were used to explore metabolite profiles from the fruit samples. Our results demonstrated that the decrease of amino acid, accompanied by the increase of sugars and organic acid, might contribute to the formation of betalains. Notably, as one of four potential biomarker metabolites, citramalic acid might be related to betalain formation.

To gain more valuable genomic information about betalain biosynthesis, the full-length transcriptome of pitaya pulp from ‘Zihonglong’ (red pulp) and ‘Jinghonglong’ (white pulp) in four fruit developmental stages was analyzed using Single-Molecule Real-Time (SMRT) sequencing corrected by Illumina RNA-sequence (Illumina RNA-Seq). A total of 65,317 and 91,638 genes were identified in ‘Zihonglong’ and ‘Jinghonglong’, respectively. A total of 11,377 and 15,551 genes with more than two isoforms were investigated from ‘Zihonglong’ and ‘Jinghonglong’, respectively. In total, 156,955 genes were acquired after elimination of redundancy, of which, 120,604 genes (79.63%) were annotated, and 30,875 (20.37%) sequences without hits to reference database were probably novel genes in pitaya. A total of 31,169 and 53,024 simple sequence repeats (SSRs) were uncovered from the genes of ‘Zihonglong’ and ‘Jinghonglong’, and 11,650 long non-coding RNAs (lncRNAs) in ‘Zihonglong’ and 11,113 lncRNAs in ‘Jinghonglong’ were obtained herein. qRT-PCR was conducted on ten candidate genes, the expression level of six novel genes were consistent with the Fragments Per Kilobase of transcript per Million mapped reads (FPKM) values. In conclusion, we firstly undertook SMRT sequencing of the full-length transcriptome of pitaya, and the valuable resource that was acquired through this sequencing facilitated the identification of additional betalain-related genes. Notably, a list of novel putative genes related to the synthesis of betalain in pitaya fruits was assembled. This may provide new insights into betalain synthesis in pitaya.

Phosphorus (Pi) is a macronutrient essential for plant growth, development, and reproduction. However, there is not an efficient available amount of Pi that can be absorbed by plants in the soil. Previously, an elite line, MSDZ 109, selected from Malus mandshurica, was justified for its excellent tolerance to low phosphorus (low−Pi) stress. To date, however, the genes involved in low−Pi stress tolerance have not yet been unraveled in this species. Currently, the physiological responses of this line for different days to low−Pi stress were characterized, and their roots as well as leaves were used to carry out transcriptome analysis, so as to illuminate the potential molecular pathways and identify the genes involved in low−Pi stress−response. After exposure to low−Pi treatment (32 µmol/L KH₂PO₄) for 20 day after treatment (DAF) the biomass of shoots was significantly reduced in comparison with that of the stress−free (control), and root architecture diversely changed. For example, the root growth parameters e.g., length, surface area, and total volume somewhat increase in comparison with those of the control. The activity of acid phosphatase (ACP) increased with the low−Pi treatment, whereas the photosynthetic rate and biomass were declining. The activity of antioxidant enzymes, e.g., superoxide dismutase (SOD), peroxidase (POD), and catalase (CAT), were substantially elevated in response to low−Pi treatment. Many enzyme−related candidate genes e.g., MmCAT1, MmSOD1 and MmPOD21 were up−regulated to low−Pi treatment. Furthermore, Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis indicated that the processes of photosynthesis, plant hormone signal transduction, and MAPK signaling pathway were affected in the low−Pi response. In combination with the physiological characterization, several low−Pi−responsive genes, e.g., PHT, PHO, were identified, and the genes implicated in Pi uptake and transport, such as MmPHT1;5, MmPHO1, MmPAP1, etc., were also obtained since their expression status varied among the exposure times, which probably notifies the candidates involved in low−Pi−responsive tolerance in this line. Interestingly, low−Pi treatment activated the expression of transcription factors including the WRKY family, MYB family, etc. The available evidences will facilitate a better understanding of the roles of this line underlying the high tolerance to low−Pi stress. Additionally, the accessible data are helpful for the use of the apple rootstock M. mandshurica under low−Pi stress.