Table 1.
Summery of the transcriptome sequencing of ‘Jincheng’ (WT) and its mutant (MT).
Table 2.
Candidate gene list and their primers for quantitative real time-PCR.
Figure 1.
Changes in the peel color of the wild type of ‘Jincheng’ sweet orange (WT) and its mutant (MT) fruit during fruit development and ripening.
The data represent the mean values with twenty-four replicates. The asterisks indicate values that were determined by Student's t test to be different (P<0.05) between the two samples. Double asterisks indicate significant differences (P<0.01). DAA, days after anthesis; the upper fruits were WT; the lower fruits were MT.
Figure 2.
Changes in the soluble sugar and acid contents of the fruit flesh of the wild type of ‘Jincheng’ sweet orange (WT) and its mutant (MT) during fruit development and ripening.
The data represent the mean values with at least three replicates. The asterisks indicate values that were determined by Student's t test to be different (P<0.05) between the two samples. Double asterisks indicate significant differences (P<0.01).
Figure 3.
Histogram presentation of clusters of orthologous groups (COG) classification.
Out of 44,413 unigenes, 9386 sequences have a COG classification among the 25 categories. A. RNA processing and modification; B. Chromatin structure and dynamics; C. Energy production and conversion; D. Cell cycle control, cell division, chromosome partitioning; E Amino acid transport and metabolism; F. Nucleotide transport and metabolism; G. Carbohydrate transport and metabolism; H. Coenzyme transport and metabolism; I. Lipid transport and metabolism; J. Translation, ribosomal structure and biogenesis; K. Transcription; L. Replication, recombination and repair; M. Cell wall/membrane/envelope biogenesis; N. Cell motility; O. Posttranslational modification, protein turnover, chaperones; P. Inorganic ion transport and metabolism; Q. Secondary metabolites biosynthesis, transport and catabolism; R. General function prediction only; S. Function unknown; T. Signal transduction mechanisms; U. Intracellular trafficking, secretion, and vesicular transport; V. Defense mechanisms; W. Extracellular structures; Y. Nuclear structure; Z. Cytoskeleton.
Figure 4.
The distribution of MT-vs-WT DEGs.
There were nearly three times more down-regulated genes than up-regulated genes. WT. the wild type of ‘Jincheng’ sweet orange; MT. the late-ripening mutant of ‘Jincheng’ sweet orange.
Figure 5.
The classification of all DEGs with annotations from at least three databases: (a) the annotation according to the Nr, COG, GO and KEGG databases; (b) the distribution of up (in white) and down-regulated (in black) unigenes in the wild type of ‘Jincheng’ sweet orange for each cluster.
Cluster A. RNA processing and modification; B. Chromatin structure and dynamics; C. Energy production and conversion; D. Cell cycle control, cell division, chromosome partitioning; E. Amino acid transport and metabolism; F. Nucleotide transport and metabolism; G. Carbohydrate transport and metabolism; H. Coenzyme transport and metabolism; I. Lipid transport and metabolism; J. Translation, ribosomal structure and biogenesis; K. Transcription; L. Replication, recombination and repair; M. Cell wall/membrane/envelope biogenesis; N. Cell motility; O. Posttranslational modification, protein turnover, chaperones; P. Inorganic ion transport and metabolism; Q. Secondary metabolites biosynthesis, transport and catabolism; R. General function prediction only; S. Function unknown; T. Signal transduction mechanisms; U. Intracellular trafficking, secretion, and vesicular transport; V. Defense mechanisms; Z. Cytoskeleton.
Figure 6.
Comparison of gene expression ratios that were obtained by RNA-seq and by quantitative real-time PCR (qRT-PCR): (a) the comparison of the gene expression value gained by RNA-seq and by qRT-PCR; (b) the liner regression analysis between the gene expression ratios obtained by RNA-seq and by qRT-PCR.
The black bars represent RNA-seq data, and the white bars represent the qRT-PCR data. The RNA-seq data were first restituted to 2×. The linear regression [(RNA-seq value) = a (RT-PCR value) + b] analysis indicated a positive relationship between them.
Figure 7.
Transcript levels of the genes in the ABA metabolism and signal transduction pathways in the wild type of ‘Jincheng’ sweet orange (WT) and its late ripening mutant (MT) during fruit development and ripening.
Actin was used as the internal control. The error bars represent SE (n = 3). NCED, 9-cis-epoxycarotenoid dioxygenase; AAO, ABA-aldehyde oxidase; ABA8ox1, ABA 8′-hydroxylase 1; ABA8ox3, ABA 8′-hydroxylase 3; AHG1, ABA-Hypersensitive germination1; AHG3, ABA-Hypersensitive germination3; ABI1, ABA insensitive 1; HAB1, Hypersensitive to ABA1; HAB2, Hypersensitive to ABA2; HAI1, Highly ABA-Induced1; PYL2, 4, 8, 9, PYR1-like proteins; PYR1, Pyrabactin resistance 1; SnRK2, Suc non-fermenting-related kinase group 2.
Figure 8.
Summary of the possible relationship of all the candidate genes in the fruit ripening regulatory mechanism.
The heat maps showed the expression level of the genes nearby. SPS, sucrose-phosphate synthase; SUS, sucrose synthase; SUC, sucrose transporter; PME, pectinesterase; PSY, phytoene synthase; ZDS, zeta-carotene desaturase; MLS, malate synthase; βLCY, lycopene β-cyclase; ZEP, zeaxanthin epoxidase; NSY, neoxanthin synthase; NCED, nine-cis-epoxycarotenoid dioxygenase; AAO, abscisic-aldehyde oxidase; ABA8ox, abscisic acid 8′-hydroxylase; AHG, ABA-Hypersensitive germination; HAB, Hypersensitive to ABA1; ABI1, ABA insensitive 1; HAI1, Highly ABA-Induced1; PYR1, Pyrabactin resistance 1; PYL, PYR1-like protein; SnRK2.2, Suc nonfermenting-related kinase group 2; ABFs, Abscisic acid response element Binding Factors; LOX, lipoxygenase; AOS, allene oxide synthase; JMT, jasmonate O-methyltransferase; COI1, coronatine insensitive 1; JAZ, Jasmonate-ZIM-domain protein.
Figure 9.
Transcript levels of the PSY gene, and the genes in the sucrose and jasmonic acid metabolism and signal transduction pathways in the wild type of ‘Jincheng’ sweet orange (WT) and its late ripening mutant (MT) during fruit development and ripening.
Actin was used as the internal control. The error bars represent SE (n = 3). PSY, Phytoene synthase; SPS, Sucrose phosphate synthase; SUS, Sucrose synthase; SUC1, 3, 4, Sucrose transporters ; LOX, Lipoxygenase; AOS, Allene oxide synthase; JMT, Jasmonate O-methyltransferase; COI1, coronatine insensitive 1; JAZ, Jasmonate-ZIM-domain protein.