Abstract
Cracks in the skin of jujube fruit reduce freshness and quality; thus,
greater understanding of the molecular mechanism that underlies
cracking is required to improve fruit production. In this study, we
profiled genes that are differentially expressed between cracked and
normal jujube fruits through RNA sequencing (RNA‐seq). We selectively
confirmed differentially expressed genes (DEGs) using quantitative
RT‐PCR. Among 1036 DEGs, 785 genes were up‐regulated and 251 genes were
down‐regulated in cracked jujube fruits. Gene Ontology and Kyoto
Encyclopedia of Genes and Genomes pathway analysis indicated that some
of these DEGs encode proteins involved in metabolic processes
(including growth hormone and surface wax production) in cracked jujube
fruits. In summary, we have identified differentially expressed
metabolic genes between cracked and normal jujube fruits, which may
serve as the basis for further studies of fruit quality control.
__________________________________________________________________
Abbreviations
AOC
allene oxide cyclase
AOS
allene oxide synthase
DEG
differentially expressed gene
ECR
trans‐2,3‐enoyl‐CoA reductase
GO
Gene Ontology
HCD
3‐hydroxyacyl‐CoA dehydratase
JA
jasmonic acid
KCR
3‐ketoacyl‐CoA reductase
KCS
3‐ketoacyl‐CoA synthase
KEGG
Kyoto Encyclopedia of Genes and Genomes
LOX
lipoxygenase
OPR3
12‐oxophytodienoate reductase 3
qPCR
quantitative PCR
qRT‐PCR
quantitative RT‐PCR
RNA‐seq
RNA sequencing
VLCFA
very long‐chain fatty acid
Ziziphus jujuba Mill. is a deciduous tree plant of the Rhamnaceae
Ziziphus Mill. Jujube is native to China, with an extensive history of
cultivation dating back more than 7000 years. It is important to note
that jujube has high nutritional value, consisting of essential amino
acids, such as histamine and arginine [[32]1], as well as mineral
elements, including potassium (K), phosphorous (P), calcium (Ca) and
manganese (Mn) [[33]2, [34]3]. Because jujube is potentially linked to
anticancer and antiallergy effects [[35]4, [36]5], it has been
officially included as a Chinese herbal medicine in the Pharmacopoeia
of the People’s Republic of China (2015 edition) [[37]6, [38]7].
China is currently the world’s largest market for jujube production and
consumption [[39]8]. However, fruit cracking is a major problem in the
jujube industry. It is striking, for instance, that the annual loss of
jujube production due to cracking is usually around 30% and that it has
reached more than 90% in some years [[40]9]. Research regarding fruit
cracking has been primarily focused on three aspects: the change of
tissue structure during the development and cracking of jujube fruit
[[41]10, [42]11], the way in which water enters the fruit [[43]12,
[44]13] and the genetic characteristics that predispose certain fruit
to cracking [[45]14, [46]15, [47]16]. Other than these processes, key
molecular events that drive fruit cracking remain poorly studied. Fruit
cracking profoundly affects a wide range of fruits, such as Malm pumila
Mill., Pmnus salicina Lind., Pmnus persica L., Pyrus spp., Pmnus avium
L., Litchi chinensis Sonn. and Vitis vinifera L. As such, understanding
the mechanism of fruit cracking would lead to better control of fruit
quality overall.
With the development of new generation sequencing technology,
transcriptome sequencing has become highly used because of its simple
technique and rapid turnaround. Transcriptome sequencing can determine
altered gene expression in response to different conditions. It can
reveal the dynamics of gene networks and their respective functions, as
well as the steady‐state level of all expressed transcripts in each
particular state [[48]17]. In 2014, Liu et al. [[49]18] completed the
entire genome sequencing of winter jujube for the first time and
preliminarily revealed the molecular mechanism of drought resistance,
fruit branch detachment, and additional fruit properties through
comparative genome and transcriptome analysis. The aim of this study is
to profile differentially expressed genes (DEGs) in cracked and normal
jujube fruits.
Materials and methods
Test materials and sample processing
‘Huping’ jujube was used for this experiment. Healthy jujube plants
obtained from the resource garden of Shanxi Agricultural University
consisted of both normal and cracked fruit at their mature stage
(Fig. [50]1). Three biological replicates were used, and these were
quickly stored in liquid nitrogen before being transported to Beijing
Baimaiker technology Co., Ltd. (Beijing, China) for RNA extraction and
transcriptome sequencing analysis. Three samples of normal fruit were
numbered T01, T02 and T03; three samples of cracked fruit were numbered
C01, C02 and C03. All plant tissues were immediately frozen in liquid
nitrogen and stored at −80 °C for later research.
Fig. 1.
Fig. 1
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Samples of normal jujube versus cracked jujube fruits. Representative
images of normal (left panel: 30 mm) versus cracked (right panel:
40 mm) jujube fruits.
Extraction and library construction of total RNA
Total RNA was extracted from the normal and cracked jujube fruit using
the RNA extraction kit (Polysaccharides Pure Polyposis‐rich) from
Tiangen Biochemical Technology (Beijing) Co., Ltd. Capture beads for
mRNA were added to the total RNA samples. After two rounds of binding,
mRNA was eluted with Tris–HCl and incubated with the first strand
synthesis reaction buffer and random primers. These short sequences
were used as templates, consisting of six bases of random hexamers, to
synthesize the first cDNA strand. Next, the buffer, dNTPs, RNase H and
DNA polymerase I were added to synthesize the second strand of cDNA.
cDNA was purified by AMPure XP beads. End repair reaction buffer and
end repair enzyme mix were added to cDNA for end repair.
Polyadenylation was performed through addition of poly(A) tails. The
sequencing joints were subsequently connected, and USER enzyme was
added to open the linker. The reaction products were supplemented with
nuclease‐free water, reaching a volume of 50 μL. They were then
transferred to a 1.5‐mL centrifuge tube for fragment selection. PCR
amplification and product purification were performed, and finally, the
cDNA library was enriched by PCR amplification.
Transcriptome sequencing and comparison with reference genomes
The high‐throughput sequencing of the transcriptome was conducted by
Beijing Baimaiker technology Co., Ltd. The cDNA library was sequenced
on the Illumina X‐TEN PE150 (San Diego, CA, USA), thereby generating
the maximum 300‐bp pair‐end reads. Raw data in fastq format were first
processed through in‐house perl scripts to obtain clean data by
removing the adapter, ploy‐N and low‐quality sequences (Q < 20). At the
same time, Q20, Q30, GC content and the sequence duplication level of
the clean data were calculated. All of the downstream analyses were
based on clean data with high‐quality clean reads. The clean reads were
aligned with hisat2 ([52]http://ccb.jhu.edu/software/hisat2) with
default parameters to the Ziziphus jujuba (assembly ZizJuj_1.1)
[[53]18] on National Center for Biotechnology Information. Transcripts
were assembled and quantified with stringtie
([54]http://ccb.jhu.edu/software/stringtie).
Identification of DEGs
DEGs were identified and analyzed using the EBSeq platform. FPKM
(fragments per kilobase of exon per million reads mapped) was
calculated as follows:
[MATH:
FPKM=cDNAFragmentsMappedFragments(Millions)×TranscriptLength(kb). :MATH]
Genes were considered differentially expressed if |log2FoldChange| > 2
and an adjusted P value using Benjamini–Hochberg procedure (false
discovery rate) was <0.01 [[55]19].
Gene annotation and Kyoto Encyclopedia of Genes and Genomes functional
enrichment analysis
To analyze the functional annotation and pathway enrichment of DEGs, we
performed differential expression analysis based on the expression
levels of genes in different samples, according to the Gene Ontology
(GO) database ([56]http://www.geneontology.org/) and Kyoto Encyclopedia
of Genes and Genomes (KEGG; [57]http://www.genome.jp/kegg/).
Quantitative RT‐PCR verification of DEGs
Quantitative RT‐PCR (qRT‐qPCR) was used on nine DEGs with significantly
different expression. The fluorescent quantitative PCR (qPCR) primers
(Table [58]1) were designed using primer premier 5.0 (Primier company,
Toronto, Canada). The jujube endogenous gene GATA binding protein 6
(Gene ID: 29300) with highly stable expression was used for reference
[forward (F): 5′‐TGGCTGGAAGATGGAAGATG‐3′, reverse (R):
5′‐ATGAAGTCTATCCCCAATCGC‐3′]. The TransScript II All‐in‐One
First‐Strand cDNA Synthesis SuperMix for qPCR (One‐Step gDNA Removal)
reverse transcription kit was used for reverse transcription into cDNA.
The components and conditions for the reverse transcription reaction
system were as follows:
* Components: Total RNA, 1 μg; 5× TransScript II All‐in‐One SuperMix
for qPCR, 4 μL; gDNA Remover, 1 μL; RNase‐free water, up to 20 μL.
* Reverse transcription conditions: 55 °C for 30 min; 85 °C for 5 s;
addition of 80 μL RNase‐free water after the reaction to dilute the
cDNA.
Table 1.
Primers for qRT‐PCR verification of DEGs in jujube fruits.
Primer Primer sequence (5′–3′)
Ju‐10633‐F TTGGAATTGGAGGTCAGAAGG
Ju‐10633‐R CTAAGTGAACCTGCTCCCATC
Ju‐18952‐F ATTACTCTATCAAGGCGGTCAG
Ju‐18952‐R AAATCCACTTCCCGTCGTAC
Ju‐19193‐F ACAGAAACTTCAAGGCCAGTG
Ju‐19193‐R CTGCACCCATCTGAGTCTATTC
Ju‐2163‐F GCATCACAAAACCCACAATCC
Ju‐2163‐R AACCCATTACACAGCTCACC
Ju‐22913‐F TTCACCAATACCAGCACCAG
Ju‐22913‐R CAAATCCCAAGCTCAACAGTG
Ju‐244‐F AGGCAAGGGAAACAGAGAAC
Ju‐244‐R TCATTGGCTGGTTCTTTGGG
Ju‐246‐F TCTTCCACCTCCTCCACCAG
Ju‐246‐R TTAGGACATGCTGCATTCTG
Ju‐30106‐F AAGTGTTCCCAGTACGATGC
Ju‐30106‐R TCTAAAAGCCCAGCACGAC
Ju‐67‐F TTCCATTCCCAAAGAGCCAG
Ju‐67‐R GAGGACCAAACACAAGCATTG
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Two samples of normal fruit and cracked fruit were detected by
real‐time fluorescence qPCR, and the detection of each gene in each
sample was repeated three times. The qPCR system consisted of forward
primer (10 μm), 0.4 μL; reverse primer (10 μm), 0.4 μL; 2× TransStart
Top Green qPCR SuperMix, 10 μL; template (diluted cDNA), 2 μL; and
ddH[2]O to a final volume of 20 μL. The PCR conditions were as follows:
94 °C for 2 min, 94 °C for 5 s, 45 cycles of 60 °C for 15 s and 72 °C
for 10 s. For the dissociation stage, the
[MATH: 2‐ΔΔCT :MATH]
method was used to determine the relative expression of the sample to
be tested. Results are expressed as the mean ± standard deviation. The
experimental data were analyzed with the Student’s t‐test using spss
(V18.0) statistical software (IBM SPSS, Amonk, NY, USA).
Results
Transcriptomic analysis of jujube fruits
To identify molecular events possibly associated with fruit cracking,
we performed comparative transcriptome analysis on cracked and normal
jujube fruits (Fig. [60]1). cDNA libraries were generated and
subsequently sequenced using the Illumina X‐TEN platform. After quality
control, 51.81 Gb of clean data was obtained, yielding approximately
26 269 299–34 063 751 clean reads. In the jujube transcriptome, GC
content made up 45.52% (Table [61]2). A fold change of 2 (false
discovery rate < 0.01) was the cutoff for the detection of DEGs. Our
analysis collectively identified 1036 DEGs, including 785 up‐regulated
and 251 down‐regulated genes, that were differentially expressed
between cracked jujube fruits and normal jujube fruits (Fig. [62]2A).
Table 2.
Summary of transcript sequencing in jujube fruits.
Sample Total reads Mapped reads Clean reads Clean bases GC content ≥Q30
HJU‐1 68 127 502 61 129 374 (89.73%) 34 063 751 10 152 619 972 45.54%
94.31%
HJU‐2 48 760 590 43 728 773 (89.68%) 24 380 295 7 265 822 642 45.75%
94.86%
HJU‐3 56 606 168 50 524 460 (89.26%) 28 303 084 8 450 170 744 45.32%
93.91%
CJU‐1 52 538 598 46 863 458 (89.20%) 26 269 299 7 843 398 644 45.58%
94.54%
CJU‐2 59 440 920 53 399 582 (89.84%) 29 720 460 8 875 766 446 45.34%
94.89%
CJU‐3 61 755 972 55 589 982 (90.02%) 30 877 986 9 224 361 284 45.56%
94.75%
Mean 57 871 625 51 872 605 (89.62%) 28 935 813 8 635 356 622 45.52%
94.54%
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Fig. 2.
Fig. 2
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Identification of DEGs by RNA‐seq. (A) The volcano plot demonstrates
that genes are differentially expressed in cracked jujube fruits
compared with normal jujube fruits. Differential expression analysis
was performed using DESeq2 from three biological replicates (|Fold
change| > 2, adjusted P < 0.01). (B) qRT‐PCR analysis showed that
selected DEGs were significantly differentially expressed in cracked
jujube fruits compared with normal jujube fruits (n = 3 independent
biological repeats) (mean ± standard error of the mean; Student’s
t‐test).
To validate the RNA‐seq results, we used qRT‐PCR to assess DEGs. Eight
up‐regulated genes and one down‐regulated gene found in cracked fruits
were randomly selected. These DEGs were mainly involved in the
biosynthesis of pectin methylesterase, swollenin and Xyloglucan
endotransglucosylases (XET). The expression levels of these DEGs were
significantly different between cracked and normal fruits, which was
consistent with the results of transcriptome analysis (Fig. [65]2B).
GO annotation was performed to explore the possible functions of DEGs.
As shown in Fig. [66]3, DEGs were significantly assigned to the
metabolic process, cellular process and single‐organism process in the
biological process category. In the cell component category, DEGs were
significantly enriched in cell and cell parts, followed by organelles
and membranes. In the molecular function category, DEGs were mainly
assigned to catalytic activity and binding. Two to three times as many
genes that were up‐regulated than those that were down‐regulated were
associated with most categories, including metabolic process, cellular
process, single‐organism process, response to stimulus, biological
regulation, cell and cell parts, and nucleic acid binding transcription
factor activity (Fig. [67]3 and Table [68]S1).
Fig. 3.
Fig. 3
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Functional annotation of DEGs based on GO categories.
Classification analysis of KEGG metabolic pathways
To further examine genes possibly involved in fruit cracking, we
carried out significant enrichment analysis of the KEGG pathway, which
allows systematic analysis of the metabolic pathways of gene products
in cells. Among them, there were 13 metabolic pathways exhibiting
significant differences between cracked and normal jujube (P < 0.05)
(Table [70]3 and Fig. [71]4). Notably, the biosynthetic metabolic
pathways annotated as plant–pathogen interactions had the most DEGs.
Moreover, amino acid and nucleotide sugar metabolism were annotated by
14 biosynthetic pathways. Twelve DEGs were enriched in the metabolism
of α‐linolenic acid associated with the biosynthesis of jasmonic acid
(JA), seven DEGs in fructose and mannose metabolism, and five DEGs in
plant endogenous hormone abscisic acid–related carotenoid biosynthesis
pathways (Fig. [72]5A). The allene oxide cyclase (AOC) gene K10525 (EC:
[73]5.3.99.6), allene oxide synthase (AOS) gene ko1723 (EC:
[74]4.2.1.92) and 12‐oxophytodienoate reductase 3 (OPR3) gene ko5894
(EC: [75]1.3.1.42) were up‐regulated, whereas lipoxygenase 2 (LOX 2)
genes (ko0454, EC: [76]1.13.11.12) were down‐regulated in cracked
jujube fruits compared with normal jujube fruits. Furthermore, four
DEGs were enriched in the synthetic pathway of cutin, a subepidermal
and wax biosynthesis related to the biosynthesis of pericarp cells
(Fig. [77]5B), among which 3‐ketoacyl‐CoA synthase (KCS; EC:
[78]2.3.1.199) (ko00062; ko01100; ko01110) was dramatically elevated in
the cracked fruits.
Table 3.
Summary of KEGG pathway analysis for DEGs of jujube fruits.
Metabolic pathway Count P Pathway ID
Plant–pathogen interaction 28 5.62E−8 ko04626
α‐Linolenic acid metabolism 12 6.20E−7 ko00592
Photosynthesis–antenna proteins 4 0.000925659 ko00196
Amino sugar and nucleotide sugar metabolism 14 0.003612874 ko00520
Porphyrin and chlorophyll metabolism 6 0.009728098 ko00860
Riboflavin metabolism 3 0.010254331 ko00740
Fructose and mannose metabolism 7 0.01283576 ko00051
Vitamin B[6] metabolism 3 0.021920369 ko00750
Carotenoid biosynthesis 5 0.024435524 ko00906
Arginine and proline metabolism 6 0.029460626 ko00330
Synthesis and degradation of ketone bodies 2 0.031697946 ko00072
Cutin, suberin and wax biosynthesis 4 0.043515195 ko00073
Thiamine metabolism 2 0.048580236 ko00730
Cysteine and methionine metabolism 8 0.051757432 ko00270
Fatty acid biosynthesis 5 0.069002897 ko00061
Anthocyanin biosynthesis 1 0.071196465 ko00942
Taurine and hypotaurine metabolism 2 0.100795311 ko00430
Glycolysis/Gluconeogenesis 8 0.123256277 ko00010
Phenylalanine, tyrosine and tryptophan biosynthesis 4 0.124521724
ko00400
Linoleic acid metabolism 2 0.124629945 ko00591
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Fig. 4.
Fig. 4
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Functional annotation of DEGs in the KEGG database. KEGG pathway
analysis identified significantly altered metabolic processes between
cracked and normal jujube fruits.
Fig. 5.
Fig. 5
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Transcriptomics links fruit cracking to differentially expressed
metabolic gene expression. This diagram illustrates the transcriptional
changes of genes mediating the JA pathway (A) and surface wax synthesis
pathway (B). Genes and their relative transcriptional changes in
cracked and normal jujube fruits are shown (cutoff: P < 0.05).
For genes up‐regulated in cracked fruits, the top 20 metabolic pathways
were enriched (Table [82]4). The pathways with the highest number of
up‐regulated genes were those involved in plant–pathogen interactions,
amino acid and nucleotide sugar metabolism, and alpha‐linolenic acid
metabolism (Fig. [83]4). Additional top‐ranked pathways included
metabolism of riboflavin, arginine and proline, cysteine and
methionine, vitamin B[6] and thiamine; biosynthesis of keratin,
subepithelium and wax, as well as phenylalanine, tyrosine and
tryptophan; and synthesis and degradation of ketone bodies
(Fig. [84]4).
Table 4.
Up‐regulation of DEGs enrichment of the KEGG pathway of jujube fruits.
Metabolic pathway Count P Pathway ID
Plant–pathogen interaction 27 3.92E−10 ko04626
α‐Linolenic acid metabolism 11 2.74E−7 ko00592
Amino sugar and nucleotide sugar metabolism 12 0.002440878 ko00520
Riboflavin metabolism 3 0.004676306 ko00740
Arginine and proline metabolism 6 0.008247456 ko00330
Vitamin B[6] metabolism 3 0.01026376 ko00750
Cutin, suberin and wax biosynthesis 4 0.017563046 ko00073
Synthesis and degradation of ketone bodies 2 0.018641963 ko00072
Anthocyanin biosynthesis 1 0.053915095 ko00942
Taurine and hypotaurine metabolism 2 0.061726118 ko00430
Fatty acid biosynthesis 4 0.084489265 ko00061
Cysteine and methionine metabolism 6 0.088048329 ko00270
Sphingolipid metabolism 2 0.16748863 ko00600
Butanoate metabolism 2 0.16748863 ko00650
Inositol phosphate metabolism 4 0.174474525 ko00562
Phenylalanine, tyrosine and tryptophan biosynthesis 3 0.175687401
ko00400
Phosphatidylinositol signaling system 4 0.179913142 ko04070
Ether lipid metabolism 2 0.187225032 ko00565
Phagosome 4 0.190958543 ko04145
Fatty acid metabolism 4 0.213664657 ko01212
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For genes down‐regulated in cracked fruits, the top 20 metabolic
pathways were enriched (Table [86]5). The pathways with the highest
numbers of down‐regulated genes included antenna proteins involved in
photosynthesis, porphyrin and chlorophyll metabolism, fructose and
mannose metabolism, thiamine metabolism, carotenoid biosynthesis and
metabolism of ubiquinone and other terpenoids. Quinone biosynthesis,
photosynthesis and the amount of gene expression of the pentose
phosphate pathway were restrained, and the expression level was
decreased.
Table 5.
Down‐regulation of DEGs enrichment of the KEGG pathway of jujube
fruits.
Metabolic pathway Count P Pathway ID
Photosynthesis–antenna proteins 4 0.00000376E−6 ko00196
Porphyrin and chlorophyll metabolism 4 0.001025742 ko00860
Fructose and mannose metabolism 4 0.00332498 ko00051
Thiamine metabolism 2 0.003352723 ko00730
Carotenoid biosynthesis 3 0.007737558 ko00906
Ubiquinone and other terpenoid‐quinone biosyntheses 3 0.008707174
ko00130
Photosynthesis 3 0.012030176 ko00195
Pentose phosphate pathway 3 0.015991172 ko00030
Propanoate metabolism 2 0.053556638 ko00640
Tryptophan metabolism 2 0.055856523 ko00380
Pentose and glucuronate interconversions 3 0.082345406 ko00040
β‐Alanine metabolism 2 0.102441332 ko00410
Glycolysis/Gluconeogenesis 3 0.122404494 ko00010
Galactose metabolism 2 0.131669638 ko00052
Valine, leucine and isoleucine degradation 2 0.137730867 ko00280
Linoleic acid metabolism 1 0.141535622 ko00591
Other glycan degradation 1 0.186645751 ko00511
Cyanoamino acid metabolism 2 0.240690341 ko00460
Starch and sucrose metabolism 4 0.246451331 ko00500
Sesquiterpenoid and triterpenoid biosynthesis 1 0.249991082 ko00909
[87]Open in a new tab
Discussion
In the market, consumers prefer juicy, crispy, and large jujube fruits.
Not only is the overall quality reduced by cracks over the fruit, but
consumer satisfaction is reduced as well. As noted, Liu et al. [[88]18]
have previously annotated the genome and gene families of jujube
[[89]21, [90]22]. However, little is known about the change in gene
expression that contributes to fruit cracking. Using RNA‐seq and
bioinformatic analysis, we collectively identified 785 up‐regulated
genes and 251 down‐regulated genes that were differentially expressed
in cracked jujube fruits compared with normal jujube fruits. To our
knowledge, we provide the first transcriptome dataset and comparative
gene expression analysis of cracked and normal jujube fruits.
The results of the GO term and KEGG pathway enrichment analysis
demonstrated that several genes related to metabolic and hormone
signaling pathways exhibit differential expression between normal and
cracked jujube fruits. Previous results indicated that phytohormones,
especially JA, play essential roles in fruit cracking in plants. Our
data indicate that genes related to α‐linolenic acid metabolism are
significantly enriched in cracked fruits. As noted, α‐linolenic acid is
the original metabolic precursor of JA. JA, a new type of growth
hormone, and its precursors and derivatives, referred to as jasmonates
(JAs), play important roles in the regulation of many physiological
processes and synthesis of metabolites in plant growth and development,
and especially the mediation of plant responses to biotic and abiotic
stresses [[91]23, [92]24]. In the biogenesis of JA, OPR3 is formed via
AOS and subsequently AOC. The intermediate produced is further
catalyzed by OPR3 to form (+)‐7‐iso –JA. Methyl jasmonate is formed
when hydrogen (‐H) on the carboxyl group of JA is replaced by methyl
(‐CH3) [[93]25]. We observed that the AOC gene K10525 (EC:
[94]5.3.99.6), AOS gene ko1723 (EC: [95]4.2.1.92) and OPR3 gene ko5894
(EC: [96]1.3.1.42) are elevated, whereas LOX 2 gene (ko0454, EC:
[97]1.13.11.12) is down‐regulated in a time‐course manner with fruit
cracking development. The dynamic changes of these genes in this study
suggest that phytohormone regulation may be related to fruit cracking.
However, further metabolic analysis of hormone production is required
to confirm a potential link between JA synthesis and fruit cracking.
KEGG analysis also revealed that the cutin, suberin and wax
biosynthesis pathways were significantly enriched (P = 0.017563046;
ko00073) for genes up‐regulated in cracked fruits. It is important to
note that surface waxes play protective roles against pathogen
infection, herbivorous insects and environmental stresses, such as
drought, UV damage and frost. Plant very long‐chain fatty acids
(VLCFAs) are known to be involved in the process of biofilm membrane
lipid synthesis and serve as precursors for the biosynthesis of stratum
corneum waxes. The synthesis of VLCFAs is catalyzed by fatty acyl‐CoA
elongase, which is a multienzyme system composed of KCS, 3‐ketoacyl‐CoA
reductase, 3‐hydroxyacyl‐CoA dehydratase (HCD) and trans‐2,3‐enoyl‐CoA
reductase. The synthesized VLCFAs enter the stratum corneum waxy
synthesis pathway by decarbonylation and acyl reduction to form various
waxy components. KCS is a rate‐limiting enzyme in the endoplasmic
reticulum that catalyzes the first step of the condensation reaction in
the synthesis of VLCFAs. It has been studied in the fruit‐setting stage
of sweet cherry fruit [[98]26] that PaKCS 6 exhibits higher expression
in rip‐prone compared with rip‐resistant varieties. In this study, we
support this idea by providing evidence that the gene encoding KCS (EC:
[99]2.3.1.199) (ko00062; ko01100; ko01110) is dramatically changed in
cracked fruits (Fig. [100]5B), which might lead to altered synthesis of
cuticle wax and consequently jujube cracking. Our findings from
transcriptome analysis are in congruence with a previous study
regarding the outer skin and pulp tissue of tomatoes by Mintz‐Oron
Mintz‐Oron et al. [[101]27].
Conclusions
Our study provides an atlas of DEGs between cracked and normal jujube
fruits. Our data may serve as a valuable resource for investigation
into the mechanisms by which jujube fruits undergo cracking.
Conflict of interest
The authors declare no conflict of interest.
Author contributions
YL and PW conceived and designed the experiments. YL, YG and XX
performed the experiments. YL and PZ analyzed the data. PZ and PW
contributed reagents, materials and analysis tools. YL, YG and XX wrote
the manuscript. All authors read and approved the final manuscript.
Supporting information
Table S1. Up‐regulated and down‐regulated DEGs in the GO terms.
[102]Click here for additional data file.^ (16.6KB, docx)
Acknowledgements