Genetics and Molecular Biology, 45, 4, e20210379 (2022)

Copyright © Sociedade Brasileira de Genética.

DOI: https://doi.org/10.1590/1678-4685-GMB-2021-0379

Plant Genetics
Research Article

Transcriptome analysis during fruit developmental stages in durian

(Durio zibethinus Murr.) var. D24

Nurul Arneida Husin1,5 , Sadequr Rahman2, Rohini Karunakaran3,4 and Subhash Janardhan Bhore1 
1
AIMST University, Faculty of Applied Sciences, Department of Biotechnology, Kedah, Malaysia.
2
Monash University Malaysia, School of Science and Tropical Medicine and Biology Platform, Malaysia.
3
AIMST University, Faculty of Medicine, Unit of Biochemistry, Kedah, Malaysia.
4
Institute of Bioinformatics, Saveetha School of Engineering, Department of Computational Biology,
Chennai, India.
5
Monash University Malaysia, Jeffrey Cheah School of Medicine and Health Sciences, Malaysia.

Abstract
Durian (Durio zibethinus Murr.) fruits are famous for their unique aroma. This study analysed the Durian fruit
transcriptome to discover the expression patterns of genes and to understand their regulation. Three developmental
stages of Durian fruit, namely, early [90 days post-anthesis (DPA)], mature (120 DPA), and ripen (127 DPA), were
studied. The Illumina HiSeq platform was used for sequencing. The sequence data were analysed using four
different mapping aligners and statistical methods: CLC Genomic Workbench, HISAT2+DESeq2, Tophat+Cufflinks,
and HISAT2+edgeR. The analyses showed that over 110 million clean reads were mapped to the Durian genome,
yielding 19,976, 11,394, 17,833, and 24,351 differentially expressed genes during 90-127 days post-anthesis. Many
identified differentially expressed genes were linked to the fruit ripening processes. The data analysis suggests that
most genes with increased expression at the ripening stage were primarily involved in the metabolism of cofactors
and vitamins, nucleotide metabolism, and carbohydrate metabolism. Significantly expressed genes from the young
to mature stage were mainly associated with carbohydrate metabolism, amino acid metabolism, and cofactor and
vitamin metabolism. The transcriptome data will serve as a foundation for understanding Durian fruit development-
specific genes and could be helpful in fruit’s trait improvement.
Keywords: Durian, Durio zibethinus, ethylene, fruit ripening, transcriptome.
Received: December 23, 2021; Accepted: October 18, 2022.

Introduction Ripening is accompanied by increased polygalacturonase

Durian fruits are extremely popular in South-East Asia. and galactosidase activity (Imsabai et al., 2002). Hydrolysis
Durian fruit is known as the “King of Fruits” because of its activity on the fruit cell wall polysaccharides leads to modifying
remarkable flavour and aroma. Both traditional and modern cell wall composition (Brownleader et al., 1999). Cell wall
breeding approaches can be used to improve the quality of polymer degradation is facilitated by various enzymes such
the fruits. In this line, understanding the gene expression as cellulase, polygalacturonase, β-galactosidase, pectate
patterns that occur during the development of durian fruit is lyase, and xyloglucan endotransglycosylase/hydrolase (XTH)
critical for its further quality improvement. The texture and (Han et al., 2016).
aroma are the two primary quality characteristics that define As of January 2021, 69,566 nucleotide sequences, 44,924
the market demand for durian fruits from the consumer’s genes, 65,547 proteins, and 14 SRA from Durio zibethinus were
perspective (Husin et al., 2018). deposited by researchers in NCBI GenBank. These DNA and
Premature fruit ripening causes significant economic mRNA sequences are helpful in the identification of genes and
losses for both farmers and consumers alike. Durian is a or transcripts. The genome draft sequence of the Musang King
climacteric fruit that softens intensively during the last stages durian cultivar has been made public (Teh et al., 2017), and most
of development. The pulp softening is regulated by endogenous recently, long PacBio reads to sequence the Musang King var.
ethylene. However, this process involves several genes that chloroplast genome has been reported by Shearman et al., 2020.
are regulated mainly for fruit softening in durian. The ability Transcriptomic studies are essential in understanding
to regulate fruit softening would have economic benefits for multiple pathways, gene expression patterns, and secondary
durian growers. Hence, genetic engineering tools for delaying metabolites biosynthesis in developing fruits or tissues of
maturation and softening processes can be desirable (Bouzayen interest. Several studies on gene expression patterns and
et al., 2010; Asif et al., 2014). gene expression profiles at the molecular level in Durian
varieties have been reported (Nyffeler and Baum, 2000;
Ruwaida, 2009; Vanijajiva, 2011, 2012; Hariyati et al., 2013;
Santoso and Saleh, 2013; Posoongnoen et al., 2015; Teh et
Send correspondence to Subhash Janardhan Bhore. AIMST
University, Faculty of Applied Sciences, Department of Biotechnology,
al., 2017; Husin et al., 2018). In transcriptomics of Durian,
Bedong-Semeling Road, Semeling, 08100, Kedah, Malaysia. E-mail: Musang King var., ripening-related gene sets included
[email protected]. genes regulated by the MADS-BOX transcription factor
 2 Husin et al.

family 29, SEPALLATA transcription factor family, and anticipated data output from HiSeq Illumina sequencing was
ethylene-related genes such as ACS (aminocyclopropane- 16.7 million reads or 5 GB per sample.
1-carboxylic acid synthase), a key ethylene-production
enzyme, are involved in ripening (Teh et al., 2017). On Raw read processing
the other hand, high-throughput sequencing has not been After sequencing, the reads (raw reads) contain low-
employed to analyse differential gene expression during quality reads and adapters, which will affect the analysis
development or to compare stages of Durian growth. Hence, quality. Therefore, it is crucial to filter the raw reads and get
the data reported in this paper will contribute to a better clean reads. Reads containing adapters, sequences with N less
understanding of durian fruit development. than 10 % (base cannot be determined), and sequences with
The ultimate goal of this study was to contribute (Qscore <= 5) base, which is over 50 % of the total base, were
fundamental knowledge about durian fruit development and filtered and removed. The quality of the raw data was assessed
ripening from a gene expression perspective. We have investigated using the FastQC software. The FastQC results showed per tile
the transcriptomic variations in Durian by performing differential sequence quality, base sequence content, sequence duplication
gene (DEG) discovery and gene expression characterisation level, overrepresented sequences, and adapter content. The
in edible fruit pulp in its young, mature, and ripened stages. pre-processing step was crucial to ensure the raw data was
We identified genes involved in ethylene biosynthesis, fruit cleaned before downstream analysis. In addition, the removal
softening, and other metabolic pathways essential for the of adapter contamination in sequence reads was a necessary
development and ripening of durian fruit. step. FastQC (Andrews, 2010) and Trimmomatic (Bolger et
al., 2014) tools were used to check and improve the quality
Material and Methods of the raw transcriptome.

Plant material Tools for the differential expression analysis

Fruit pulp samples from three different stages (young, Four DEG/transcript identification methods were used
mature, and ripening) of Durian variety (clone D24) fruits (Figure S1). When the absolute expression log2 fold change
were collected freshly in triplicate at the Agriculture Park of was greater than 1.5, and the FDR-corrected p-value was less
Universiti Putra Malaysia (UPM), Selangor, Malaysia (Figure 1). than 0.05, the analysis was considered statistically significant
Fruit pulp tissues were separated from the husk (and seeds), (Padovan et al., 2013; Aarhus, 2015; Zhu et al., 2017; Sebastian
frozen in liquid nitrogen, and stored at ₋80 °C until the total et al., 2018). A series of analyses, such as the number of
RNA isolation. The young fruits were collected on the 90th expressed genes/transcripts, the number of up and down-
day after the anthesis. The mature fruits were left at room regulated genes/transcripts, and the number of differentially
temperature for seven days to let them ripe naturally. The expressed genes/transcripts, were determined.
fruit pulp tissue was separated from the ripened fruit stage. CLC Genomic Workbench: Several QC trimming


methods were used within the CLC Genomic workbench

RNA isolation, cDNA library construction, software before mapping to the reference Durio zibethinus
and HiSeq Illumina sequencing genome. A reference-guided assembly was performed to
An RNA extraction kit, namely the GeneAll RibospinTM assemble the sequencing reads by mapping the reads to the D.
Seed/Fruit RNA mini kit, was used to isolate the total RNA zibethinus reference genome with the defined mapping options
from young, mature, and ripened Durian pulp tissues. RNA for RNA seq, followed by the empirical analysis of differential
samples with RIN numbers more than 7.0 were considered gene expression (EDGE test), functional annotations, and
for constructing the cDNA library as guidelines. categorisation of the assembled reads (Aarhus, 2015).
Poly-A mRNAs were purified from 1 µg of total RNA DESeq2: Principal component analysis (PCA) was
from respective samples using 20 µl of NEBNext Oligo performed with rlog-transformed transcripts count from htseq
d(T)25 beads as per illustrated in NEB Next Poly (A) mRNA in DESEq2 to verify each library’s identity and suitability for
magnetic isolation module. RNA mixtures were placed on differential expression (DE) analysis. The data analysis consists
a thermal cycler at 65 °C for 5 minutes and held at 4 °C to of pre-processing raw reads, mapping reads with HISAT2,
denature the RNA and facilitate binding the poly-A mRNA to transcript assembly using StringTie, gene counts with ht-seq,
the beads. The first and second strand of cDNA synthesis was and differential analysis with DESeq2 (Love et al., 2014).
performed with purified mRNA using the NEB Next Ultra RNA edgeR: MDS plot was constructed to assess the level of
Library Prep Kit (Ilumina). Messenger RNAs (mRNAs) were similarity between samples and their groups. This data analysis
eluted from the beads by adding the pre-prepared First-Strand consists of pre-processing raw reads, mapping reads with
Synthesis Reaction Buffer and Random Primer mix (2X). After HISAT2, transcript assembly using StringTie, and gene counts
incubation in a thermal cycler, second-strand cDNA synthesis with htseq (Robinson et al., 2009; McCarthy et al., 2012).
was performed immediately by adding the mixture of second- CuffDiff: This data analysis consists of pre-processing
strand synthesis reaction buffer and enzyme mix. The adaptor raw reads, mapping reads with TopHat, transcript assembly
ligation was proceeded immediately by adding the TA ligase using cufflinks, and differential expression analysis with
master mix and NEBNext adaptor. The final purification of CuffDiff. The up-regulated and down-regulated genes and
the PCR reaction was carried out using AmPure XP beads. transcripts were ranked and determined using the q value and
Before sequencing, the cDNA library’s quality was assessed fold change. FPKM value was used to evaluate the abundance
using the Qubit 2.0 Fluorometer and Agilent Tape station. The of the genes in the differential group (Trapnell et al., 2012).
 Durian fruit transcriptome 3


Figure 1 − Durian fruits and pulp tissue. (a-b) Durian fruits at its young stage of growth and development (90 days); (c-d) Durian fruit at its mature stage
of growth and development (120 days); and (e-f) Durian fruit at its ripening stage of growth and development (127 days).

Functional annotation of transcripts were used for their downstream analysis. The high-throughput
and pathway analysis sequence data for nine samples were submitted to GEO (Gene
The Blast2GO 5 (Conesa and Götz, 2008) Basic software Expression Omnibus), at NCBI. Transcriptome datasets are
was used. The differential group sequence in FASTA format available through the NCBI under the accession number series
was uploaded to the software. Then, the pathway analysis GSE136290 (release date: March 31, 2023).
was conducted with the KEGG Blast2GO function. All genes
Comparison of all mapping tools
that have a q-value less than 0.05 were added to the GO
categories “biological process,” “molecular function,” and Three different mapping methods, namely CLC Mapping,
“cellular components.” TopHat, and HISAT2 were used for mapping the reads to the
Durian reference genome. The number of mapping reads using
Results CLC is 49.82-59.42 %, TopHat 84.5-90.6 %, and HISAT2
88-95 %. Figure 2 shows the graphical representation of
Sequencing, annotation, and mapping mapped and unmapped reads using three mapping tools.
to the Durian genome CLC mapping shows lower mapping rates, while TopHat and
The sequencing was carried out with the Illumina Hiseq HISAT2 offer high and competitive mapping rates. Overall,
150 PE Run by a commercial service provider. The data output HISAT2 outperformed TopHat significantly in aligning FASTQ
was around 16.7 million reads per sample, equal to 5 GB. reads to the Durian genome. TopHat and HISAT2 are a type
Total raw reads were 193,416,352 M, and filtered reads were of splice-aware aligners suitable for RNA reads. This can
166,709,698 M, with a ≥ Q30 percentage. The quality of the raw split reads at intron-exon boundaries. The high mapping rate
data was assessed with the FastQC software. Trimmomatic and could be due to the tools’ ability to handle the RNA sequences’
Fast QC were tools used to check and improve the quality of splicing sites. Also, HISAT2 is an improved TopHat version
the raw transcriptome. In total, 110,351,584 M clean sequences (Trapnell et al., 2009, Kate Shannon, 2016).
 4 Husin et al.

Figure 2 − Comparison of the percentage of mapped and unmapped reads using CLC Mapping, TopHat, and HISAT2. (a) CLC Mapping, (b) TopHat
Mapping, and (c) HISAT.

Compared with other research, the selection of mapping total variation of PC1 and PC2 for YSMS was 95 %. There
tools has not given any significant indicator to determine the was a strong correlation in their particular groups at the YS
correct mapping for the aligned reads. Raplee et al. (2019) vs. ripening stage (RS). The total variation of PC1 and PC2
stated that the generally low proportion of aligned reads for YSRS was 91 %. The total variation of PC1 and PC2 for
for all input reads for HISAT2 and STAR is likely due to MSRS was 100 %. The PCA for all samples in three different
its quality. They also suggest that many input reads were groups was calculated. Principal component 1 (PC1) and
poly(A) sequences, Illumina adapter sequences, and reads principal component 2 (PC2) were identified by variance
from libraries are too uninformative for accurate mapping stabilising transformation in all three groups. The percentage of
to correspond to the very 3-end of mRNAs (Raplee et al., variance indicates how much variance was explained by PC1
2019). This study also contrasts with other previous studies, and PC2. These comparative principal component analyses
which reported that a mapping method has a limited impact demonstrate that biological replicates from all differential
on the final analysis of DE genes (Costa-Silva et al., 2017). groups are highly similar.
Table 1 shows the mapping tools’ performance in this study.
The mapped reads’ output was used to compare the number of Comparative transcriptome analysis and differential
DEGs analyzed with four selected methods. It is also known gene expression using merged DEGs


that selecting a suitable mapping tool relies on a variety of RNA-seq was used with the Illumina platform technology
other variables, such as RNA quality, cDNA libraries, genome to explore dynamic changes in gene expression in durian fruit
size, intron length, etc... pulp tissues from three developmental stages, young, mature,
and ripening. Various techniques are available to assess gene
Principal component analysis (PCA) for differential expression, each of which produces distinct results for rapid
expression groups RNA-seq growth. However, there are no clear rules as to which
Each differential studied group was subjected to PCA technique yields the best accurate gene expression estimations.
analysis to identify whether the samples clustered within In this study, four statistical techniques were used to produce a
each group or with other groups. At the young stage (YS) more accurate list of DE genes. Other researchers used similar
vs. mature stage (MS), the PCA results show that the YS techniques to study the transcriptomic data (Rajkumar et al.,
and MS samples were clustered together in their group. The 2015; Costa-Silva et al., 2017).

Table 1 − Statistics of the reads and the mapping percentage using CLC Mapping, TopHat, and HISAT2 in the present study.

Total Clean CLC Mapping: TopHat: Mapped HISAT2: Mapped

Samples Raw Reads Q20 Q30
Reads Mapped Reads (%) Reads (%) Reads (%)
YS_01 19,073,485 16,032,311 51.77 89.0 94.05 96.39 91.55
YS_02 22,376,330 18,890,648 49.81 90.1 95.14 96.60 91.93
YS_03 28,285,344 22,928,914 50.61 89.6 94.94 96.37 91.41
MS_01 21,308,808 17,586,886 49.65 89.5 94.93 96.33 91.47
MS_02 19,405,436 16,103,585 49.79 90.1 95.36 96.33 91.48
MS_03 21,699,619 19,093,624 49.61 90.6 95.31 96.33 91.45
RS_01 21,124,070 19,682,714 50.77 86.1 90.45 95.84 90.69
RS_02 20,261,496 18,614,759 49.82 85.6 89.83 95.92 90.75
RS_03 19,881,764 17,776,257 59.42 84.5 88.10 95.91 90.63

YS, young stage; MS, mature stage; RS, ripening stage; DPA, days post anthesis.
 Durian fruit transcriptome 5

CLC was used to investigate the utilisation of commercial Five different genes, namely, LOB domain-containing
software for Durian RNA seq experiments in this study. protein 18 (LOC111304630), LOB domain-containing protein
CuffDiff was chosen in conjunction with Top Hat, as it is 42 (LOC111282412), LOB domain-containing protein
developed explicitly from transcripts, spliced regions, and 40 (LOC111290435), LOB domain-containing protein 1
promoters for DGE analysis. In the comparison, DESEq2 and (LOC111297059), and LOB domain-containing protein 19
edgeR were combined to investigate the gene-level expression, (LOC111305909), were expressed during the early stage of
as this method works by integrating the raw reads using Ht- durian fruit pulp development. These five genes are from the
seq count. If the absolute value of the expression log2 fold LOB (lateral organ boundaries)-domain gene family. Durian’s
changes > 1.5 and < -1.5, the differentially expressed genes LOB gene family members exhibited a 9-fold increase in
and the transcript were considered statistically significant. expression. Several studies have suggested that LBD genes
Only those genes with expression identified as meaningful have a broad range of functions (Luo et al., 2016). Genes
with q value of < 0.05 (5 % of a gene for each comparative from the plant-specific Lateral Organ Boundaries Domain
group, false rate of discovery, FDR) were considered. After (LBD) family encode transcriptional regulators with roles in
mapping the reads to the reference genome using one of CLC various physiological and developmental processes in plants
mapping, TopHat or HISAT2, transcripts were assembled (Luo et al., 2016).
in separate events using the CLC assembler, Cufflink, and One of the MGL gene isoforms, namely methionine
StringTie. Table 2 highlighted the number of significant genes gamma-lyase-like (LOC111287425), responsible for the
identified in up and down-regulation among the four studied Volatile sulfur compounds (VSC) ’s production, was up-
methods. Among four methods used for RNA - seq analysis, regulated during the transition from the young to the mature
edgeR detected more DE genes in the durian transcriptome. stage. In a differential analysis of Durian, this gene is found
This finding is similar to other researchers’ findings, as they up-regulated with a fold change of 10.163. This gene is
reported that edgeR had identified more DEGs than other tools involved in the transsulfuration metabolic pathway, where
used (Fischer, 2003; Kvam et al., 2012; Seyednasrollah et al., sulfur transfer from homocysteine to cysteine occurs. The
2013; Gallego Romero et al., 2014; Rajkumar et al., 2015). pathway leads to the generation of several sulfur metabolites,
including cysteine, GSH, and the gaseous signalling molecule
Differentially expressed genes in Durian during hydrogen sulfide (H2S) (Sbodio et al., 2019).
its fruit development ATP- binding cassette (ABC) transporters are essential
Genes are differentially regulated to bring about changes for plant development in processes such as gametogenesis,
in durian fruit from a young to a mature stage. The differentially seed development, seed germination, organ formation,
expressed genes were identified in the young and mature secondary growth, protective layer formation, and
stages (Tables S1 and S2). phytohormone transport (Ha et al., 2017). In this study,
Pectinesterase 2-like (LOC111304600) had an 11- four different ABC transporter gene families, namely, ABC


fold increase in expression, and the endoglucanase-like transporter C family member 13 (LOC111274386), ABC
(LOC111278395) gene had a 10-fold rise in expression. Both transporter G family member 31 (LOC111301322), ABC
of these genes are involved in cell wall metabolism. Glucan transporter G family member 14 (LOC111286089), and ABC
endo-1,3 beta-glucosidase 11-like (LOC111287487) and transporter G family member 11 (LOC111316978) were found
cellulose synthase-like protein G2 (LOC111280213), both significantly up-regulated during the early stage. Members
implicated in the starch-sucrose breakdown, had a 9-fold and of the ABC transporter gene family in Durian exhibited a
6-fold expression, respectively. 10-fold increase in expression.
The analysis suggested that the Polygalacturonase
inhibitor-like (LOC111311552) gene was expressed highly (an Differentially expressed genes in Durian during
8-fold increase in expression) and is responsible for protein its fruit ripening
binding. Polygalacturonase inhibiting proteins (PGIPs) are cell Genes that play an essential role in the Durian fruit
wall proteins that inhibit the pectin-depolymerising activity pulps’ growth and development and are responsible for the
of polygalacturonases and play an essential role in the plant transition from a mature to a ripening stage are depicted in
defence system (Kalunke et al., 2015). Tables S3 and S4.

Table 2 − Total number of identified DEGs using four tools of CLC, CuffDiff, DESEq2, and edgeR.

Differential Group Expression CLC CuffDiff DESeq2 edgeR

YS/MS Up-regulated 2,565 1,461 5,790 5,117
Down-regulated 5,793 3,607 1,801 3,426
YS/RS Up-regulated 1,611 1482 3,452 2,872
Down-regulated 3,296 2611 1,820 1,894
MS/RS Up-regulated 4,141 2191 1,265 5,172
Down-regulated 2,570 926 3,705 5,870

YS, young stage; MS, mature stage; RS, ripening stage.

 6 Husin et al.

Four family members of xyloglucan endotransglucosylase Venn analysis of all differentials expressed genes
(XTH) were present, namely, xyloglucan endotransglucosylase/ Venn analysis was carried out for all differential expressed
hydrolase protein 33 (LOC111317417), xyloglucan genes to observe the specific and overlapping sequences among
endotransglucosylase/ hydrolase 2- like (LOC111287953), the three stages. Figure 3 shows the intersection among YSMS
xyloglucan endotransglucosylase/ hydrolase protein 6 and YSRS and MSRS, with 67 up-regulated and 42 down-
(LOC111316166), and xyloglucan endotransglucosylase/ regulated genes overlapped in all their gene sets. The Venn
hydrolase protein 6 (LOC111292968). These XTH family diagram analysis revealed a total of 937, 504, and 1,666 of the
members were directly annotated to the term cellular glucan specific differentials upregulated expressed genes, respectively,
metabolic process. The most significant increase in the in the young, mature, and ripening stages of growth. The
expression during durian ripening was observed in this Venn diagram analysis showed a total of 1,965, 724, and 635
XTH gene family. Similar observations were also reported of the specific differentials downregulated expressed genes,
for the banana and papaya fruit softening process (Asif respectively, in the young, mature, and ripening growth stages.
et al., 2014; Yao et al., 2014). Previously reported gene
families include expansins, pectate lyases, and xyloglucan Functional analysis of differentially expressed genes
endotransglycosylases responsible for softening banana fruit Blast2GO 5 Basic was used to identify the biological
(Ha et al., 2017) Most of the genes involved in cell wall significance of each group’s transition stage. The entire DEGs
hydrolysis are also members of multigene families, and many from each group generated using CuffDiff were subjected to
have highly specialised functions in cell wall metabolism GO analysis to achieve a broader functional characterisation.
(Asif et al., 2014). The GO analysis was classified into three major categories,
Three family members, namely, glucan endo-1,3 namely, biological process (BP), molecular function (MF),
beta-glucosidase (LOC111285741), glucan endo-1,3 beta- and cellular component (CC)). The total DEGs mapped to
glucosidase 12-like (LOC111275649), and glucan endo- the three GO categories for YSMS, YSRS, and MSRS were
1,3 beta-glucosidase (LOC111295531) were among the 6,735, 3,898, and 7,310 (Table 3). All selected transcripts with
expressed transcripts. They are known for their hydrolysis q value > 0.05 were uploaded to Blast2GO for annotation to
activity (Hrmova and Fincher, 2001; Singh et al., 2016). assign the putative functions to the DEGs. After running with
These genes and galactinol-sucrose galactosyltransferase InterProscan and Annex, the transcripts were assigned to the
5 (LOC111316628), beta-amylase 3, and chloroplastic-like GO terms within three main categories (BP, MF, and CC).
(LOC111305012) are also involved in sugar metabolism, and In developmental stage YS/MS, for biological process
responsible for the degradation of starch to sugar. (BP), major sub-categories were 1,416 DEGs in the metabolic
Polygalacturonase (PG), LOC 111311521, was process (GO: 0008152), followed by 1,401 DEGs in the
significantly expressed in durian. It is responsible for fruit cellular process (GO: 0009987) and 395 DEGs in response
softening (García-Gago et al., 2009; Anand et al., 2018). Its to stimulus (GO: 0050896). As for molecular function (MF),


high expression of 12.6-fold was noticeable while doing the binding (GO: 0005488) and catalytic activity (GO: 0003824)
data analysis. This gene is also involved in starch and sucrose were the highest genes mapped to these GO terms, with a total
metabolism. Other significant up-regulated genes involved in number of 1,427 and 1,137, respectively. Cell (GO: 0005623),
the hydrolysis activities were carboxylesterase SOBER1-like cell part (GO: 0044464), and organelle (GO: 0043226) with
(LOC111275243), endoglucanase-like (LOC111278395), and total DEGs of 1,297, 1,272, and 1,049 were enriched in cellular
beta-glucosidase 11 (LOC111305070). The findings on Carica component (CC). In YS/RS, the major sub-categories for
papaya L. var solo eight (8) fruits at the post-harvest stage biological process (BP) were 862 for metabolic process, 806
reported by Yao et al. (2014) reveal that the loss of the papaya’s for cellular process, and 227 for response to the stimulus. As for
firmness was positively related to the hydrolytic enzyme molecular function (MF), binding (GO: 0005488) and catalytic
activities and the sweet taste of the presence of simple sugars activity (GO: 0003824) were the genes mapped to these GO
such as galactose liberated from the polysaccharide complexes. terms with a total number of 730 and 597, respectively. Cell
The data analysis suggests that Sulfate transporter (GO: 0005623), cell part GO: 0044464), and organelle (GO:
1.3, SULTR (LOC 111294357) is also activated during 0043226) with total DEGs of 775, 746, and 533 were enriched
durian ripening. It is involved in sulfur metabolism (Leustek in cellular component (CC). The number of DEGs for all GO
et al., 2000; Gigolashvili et al., 2014). Sulfur is required terms was lower compared to YS/MS. In late-stage MS/RS,
for the biosynthesis of proteins, co-enzymes, prosthetic 1509, 1415, and 393 DEGs represented major sub-categories
groups, vitamins, amino acids like Cys and Met, GSH, and in biological process (BP) for metabolic process, cellular
secondary metabolites such as GSL and sulfoflavonoids. process, and response to the stimulus. As for molecular
Sulfate transporters are the most prominent S-metabolite function (MF), binding (GO: 0005488) and catalytic activity
transporters in plants, as sulfate is the primary source of sulphur (GO: 0003824) were the highest genes mapped to these GO
taken from the soil. It is the most abundant S-containing terms, with a total number of 1,571 and 1,094, respectively.
metabolite in plant cells (Gigolashvili et al., 2014). The Cell (GO: 0005623), cell part (GO: 0044464), and organelle
process is assisted by several sulfate transporter members (GO: 0043226) with total DEGs of 1,354, 1,269, and 969
(SULTR) (Pinsorn et al., 2018). were enriched in cellular component (CC).
 Durian fruit transcriptome 7

Figure 3 − a. Venn diagram for upregulated DEGs from three comparisons, namely YS/MS, YS/RS, and MS/RS. A total of 5,134 genes were expressed in
all three stages. The number of tissue-specific genes are 1,965, 724, and 635, respectively. b. Venn diagram for upregulated DEGs from three coparisons,
namely YSMS, YSRS, and MSRS. A total of 4,087 genes were expressed in all three stages. The number of tissue-specific genes are 937, 504, and
1,666, respectively.

Table 3 − Analysis of GO terms for differently expressed sequences. Enrichment of the KEGG Pathway
GO:0008150 GO:0003674 GO: 0005575 The Kyoto Encyclopedia of Genes and Genomes
Differential
Biological Molecular Cellular (KEGG) platform (https://www.genome.jp/kegg/) hosts various
Group
process Function Component databases and provides tools for a systematic annotation and
YS/MS 1,870 2,876 1,989 analysis of cell metabolic pathways and functions of the gene
YS/RS 1,149 1,646 1,103 product. To further investigate the functional studies, all these
MS/RS 2,038 3,160 2,112 up-regulated DEGs were enriched and annotated using the
KEGG database to obtain the link to the Enzyme Commission


YS, young stage; MS, mature stage; RS, ripening stage. number (EC). The EC was finally mapped to the relevant
KEGG pathway to obtain the annotated pathway maps. The
In the developmental stage of growth from young to mature percentage of the mapped reads to the KEGG pathway for
(YS/MS), a total of 210 DEGs mapped to the developmental each differential group was 96.50 % (YS/MS), 60.20 % (YS/
process (GO: 0032502) and 210 DEGs in anatomical structure RS), and 35.30 % (MS/RS). Table 4 shows the number of
development (GO: 0048856). Both GO terms were not present the mapped pathway, the number of mapped sequences, and
in the MS/RS. The DEGs are important for durian fruit growth the EC number for each differential group. A total of 2,705
and development. Several other GO terms of BP, MF, and DEGs were assigned to 382 EC. The EC were subsequently
CC that were not active in the developmental stage were grouped into 284 biochemical pathways.
localisation, catabolic process, and establishment of localisation, The top five KEGG class results from the young to
transport, non-membrane-bounded organelle, and intracellular mature stage data analysis indicate that most transcript-
non-membrane-bounded organelle. The highest DEGs of GO encoding enzymes were linked to carbohydrate metabolism
term associated with response to stress were in the ripening (254), metabolism of cofactors and vitamins (200), amino
stage, MS/RS with 291, followed by YS/MS with 277 DEGs. acid metabolism (176), nucleotide metabolism (142) and
As shown in Figure 4, the developmental process, biosynthesis of other secondary metabolites (82). Carbohydrates
cellular component organization, anatomical structure are highly essential due to its contribution to texture, flavour,
development, protein modification process within the color, and nutritional value in horticultural commodities (Yahia
biological process, and RNA binding within the molecular et al., 2019). The classification suggests that the highest
function were the unique groups in YSMS. Localization, number of enzyme activities in Durian growth in the young
catabolic process, the establishment of localization and stage were related to carbohydrate metabolism. This indicates
transport within the biological process, and non-membrane- that many pathways related to carbohydrate metabolism were
bounded organelle, an intracellular non-membrane-bounded activated to support the durian fruit’s growth and development.
organelle within the cellular component, were the unique Understanding the gene expression patterns in carbohydrate
groups in MSRS. This finding revealed that the DEGs metabolism will facilitate the investigation of durian fruit
classified into the groups might be playing a tissue-specific quality. Durian fruits development involves the accumulation
role during fruit development (Table S5). of starch and sucrose. According to KEGG, 254 genes were
 8 Husin et al.

associated with carbohydrate metabolism, and these genes 2-fold change in expression level, indicating its role in fruit
were classified into several metabolic pathways. The highest pulp softening. Endoglucanase also showed a high level (9-
number of expressed genes during the early fruit development fold) of change in its expression.
were from starch and sucrose pathways. Starch is present in Other softening genes that showed more than 2-fold
unripe durian, mainly in its pulp, which is transformed into expression change in the ripening stage were pectinesterase,
sugars during the ripening process. These sugars contribute U-box domain, xyloglucan endotransglucosylase/hydrolase,
to the level of sweetness of the fruits. In the transition from beta-galactosidase, cellulose synthase, endonuclease 1,
the young to the ripening stage, GO analysis produced 4,154 expansin-A (also called α-expansins), beta-glucosidase, and
sequences mapped with GO terms, and 2,248 transcripts pectin. It appears that more genes were expressed during the
encoding enzymes were annotated. ripening stage than the developmental stage of durian fruits.
The top five KEGG class results showed that the
expressed genes during the transition from the young to Ethylene synthesis and signal transduction
ripening stage were mainly for the metabolism of cofactors pathway in Durian
and vitamins (109), carbohydrate metabolism (102), lipid The molecular level of ethylene-controlled ripening
metabolism (77), nucleotide metabolism (75), and amino acid in Durian has not been investigated in detail. Most of the
metabolism (65). The pathways for nitrogen and glutathione studies conducted refer to a single gene or a single family
metabolism contained the greatest number of expressed genes. of genes. The genes involved in ethylene biosynthesis and
During the transition from the mature to ripening stage, signal transduction are significantly important in the growth
GO analysis produced a total of 7,629 sequences mapped with and development of Durian fruit. Ethylene biosynthesis
GO terms, and of these, 4,096 transcripts encoding enzymes were is essential for the ripening of fruits; hence, the data were
annotated. The top five KEGG class results were the metabolism analysed to study the genes involved in this process. Durian
of cofactors and vitamins (200), nucleotide metabolism (192), shows a burst of respiration and a gaseous hormone ethylene
carbohydrate metabolism (85), lipid metabolism (61), and biosynthesis at the beginning of its ripening, which regulates
amino acid metabolism (56). During the late stage of fruit the fruit-maturing aspects.
development, the sulphur metabolism pathway had the highest The genes involved in ethylene biosynthesis, signalling
number of expressed genes, indicating the durian’s strong odour. pathway, and regulatory response process were identified from
In contrast, the classification of transcripts suggests that the transcriptome data (Table S8). S-adenosyl-L-methionine
the highest number of metabolism of cofactors and vitamins (SAM) synthase converts methionine to SAM with a 2-fold
outperformed the other pathways in the late stage of Durian expression during fruit ripening (Bouzayen et al., 2010). Several
growth. In KEGG, 180 genes were identified to be associated genes linked with ethylene biosynthesis have been identified
with thiamine metabolism to support the nutritional quality and with six ACS gene members. The ACS genes are involved
health benefit of durian fruit, mainly in the energy metabolism in converting SAM to 1-aminocyclopropane-1-carboxylic
(Figure 5 and Table S6) (Lonsdale, 2006). acid (ACC) with 2-fold expression in both stages. Most


1-Aminocyclopropane-1-Carboxylic Acid Oxidase (ACO)

Genes involved in Durian fruit softening
genes with high expression of 4-fold increase were identified
During the fruit ripening developmental stages, a set of at the stage of ripening. This ACC oxidase is known to play
distinct softening genes are expressed. The significant clusters, a role in converting ACC to ethylene (Bouzayen et al., 2010).
young vs. mature, and mature vs. ripening annotation, are In addition to this, an array of genes that are associated
shown in Figure 6 and Table S7. In developmental stages, with ethylene signal transduction have been identified in this
several genes that showed more than a 2-fold change in study. Fifteen selected gene family members of mitogen-
expression level were pectinesterase 3-like, U-box domain- activated protein kinase (MAPK) and genes linked to
containing protein, expansin-like B1, and probable xyloglucan. transcription factors such as EIN3, ethylene-like receptor,
These genes coordinate to soften durian fruit in the transition protein kinase constitutive triple response1 (CTR)-like were
from the young to the mature stage. identified and grouped under the ethylene signalling pathway
Polygalacturonase inhibitors showed the highest (Binder, 2020). The ethylene signal transduction pathway has
expression of 8-fold in the developmental stage. This plant been extensively studied in fruits as ethylene affects fruit’s post-
protein can inhibit polygalacturonase (PG) enzymes in the harvest physiology and storage requirements (Binder, 2020).
young to mature durian growth stage. In contrast, this gene is The ethylene response factors (ERFs) that act downstream
down-regulated in the ripening stage with -8-fold expression are the last component of the ethylene signalling pathway to
to activate durian fruit pulp softening genes. regulate the ethylene-responsive gene’s expression. ERFs have
It is known that expansins A affect preferentially been reported to play essential roles in plant development,
xyloglucan-rich type-I cell walls characteristic of flower abscission, fruit ripening, and defence responses (Gao
dicotyledonous plants (Sharova, 2007; Marowa et al., 2016). et al., 2020). Fifty-six ERF members expressed the ethylene
In contrast, expansins B modify type-II cell walls rich in signalling pathway to regulate the ethylene response for the
arabinoxylans and β-glucans (Sharova, 2007). Only proteins developmental and ripening processes. ERFs mediate the
from the alpha-expansin and beta-expansin families have ethylene-dependent ripening gene responsible for the Durian
been found to weaken cell walls. The roles of expansin-like fruit’s significant texture, flavour, and taste (Binder, 2020;
A and expansin-like B, on the other hand, remain unknown. Thirugnanasambantham et al., 2015). We have presented
(Palapol et al., 2015). While doing data analysis, we found the ethylene synthesis and signal transduction pathway for a
that the expansin-B is expressed in Durian with more than a simplified explanation purpose (Figure 7).
 Durian fruit transcriptome 9


Figure 4 − GO terms classification in a) YS/MS, b) YS/RS, and v) MS/RS.

 10 Husin et al.

Table 4 − No of mapped pathways and sequences. pulp samples, Durio zibethinus methionine gamma-lyase-like
No of Mapped No of Mapped (LOC111287425), transcript variant X1, mRNA, D. zibethinus
Stage No of EC methionine gamma-lyase-like (LOC111308026), transcript
Pathway Sequences
YS/MS 96 1,279 114 variant X3, misc_RNA, and D. zibethinus methionine gamma-
lyase-like (LOC111290112), partial mRNA, were found,
YS/RS 85 689 95
respectively. MGL genes abundantly expressed in the mature
MS/RS 103 737 173
and ripening stage were D. zibethinus methionine gamma-
YS, young stage; MS, mature stage; RS, ripening stage. lyase-like (LOC111308047), mRNA, and D. zibethinus
methionine gamma-lyase-like (LOC111315809), mRNA.
The correlation matrix was performed to compare the five
Role of MGL genes and VSC production in Durian` MGL gene copies to observe its expression value in three
To study the biological process related to the Durian developmental stages. There were two major clusters, major
fruit’s strong aroma, the heatmap analysis between isoforms cluster 1 (C1) comprised of 2 minor clusters (C1a and C1b).
of MGL (methionine gamma-lyase-like) gene responsible Major cluster 2 comprised of C2, the outlier. C1a showed a
for volatile sulphur compounds (VSC) production was relationship between MGLa1 and MGLa2. Both MGL genes
carried out. The VSCs have been identified as important in cluster C1a showed a varying high level of expression
factors determining the degree of aroma and taste of Durian value in the ripening stage. While C1b comprises MGLb1
fruit pulp. MGL enzymes break methionine and cysteine and MGLb2, it showed a similar expression pattern from
into methanethiol, ethanethiol, and ethionine (Fischer and the mature to ripening stage. MGL genes were up-regulated
Steinhaus, 2019). from the mature to the ripening stage. There were two
MGL genes produce VSC. Durian fruit is unique in the transcripts under MGLb2; namely XM_022906389.1 and
sense of its aroma conferred by VSCs. A study on the Durian XM_022906396.1. Major cluster C2 was an outlier, as this
genome reveals the presence of four copies of MGL, which MGL gene, MGLc, showed an uneven expression level only
contributes to making the Durian fruit pulp aroma strong (Teh in the young stage of growth. This gene was downregulated
et al., 2017). There are two main groups of volatile compounds; in the mature to ripening stage. Under this gene, there were
sulfur-containing volatiles, such as thiols, disulfides, trisulfides, three transcripts; XM_022877994.1, XM_022878003.1 and
and esters associated with a fruity aroma. MGL genes control XM_022877983.1. Overall, the highest-level expression value
the VSCs level. A distinctive sulfuric aroma can be smelled of the MGL gene was expressed in MGLb1 in the transition
in durian fruit pulp due to VSCs produced by the MGL stage from mature to ripening.
enzyme (Teh et al., 2017). Seven low molecular weight The structural analysis of MGL proteins published in
sulfurs containing compounds are reported in durian fruit the 2018 International Conference on Tropical Fruit Pests
pulp, including hydrogen sulphide, methanethiol, ethanethiol, and Diseases suggests that all four MGL genes in Durian


and propane-1-thiol (Cannon and Ho, 2018). have 89 % to 93 % similarity at the protein sequence level.
While annotating transcripts, we noticed that Durian Phylogenetic analysis demonstrated that the MGL genes in
fruit pulp contains five different MGL isoforms expressed in Durian are evolutionary-related with high genetic diversity,
three different stages of growth, YS, MS, and RS. One outlier separating MGLb_1 into different clades (Yusof, 2018). The
of the MGL gene, MGLc (LOC111287425), is found in the active sites in MGL protein sequences are highly conserved.
early stage of Durian fruit pulp. However, the regions proximal to the active sites in MGLb_1
A Heatmap showing the gene abundance of MGL showed more residue substitutions than others. Their sequence
isoforms (FPKM) in YS, MS, and RS is depicted in Figure 8. analysis also showed that LOC111315809, MGLb_1 (accession
This heatmap was generated using StringTie. The abundance number XP_022773569) contained more residue substitutions
of each reference gene was estimated with StringTie. The than other MGL genes. This gene expression was highly
output of FPKM (Fragment per kilobase) and TPM (Transcript abundant in the ripening stage, suggesting that it produces
per kilo base million) values were calculated based on the more VSCs than other isoforms.
normalisation of the sequencing depth and gene length. Furthermore, they also suggested some possible residue
The highest FPKM or TPM value was considered the most substitutions in MGLb_1 that may affect the activity of MGL
abundant genes for the particular sample. FPKM and TPM in the recognition and elimination of methionine, which
values were used to compare the relative gene expression eventually contributes to the pungent odour of ripening
levels within a sample. Durian fruit (Yusof, 2018). Our findings were similar.
We found that durian fruits possess various isoforms MGLa2 (LOC111315809) was expressed abundantly in the
of the MGL genes. The MGL gene isoforms are abundantly ripening fruit pulp tissue samples. These findings explain
expressed. The transcripts were found in young, mature, and why the strong aroma of Durian is felt when fruit reaches
ripening fruit pulp samples. In young, mature, and ripened fruit the ripening stage.
 Durian fruit transcriptome 11


Figure 5 − Classification of the sub-categories of KEGG pathways in a) YSMS, b) YSRS, and c) MSRS.
 12 Husin et al.

Figure 6 − Hierarchical clustering analysis, heatmap, and key regulatory genes involved in Durian fruit softening development and ripening stage. Blue
and orange bands indicate the high and low expression of genes, respectively. The color scale representing log2 fold change values is shown; young to
mature stage (YSMS), young to ripening stage (YSRS), and mature to ripening stage (MSRS).


Figure 7 − Selected members of gene families involved in ethylene biosynthesis and signal transduction in durian fruit during its developmental and
ripening stages. The colour scale is representing the log2 fold change values.
 Durian fruit transcriptome 13


Figure 8 − Heatmap showing the expression of MGL (Methionine gamma lyases) gene isoforms in three different growth stages of durian fruit pulp.
YS represents for the young stage; MS represents the mature stage, and RS represents ripening stage. The FPKM value and Pearson’s distance are used
as the metric.

Discussion showed that HISAT2 is a highly sensitive approach to mapping

This paper describes the use of next-generation transcriptome data to the Durian Reference Genome, with
sequencing (Hi-Seq Platform) to understand the molecular the highest mapping rate of 95 % (Sutthacharoenthad et al.,
attributes of Durian fruit in its young, mature, and ripen 2019). Differential expression analysis has revealed a different
stages. A better understanding of how these processes are number of Durian DEGs for all used tools (CLC, CuffDiff,
genetically regulated will facilitate the potential capacities and DESEq2, and edgeR) specific to their level of developmental
development of effective strategies to improve local durian stages in differential expression analysis. The reason is mainly
fruits by identifying key regulatory genes and their manipulation due to the different statistical methods unique to each tool, and
using genetic engineering tools (Husin et al., 2018). the number of mapped reads specific to the tools used is not
We have used three different mapping tools, CLC determined by high or low mapping rates. We have learned
(Aarhaus, 2015), Top Hat (Trapnell et al., 2009), and HISAT2 from our results that higher rates of mapping do not indicate
(Kim and Yang, 2015), to map the reads against the Durian a higher DEG identification. Venn analysis was carried out
Reference Genome. A comparison of these mapping tools further to find the overlapped DEGs identified by four different
 14 Husin et al.

tools used. As a result, a comparison of the top 50 highly in ripened jackfruit (Hu et al., 2016). Some of the genes
significant genes revealed the similarities and dissimilarities identified in jackfruit are also expressed in Durian fruit pulp
between these four pipelines. Therefore, it is advantageous to tissue. The commonly expressed genes, namely 1,4-alpha-
combine the results of different tools to obtain a more detailed glucan-branching enzyme 2-1, chloroplastic/amyloplastic-like,
and reliable DEGs results output. fructokinase-like 1, chloroplastic, and hexokinase-3-like,
Previous studies published by other research groups also are expressed during the transition from young to mature
support selecting top candidate genes to explore further using stage. Similarly, during the transition from the mature to
several tools for identifying DEGs (Costa-Silva et al., 2017; ripening stage, genes, namely hexokinase-3-like, sucrose-
Raplee et al., 2019). Schurch et al. (2016), recommended to phosphatase 2-like, probable sucrose-phosphate synthase 1,
use edgeR for samples of less than 12 replicates due to the glucan endo-1,3-beta-D-glucosidase-like, and fructokinase-like
superior combination of a truly positive and false positive. 1, chloroplastic are also expressed in Jackfruit (Hu et al., 2016).
DESeq2 is recommended to use for higher replicates of As a whole, this study has successfully provided the
samples. Only DESeq2 and edgeR (TMM) can maintain a transcriptome data and gene expression data specific to
reasonable false-positive rate in the presence of top-count young, mature, and ripened developmental stages of Durian
genes without any loss of power. fruit pulp. The research findings reported in this paper will
Results suggest that the total number of identified up serve as preliminary genomics expression data, which may be
and down-regulated expressed genes in all groups is higher helpful in developing a new strategy for genetic engineering
using DESeq2 and edgeR compared with CLC and CuffDiff. to create a new Durian variety with desirable traits beneficial
The highest range of overlapping gene similarities between for consumers and Durian growers.
DESEq2 and edgeR is 72.1-85.4 %. Unknown genes and
functions dominate most of the top DEGs associated with Acknowledgements
DESeq2 and edgeR. These obscure results need further research The authors want to acknowledge that the research
work using both tools in the identification of novel genes. funding for this project was provided by AIMST University,
DESeq2 and edgeR tools identified the highest number Malaysia, under its internal research grant scheme. The
of up-regulated genes compared to other tools in the transition authors also want to thank the Agriculture Park of Universiti
of young to mature and mature to the ripening stage. EdgeR Putra Malaysia (UPM), Selangor, Malaysia, for providing the
has successfully identified the highest number of DEGs in Durian (clone D24) fruit samples for the study.
up and down-regulated genes in the transition from mature to
ripening compared with other tools. For comparative functional Conflict of Interest
analysis and validation between four tools, the top 50 DEGs
The authors declare no conflict of interest.
in up and down-regulated were selected from each tool. The
function of the top significant genes between stages shows Author Contributions


almost similar patterns. The most common up-regulated

genes were involved in cell wall development, cell membrane NAH collected the fruit samples, carried out the
and cytoplasm, and defence activation in early fruit growth. laboratory work, performed bioinformatics data analysis,
In the late stage of growth, the most common up-regulated validated the data analysed, and prepared the manuscript draft.
genes were involved in the critical process of growth and SJB conceived the idea and developed the project proposal and
development, regulated organ development, stress, defence experimental strategies; he reviewed and edited the manuscript
against pathogen attack, and disease resistance. to finalise it. SJB, SR, and RK served as the main supervisor,
Transcriptome analysis also revealed that genes field-supervisor, and co-supervisor for NAH, respectively. SR
associated with cell wall softening, such as polygalacturonase, and RK provided their input for manuscript improvement.
pectin, etc., were significantly up-regulated at the ripening
stage of 127 DPA. To delay durian fruit pulp softening,
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