De novo transcriptome assembly and characterization of nine tissues of Lonicera japonica to identify potential candidate genes involved in chlorogenic acid, luteolosides, and secoiridoid biosynthesis pathways
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Lonicera japonica is one of the most important medicinal plants with applications in traditional Chinese and Japanese medicine for thousands of years. Extensive studies on the constituents of L. japonica extracts have revealed an accumulation of pharmaceutically active metabolite classes, such as chlorogenic acid, luteolin and other flavonoids, and secoiridoids, which impart characteristic medicinal properties. Despite being a rich source of pharmaceutically active metabolites, little is known about the biosynthetic enzymes involved, and their expression profile across different tissues of L. japonica. In this study, we performed de novo transcriptome assembly for L. japonica, representing transcripts from nine different tissues. A total of 22 Gbps clean RNA-seq reads from nine tissues of L. japonica were used, resulting in 243,185 unigenes, with 99,938 unigenes annotated based on a homology search using blastx against the NCBI-nr protein database. Unsupervised principal component analysis and correlation studies using transcript expression data from all nine tissues of L. japonica showed relationships between tissues, explaining their association at different developmental stages. Homologs for all genes associated with chlorogenic acid, luteolin, and secoiridoid biosynthesis pathways were identified in the L. japonica transcriptome assembly. Expression of unigenes associated with chlorogenic acid was enriched in stems and leaf-2, unigenes from luteolin were enriched in stems and flowers, while unigenes from secoiridoid metabolic pathways were enriched in leaf-1 and shoot apex. Our results showed that different tissues of L. japonica are enriched with sets of unigenes associated with specific pharmaceutically important metabolic pathways and, therefore, possess unique medicinal properties. The present study will serve as a resource for future attempts for functional characterization of enzyme coding genes within key metabolic processes.
KeywordsDe novo transcriptome assembly Chlorogenic acid Luteolosides Secoiridoid
Geranyl diphosphate synthase
7-Deoxyloganetic acid glucosyl transferase
Loganic acid O-methyltransferase
Phenylalanine ammonia lyase
Cinnamic acid 4-hydroxylase
p-Coumaric acid 3-hydroxylase
4-Hydroxycinnamoyl-CoA ligase/4-coumarate-CoA ligase
Hydroxycinnamoyl-CoA shikimate/quinate hydroxycinnamoyl transferase
Hydroxycinnamoyl-CoA quinate hydroxycinnamoyl transferase
Lonicera japonica Thunb, also known as Japanese honeysuckle, ‘Jin Yin Hua’, and ‘Ren Dong’, belongs to the Caprifoliaceae family and is often used in traditional Chinese and Japanese medicine . L. japonica is native to eastern Asia, and is cultivated worldwide, particularly in China, Japan, and Korea due to its medicinal properties, and as an ornamental plant due to its pleasant smelling flowers, and attractive evergreen foliage . However, as it is highly invasive to the ecology of some countries, such as New Zealand and several other countries including North America, it is considered a major nuisance and is restricted . L. japonica has been used as traditional medicine in China for over thousands of years, and has been listed as top grade in ‘Ming Yi Bie Lu’ and ‘Shen Nong Ben Cao Jing’, and described in ‘Ben Cao Gang Mu’, the famous classical book of Chinese Materia Medica, as early as the seventeenth century, for applications in various diseases such as to clean away the heat-evil or heal the swelling . Different parts of L. japonica have been reported to possess unique medicinal properties, with flowers and floral buds being highly used in Chinese traditional medicine, while the leaves and stems are used in Japan [2, 4, 5]. The commercial value of L. japonica in the herbal medicine trading market has increased by several hundred-fold in recent years, and >30 % of current traditional Chinese medicine prescriptions contain extracts from different plant parts of L. japonica . Since 1995, L. japonica has been included in the Chinese Pharmacopoeia, with >500 prescriptions containing L. japonica being used for the treatment of various diseases .
Whole plant or aerial parts of L. japonica, particularly leaves and floral buds are used to derive bioactive metabolites for various preparations and medicinal uses . Modern pharmacological studies have shown that extracts from L. japonica possess a wide range of bioactive properties, such as anti-bacterial, anti-inflammatory, anti-viral, anti-pyretic, anti-oxidant, anti-hyperlipidemic, and anti-nociceptive among others [2, 5, 8, 9, 10, 11, 12, 13, 14, 15]. Extracts from L. japonica were used to prevent and treat severe acute respiratory syndromes, H1N1 influenza, and hand, foot and mouth diseases, and were reported to be effective against SARS coronavirus . Apart from its application in traditional medicine, L. japonica has also been used as a health beverage such as ‘Jin Yin Hua’ tea or ‘Jin Yin Hua’ wine, as cosmetics such as ‘Jin Yin Hua’ floral water, or even as an active ingredient of toothpaste to prevent oral cavity diseases .
The major chemical constituents of L. japonica extracts include phenolic acids [16, 17], flavonoids [18, 19], volatile oils [20, 21], and saponins [22, 23, 24, 25, 26, 27], and predominantly account for a wide range of attributed pharmacological properties. Chlorogenic acid (CGA) is a potent phenolic acid derived from phenylalanine and is considered to have several important biological activities. CGA, a group of esters created from certain trans-cinnamic acids such as caffeic acid, ferulic acid, and quinic acid, is a primary phenylpropanoid generated from the shikimic acid pathways with high anti-oxidant activities and, therefore, are often used in the form of medicines or foods. Studies have shown strong anti-bacterial, anti-oxidant and anti-diabetic activities attributed to CGA [1, 28, 29]. Luteolin, and its sugar-conjugated derivative, luteolosides, are also derived from phenylpropanoid metabolic pathways, and are major constituents of L. japonica extracts. Studies have shown luteolin and luteolosides to possess anti-oxidative, anti-inflammatory, anti-tumor, and anti-5-lipoxygenase activity . CGA and luteolosides are the major constituents of L. japonica and are used as standard compounds for assessing its quality . Besides CGA and luteolosides, secoiridoids such as loganin, secologanin, sweroside, and kingiside among others have been identified from extracts from L. japonica. In the past decades, >30 iridoids from L. japonica have been identified and reported [1, 27, 31, 32]. Iridoids and secoiridoids are pharmaceutically active metabolites, and are known to possess anti-tumor, anti-inflammatory, and anti-oxidant activities and hepatoprotective effects [32, 33, 34, 35, 36, 37]. In Japanese pharmacopoeia, loganin along with CGA are recommended as a means to evaluate the quality of L. japonica. Several studies on chemical constituents across different tissues have shown a higher content of CGA and luteolosides in floral buds, leaves and stems of L. japonica [1, 5, 7]. The CGA content in L. macranthoides, a species closely related to L. japonica, was reported to be higher in young leaves and young stems compared to flowers . The content of CGA, luteolosides, and other bioactive constituents of L. japonica varies based on tissue, extraction period or season, and their habitat.
Recent advances in next-generation sequencing, and computational resources to perform de novo transcriptome assembly and analysis has revolutionized the field of phytochemistry, especially for non-model plants [39, 40, 41]. RNA-seq-based transcriptome profiling provides a broad overview of different active metabolic processes, and their localization. Using a different statistical approach leads to the identification of potential genes involved in the pathway of interest. Previous transcriptome-based studies on L. japonica described transcripts across leaves and different floral developmental stages, and were focused on CGA, luteolosides, and flavonoid biosynthesis [2, 6]. However, the number of tissues used to perform de novo transcriptome assembly was limited and, therefore, does not represent a complete transcriptome for L. japonica. Furthermore, genes involved in secoiridoid metabolic pathways, one of the major chemical constituents with important pharmaceutical properties, have not been studied in L. japonica. Our study attempts to bridge this gap. We performed deep RNA sequencing for nine different tissues of L. japonica, yielding over 24 Gbps reads, which upon de novo transcriptome assembly, by combining three popular assemblers, resulted in 243,185 unigenes. The transcriptome assembly thus obtained is a more complete representation of the transcripts and ongoing metabolic processes of L. japonica. Through multiple transcriptome assemblers and integration of their resulting assemblies to obtain final de novo transcriptome assembly of L. japonica, we managed to capture diverse transcripts with improved N50 values and number of contigs assembled. Homologs for all enzymes from CGA, luteolin, and secoiridoid metabolic pathways were identified. Transcriptome abundance estimation across all nine tissues of L. japonica showed unigenes associated to key metabolic pathways were highly expressed in the young leaf and shoot apex. We also identified cytochrome P450s and UDP-glycosyl transferases, two major enzyme families involved in secondary metabolic pathways, which will serve as a basis for future validation and characterization. This study therefore presents a comprehensive transcriptome profiling and analysis for L. japonica, and will be useful as a resource for future functional characterization of enzymes of interest.
Results and discussion
Sample preparation, and Illumina sequencing
Raw reads generated from Illumina HiSeq™ were pre-processed using the Trimmomatic program  for the removal of adaptor sequences, reads with a sequence length <500, low quality and ambiguous reads, yielding over 110 M paired-end clean reads, or 22 Gbps (base pairs) of reads in total (Table S1). Mean phred score, which serves as a bench mark for assessing the quality of the sequenced reads, were >36 across all nine tissues of Lonicera japonica; <1 % of raw reads were dropped by the Trimmomatic program based on low-quality reads or being adaptor sequences. This indicates that our RNA-seq data was of high quality, and adequate for de novo transcriptome assembly. The study overview is shown in supplementary Fig. S1.
De novo transcriptome assembly for L. japonica
Success for any transcriptome-based study, especially when complete genome sequences are not available, depends upon the completeness and quality of an assembled transcriptome, which in turn depends upon the assembler program, and assembly parameters, particularly kmer size [43, 44]. Although, most de novo transcriptome assemblers rely on partitioning the sequence data into many individual de Bruijin graphs based on certain kmer size, where kmers are shorter than the reads length, output from each assembler is very different. Comparison of several popular transcriptome assemblers using different datasets revealed that none of them consistently performed to generate best assemblies . Recent studies, therefore, have proposed the use of multiple assemblers in order to maximize diversity of the de novo assembled transcripts [46, 47, 48]. Therefore, in order to generate a complete de novo transcriptome assembly for L. japonica, we used three popular assemblers, namely, SOAPdenovo-Trans , Trinity , and CLC Genomics Workbench 8.0.3 (https://www.qiagenbioinformatics.com/).
Summary of assembly statistics for de novo transcriptome assembly resulting from three different assemblers and their combination
No. of contigs
49,831 (37.7 %)
22,776 (17.2 %)
175,121 (49.8 %)
97,341 (27.7 %)
52,789 (43.7 %)
29,066 (24.1 %)
52,362 (41.3 %)
28,570 (22.5 %)
49,743 (37.8 %)
27,048 (20.6 %)
44,775 (34.4 %)
24,670 (19.0 %)
39,788 (36.0 %)
22,709 (20.5 %)
20,425 (56.5 %)
12,687 (35.1 %)
122,493 (50.4 %)
69,659 (28.6 %)
The transcriptome assemblies, thus obtained from SOAPdenovo-Trans (kmer31), Trinity, and CLC Genomics Workbench were combined, and sequence redundancies were removed using the CD-HIT-EST program [51, 52], resulting in a final de novo transcriptome assembly for L. japonica by incorporating 220,651,304 bps into 243,185 unigenes, with an N50 value of 1561 and the number of unigenes with sequence length >500 bps as 122,493 (50.4 %) (Table 1). Comparison of transcriptome assemblies resulting from individual assemblers, or one resulting by combining the output of three assemblers showed an advantage for this approach of combining multiple assemblers, as we observed a significant gain in N50 values, average unigene length, mean unigene length, and percentage of sequences with a length >500 bps for the combined assembly. The guanine-cytosine (GC) % and length distribution for resultant transcriptome assembly for L. japonica is shown in Fig. S2a, b, respectively, with average GC % for all unigenes being 40.82 %, while 10,374 unigenes had a sequence length >3000 bps. The resultant de novo transcriptome assembly for L. japonica was improved compared to earlier published transcriptome assemblies, with a significant increase in N50 value, and overall contig length distribution.
Functional annotation and classification of L. japonica
The unigene sequences derived from L. japonica transcriptome assembly were subjected to further characterization. A Blastx program-based [53, 54] homology search was performed for L. japonica unigenes against the NCBI non-redundant (nr) protein database (http://www.ncbi.nlm.nih.gov; formatted on Oct 2015) using an E value cut-off of <10−5, and the maximum number of allowed hits for each query was limited to 20. The top hit for each query sequence was used for the transcriptome annotation, and subsequent analysis and characterization. A Blastx-based homology search for L. japonica resulted in the annotation of 99,938 (41.1 %) unigenes (Table S2), while 143,251 unigenes had no significant sequence homology against the NCBI-nr database (Fig. S3a). Blastx results were used to extract associated gene ontology (GO) terms, to assign an enzyme commission (EC) number, and associated Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway. A total of 91,745 unigenes were assigned to at least one GO term or KEGG pathway information (Fig. S3a). An E-value distribution plot for unigenes with a blast hit showed >89 % of aligned sequences having significant sequence homology against the NCBI-nr database (Fig. S3b). Sequence similarity distribution analysis for sequences with a blast hit showed 65,213 (65.23 %) unigenes having sequence similarity >75 % (Fig. S3c). These results, therefore, suggest that the annotation unigenes from Blastx results can be used reliably for further functional characterization.
Top-hit species distribution analysis for unigenes showed >85 % of all annotated transcripts having high sequence similarity against six plant species, namely, Vitis vinifera, Populus trichocarpa, Ricinus communis, Glycine max, Medicago truncatula, and Arabidopsis thaliana (Fig. S3d). Within these six plant species, L. japonica transcriptome assembly showed highest similarity to Vitis vinifera, with 50 % of annotated top-hit unigenes being derived from it. Top-hit species distribution results were similar to previous reports, where >50 % of annotated transcripts were assigned to Vitis vinifera .
KEGG database-based functional characterization of L. japonica transcriptome assembly
Identification of simple sequence repeats (SSRs)
Statistics of SSRs detected in Lonicera japonica
Results of SSR searches
Total number of sequences examined
Total size of examined sequences (bp)
Total number of identified SSRs
Number of SSR-containing sequences
Number of sequences containing >1 SSR
Number of SSRs present in compound formation
Distribution to different repeat type classes
Transcriptome expression analysis for nine tissues of L. japonica
Transcriptome expression profiling provides a key insight into the different ongoing cellular processes under various conditions. To estimate expression abundance for unigenes across all nine tissues of L. japonica, clean paired-end reads were aligned to the de novo transcriptome assembly using the Bowtie 2 program , and transcript expression as direct count and the FPKM (fragments per kilobase of exon per million mapped fragments) values were determined by the RSEM program . Among nine tissues of L. japonica, green and white floral bud tissues with 169,203 (69.57 %) and 160,454 (66 %) unigenes, respectively, showed the highest number of transcriptionally active unigenes (FPKM >0), while yellow flower and leaf-1 with 138,138 (56.8 %) and 141,099 (58 %), respectively, represented tissues with the lowest number of transcriptionally active unigenes (Table S6). Transcriptome expression analysis showed greater overlap in terms of transcriptionally active unigenes, with 15,551 (6.39 %) unigenes being expressed in only one of the nine tissues of L. japonica. Overall, FPKM value distribution for unigenes across all nine tissues was uniform except for leaf-1 and leaf-3, which showed the majority of its unigenes having lower FPKM values but the number of unigenes with an expression value >500 FPKM were highest when compared to the rest of the tissues.
Identification of potential candidate unigenes involved in CGA biosynthesis pathways
Identification of potential candidate unigenes involved in secoiridoid biosynthesis pathways
Cytochrome P450 (CYP) represents a large superfamily that plays an important role in oxidation and hydroxylation reactions, and is involved in key secondary metabolic pathways. UDP-glucosyl transferases (GTs) represent another super family which participates in conjugation of sugar moieties to secondary metabolites, and is responsible for huge metabolic diversity in plants. Biosynthesis of CGA, luteolin, and secoiridoids involves several CYP enzymes, while GTs play an important role in bringing metabolic diversity and regulating pools of bioactive metabolites. In this study, a total of 285 and 470 unigenes, with sequence lengths >500 bps were annotated CYPs and GTs, respectively, and are listed in Supplementary Tables 10 and 11, respectively. These unigenes are regarded as important enzyme coding genes in many secondary metabolic processes, and will serve as an important resource for future functional characterization attempts.
Materials and methods
Plant material preparation, RNA extraction, and library preparation
All nine tissues for L. japonica, namely, shoot apex, stem, leaf-1 (youngest leaf near shoot apex), leaf-2 (second leaf), leaf-3 (mature leaf), green floral bud, white floral bud, white flower, and yellow flower were harvested in June 2014. L. japonica plants were cultivated in the natural environment of Chiba University pharmaceutical garden, Chiba (located at 35°36′17.7″N; 140°08′06.9″E). All tissues from L. japonica were harvested on ice, cut into small pieces, and were snap-freezed by liquid N2 before storing at −80 °C prior to RNA extraction.
The frozen tissues from L. japonica were powdered using a multi-bead shocker (Yasui Kikai, Japan), and were used for subsequent extraction of total RNA using RNeasy Plant Mini Kit (Qiagen, USA) according to the manufacturer’s instructions. RNA quality was assessed using Agilent Bioanalyzer 2100 (Agilent Technology, USA), and RNA samples with RNA integrity number (RIN) above 8 were used for cDNA library preparation.
mRNA for each sample was isolated from the total RNA by using beads with oligo (dT), and were added with fragmentation buffer to shear mRNA into short fragments, which were then used as a template for the synthesis of first-strand cDNA using random hexamer primers. cDNA library for Illumina sequencing was prepared using SureSelect Strand specific RNA library kit (Agilent Technology, USA) according to the manufacturer’s instructions.
Illumina sequencing and pre-processing of raw reads
A cDNA library was sequenced using Illumina HiSeq™ 2000 sequencer (Illumina Inc., USA) to obtain paired-end reads with an average length of 101 bps. cDNA library preparation and sequencing were performed at Kazusa DNA Research Institute, Chiba, Japan. The raw read sequences, transcriptome assembly, and RSEM-based transcript abundance data for nine tissues of L. japonica discussed in this study have been deposited in the NCBI’s Gene Expression Omnibus (GEO), and are accessible through GEO Series accession number GSE81949.
Raw reads thus obtained through Illumina sequencing were pre-processed using the Trimmomatic program  for the removal of adaptor sequences, empty reads, reads with ambiguous ‘N’ base >5 %, low-quality raw reads (Phred score <20), and raw reads with an average length <50 bps. The clean reads thus obtained were in the form of paired reads, or unpaired clean reads (forward and reverse), and were all used to perform de novo transcriptome assembly.
De novo transcriptome assembly and transcriptome expression analysis
De novo transcriptome assembly for L. japonica was obtained by merging three popular assemblers, namely, SOAPdenovo-Trans, Trinity v 2.0.6, and CLC Genomics workbench v8.0.3 (https://www.qiagenbioinformatics.com/) (Qiagen, USA). For SOAPdenovo-Trans, we performed six independent de novo transcriptome assemblies using kmer sizes as 31, 41, 51, 63, 71, and 91, and resultant assemblies were analyzed using perl script from assemblathon_2 to obtain N50 values and other assembly-related stats . De novo transcriptome assembly using Trinity and CLC Genomics Workbench were performed using default kmer size and default parameters. Resultant transcriptome assemblies from SOAPdenovo-Trans using kmer size as 31 emerged as the best assembly on the basis of different assembly parameters, which were then pooled together with assemblies from Trinity  and CLC Genomics Workbench into one merged assembly, and were processed by CD-HIT-EST v 4.6 (built on Mar 5, 2015) [51, 52] with parameters used as ‘−c 0.95 −n 8’ to remove sequence redundancy. Sequences with a length <200 bps were dropped, and the resulting de novo transcriptome assembly was used for further characterization. For transcriptome expression analysis, clean paired reads for each tissue were used for alignment over L. japonica transcriptome assembly using the Bowtie 2.0 program , and the RSEM program  was used for abundance estimation. To calculate unigene expression, we used the FPKM method. Unsupervised principal component analysis for all nine tissues was performed by the DESeq2 program  using count data for unigenes obtained from the RSEM program. GC content and basic statistic values for unigenes were calculated as described previously .
Functional annotation and classification of de novo transcriptome assembly
We performed a homology search based on the Blastx program using L. japonica transcriptome assembly as a query against the NCBI-non redundant (nr) protein database (http://www.ncbi.nlm.nih.gov; formatted on Oct, 2015) using a cut-off E value of <10−5 with a maximum number of allowed hits of 20. The top hit for each unigene was used to annotate the transcriptome. For further characterization of L. japonica transcriptome assembly, we used the Blast2GO v 3.0 program  to assign GO terms, EC number, and KEGG pathway information to the unigenes using associated Blastx results. GO level distribution, and visualization of the top 20 GO terms from three broad categories (biological process, molecular function, and cellular component) at level 3 for L. japonica transcriptome assembly were performed using Blast2GO.
Simple sequence repeat (SSR) detection
The transcriptome assembly for L. japonica was searched to identify the composition, frequency, and distribution of SSRs using the microsatellite identification tool (MISA) (http://pgrc.ipk-gatersleben.de/misa/) . The search parameters for maximum motif length group were set to recognize hexamers with each SSR length-based category to have at least ten repeats.
In this study, we performed deep RNA sequencing, and de novo transcriptome assembly for nine tissues of L. japonica using three popular transcriptome assemblers. With a total of 22 Gbps clean reads, transcriptome assembly for L. japonica was established, consisting of 243,185 unigenes with an N50 value of 1561 bps. The transcriptome assembly presented here represents much wider coverage, and longer contigs than previous reports and, therefore, improves overall transcript-associated knowledge available for L. japonica. Correlation-based analysis between nine tissues showed association, explaining the relationships between tissues at the developmental stages, thus suggesting that our data reliably represent transcripts for all tissues of L. japonica included in this study. Homologs for all genes associated with CGA, luteolin, and secoiridoid metabolic pathways were identified in L. japonica. Transcriptome expression analysis for unigenes associated with these key metabolic pathways revealed tissue-based transcript enrichment in L. japonica. Unigenes associated with CGA were highly enriched in the stem and leaf-2, while unigenes associated with luteolin were highly enriched in the stem and flowers. Transcripts from secoiridoid metabolic pathways showed the highest expression in leaf-1 and shoot apex. Our results therefore indicate that transcriptome abundance for key metabolic pathways is enriched in a tissue-dependent manner and, therefore, different tissues of L. japonica possess unique medicinal properties. Analyzing metabolite profiling of these tissues together with our transcriptome study to characterize relationships between gene expression and accumulation of metabolites will be highly desired for effective use of L. japonica as an important source of medicinal compounds. We believe that this study will serve as a milestone for functional characterization of key biosynthesis enzymes in L. japonica.
This study was supported, in part, by a Health and Labour Sciences Research Grant on the enhancement of ‘Comprehensive Medicinal Plant Database’, by the Grants-in-Aid for Scientific Research of The Japan Society for the Promotion of Science (JSPS), and by the Strategic Priority Research Promotion Program of Chiba University. HT was partially supported by MEXT KAKENHI (Number 221S0002). The super-computing resource was provided by the National Institute of Genetics, Research Organization of Information and Systems, Japan. The computing resources were provided by the National Institute of Genetics, Research Organization of Information and Systems, and the Medical Mycology Research Center, Chiba University, Japan.
Compliance with ethical standards
Conflict of interest
The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.
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