Use of the de novo transcriptome analysis of silver-leaf nightshade (Solanum elaeagnifolium) to identify gene expression changes associated with wounding and terpene biosynthesis
BMC Genomics volume 16, Article number: 504 (2015)
Solanum elaeagnifolium, an invasive weed of the Solanaceae family, is poorly studied although it poses a significant threat to crops. Here the analysis of the transcriptome of S. elaeagnifolium is presented, as a means to explore the biology of this species and to identify genes related to its adaptation to environmental stress. One of the basic mechanisms by which plants respond to environmental stress is through the synthesis of specific secondary metabolites that protect the plant from herbivores and microorganisms, or serve as signaling molecules. One important such group of secondary metabolites are terpenes.
By next-generation sequencing, the flower/leaf transcriptome of S. elaeagnifolium was sequenced and de novo assembled into 75,618 unigenes. Among the unigenes identified, several corresponded to genes involved in terpene biosynthesis; these included terpene synthases (TPSs) and genes of the mevalonate (MVA) and the methylerythritol phosphate (MEP) pathways. Functional characterization of two of the TPSs showed that one produced the sesquiterpene (E)-caryophyllene and the second produced the monoterpene camphene. Analysis of wounded S. elaeagnifolium leaves has shown significant increase of the concentration of (E)-caryophyllene and geranyl linalool, two terpenes implicated in stress responses. The increased production of (E)-caryophyllene was matched to the induced expression of the corresponding TPS gene. Wounding also led to the increased expression of the putative 1-deoxy-D-xylulose-5-phosphate synthase 2 (DXS2) gene, a key enzyme of the MEP pathway, corroborating the overall increased output of terpene biosynthesis.
The reported S. elaeagnifolium de novo transcriptome provides a valuable sequence database that could facilitate study of this invasive weed and contribute to our understanding of the highly diverse Solanaceae family. Analysis of genes and pathways involved in the plant’s interaction with the environment will help to elucidate the mechanisms that underly the intricate features of this unique Solanum species.
Solanum elaeagnifolium (common name: silver-leaf nightshade) is a perennial weed of the family Solanaceae, native to north Mexico and south USA , now extended to nearly all the Mediterranean . The weed constitutes a big threat to major crops such as cotton, wheat and tomato, while it endangers city parks in metropolitan areas. Its highly invasive nature is due to its fine adaptation to diverse environmental and soil conditions (especially drought), and its reproductive mode which includes both sexual reproduction by seeds and asexual reproduction by underground regenerating buds [3, 4]. S. elaeagnifolium plants are also hosts to several dangerous plant viruses like potato virus Y (PVY)  and tomato yellow leaf curl virus (TYLCV) .
Although S. elaeagnifolium fruit is toxic to many animals , whole plant extracts were recently shown to exhibit analgesic, anti-inflammatory, antioxidant and hepatoprotective activities . Many of these functions were attributed to the high amount of phytosterols, which amounted to more than 11 % of the plant’s extract . Sterols belong to the large family of plant terpenes whose biosynthesis in plants is extremely important due to their role as phytohormones and photosynthesis pigments but more importantly as mediators of plant’s interaction with a variety of biotic and abiotic factors. Tomato breeding has been focused lately in improving the biosynthetic pathways that lead to the production of terpenes in an effort to increase herbivore resistance . Wild Solanum species are considered a valuable source of genetic variability towards this goal . Plant terpenes are produced by prenyl diphosphates, such as dimethylallyl diphosphate (DMAPP), geranyl diphosphate (GPP), farnesyl diphosphate (FPP), and geranylgeranyl diphosphate (GGPP), via two pathways, the MVA pathway and the MEP pathway . Sesquiterpenes (C15) and triterpenes (C30) are produced by the cytosolic MVA pathway while monoterpenes (C10) and diterpenes (C20) are produced by the plastidial MEP pathway. However, in Solanum species the production of many monoterpenes and sesquiterpenes rather derives from GPP, (Z,Z)-FPP and neryl diphosphate (NPP) located in the plastids [11–13]. Prenyl diphosphates are the substrates on which the enzymes responsible for the production of terpenes act. The specific enzymes are TPSs and expression of their coding genes is frequently induced in response to biotic and abiotic stress . Plant terpenes are implicated in a variety of plant processes such as the formation of plant hormones gibberellins (GA) and abscisic acid (ABA), the production of phytoalexins, allelopathic substances  and substances that attract pollinators or repel herbivores . Tomato terpenes, which have been studied extensively, are abundant in the glandular trichomes of leaves, stems, young fruits and flower parts.
Although S. elaeagnifolium is a species that gained significant agronomic and scientific attention, only 169 expressed sequence tags (ESTs) sequences exist in GenBank. At the molecular level, it was only recently that specific EST- simple sequence repeat (SSR) molecular markers were developed and used for estimating the genetic diversity of S. elaeagnifolium natural accessions collected from nine sites of southeastern Australia . SSR markers from other Solanum species have been used before for estimating the genetic variability of S. elaeagnifolium populations . Transcriptome analyses of species such as tomato (Solanum lycopersicum), pepper (Capsicum annuum) and tobacco (Nicotiana tabacum) have shown that a high level of sequence conservation exists among Solanaceae .
In this study aiming to obtain transcriptome sequences, next-generation sequencing was performed in a pool of mRNAs isolated from S. elaeagnifolium leaves and flowers. By the use of computational methods transcript abundance was estimated. To assess aspects of stress resistance in S. elaeagnifolium, terpene biosynthesis associated with stresses and the plant’s response to leaf wounding was examined. In this context, two terpene synthases were isolated and characterized in yeast, a monoterpene synthase mostly producing camphene and lesser amounts of β-myrcene and limonene, and a sesquiterpene synthase producing mostly caryophyllene and lesser α-humulene. Leaf wounding experiments showed both transcriptional induction and caryophyllene production in wounded tissues.
High-throughput sequencing and transcriptome assembly
The sequencing output of S. elaeagnifolium flowers and leaves mRNA is shown in Table 1. Clean reads were assembled into contigs using Trinity . Then the reads were mapped back to contigs. An amount of 138,604 contigs were generated with a mean length of 385 nucleotides (nt) (N50 824 nt). Contigs were re-assembled into 75,618 unigenes with mean length of 1,082 nt (N50 1,778 nt). For a detailed graph of contigs and unigenes length see Additional file 1: Figure S1. A total of 33,893 clusters (prefix cl) were created from unigenes while 41,725 unigenes remained as singletons (prefix unigene).
Functional characterization of unigenes
Based on basic local alignment search tool (BLAST) searches in the non-redundant (NR) database at NCBI (download 14 April 2014), the majority of S. elaeagnifolium unigenes (39.8 %) shares similarity with grape sequences while less than 6 % of sequences shares similarity with other Solanaceae sequences (Fig. 1). Most unigenes (66.3 %) show significant similarity above 60 % with NR entries from which 25.4 % exceeds 80 % similarity.
All unigenes were employed in Blastx searches against the NR, Swiss-Prot, Kyoto encyclopedia of genes and genomes (KEGG), gene ontology (GO) and clusters of orthologous groups (COG) databases with an e-value of 10−5. The information obtained was used to extract coding DNA sequence (CDS) from unigenes and translate them into amino acid sequences. The CDS of unigenes that had no Blastx hit was predicted based on the ESTScan results and their translation into amino acid sequences; these unigenes were singificantly less than those whose prediction of CDS was based on BLAST results. The predicted CDS length (predicted from both BLAST results and ESTScan) was less than 500 nt with the majority of CDS being approximately 300 nt size.
Among the 36,504 unigenes with one at least GO-term given, 40.6 % were annotated in the biological process, 38.9 % in the cellular component and 20.4 % in the molecular function (for the detailed classification of the unigenes in the individual GO-terms of the three GO ontology domains see Additional file 2: Figure S2). Furthermore 19,911 unigenes were classified in 25 COG functional categories. For most of the unigenes only a general function prediction is possible (6,606 unigenes) while the next most abundant categories are transcription (3,333 unigenes), replication, recombination and repair (3,192 unigenes) and signal transduction mechanisms (2,905 unigenes) (for the detailed classification of S. elaeagnifolium unigenes according to COG see Additional file 3: Figure S3).
Expression of unigenes
Transcript abundances were estimated for S. elaeagnifolium unigenes by the RSEM software . The complete list of the 20 most expressed genes in S. elaeagnifolium leaves and flowers is presented in Table 2. The comparison of S. elaeagnifolium leaf and flower transcriptome expression results of the present study, produced by RSEM analysis, with other Solanaceae transcriptomes has shown that the majority of the most abundant transcripts are common inside the family. For instance, the most abundant transcripts in S. elaeagnifolium leaves and flowers encode a putative subunit of the ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) protein, a Rubisco activase, putative lipid-transfer proteins, proteins involved in chlorophyl binding and photosystem I and II, a S-adenosylmethionine decarboxylase (SAMDC) etc. Most of these transcripts are universally identified as strongly expressed in Solanum databases (tomato, potato transcriptomes) [21, 22]. Transcripts strongly expressed that code for metallothioneins (MTs) are also found. MTs are proteins that bind metal ions and are classified in four classes/types depending on the amount and the arrangement of their cysteine-rich domains . MT proteins are known to respond to metal presence but also may play a role in reactive oxygen species detoxification [for a review on MT roles see . An additional abundant S. elaeagnifolium transcript encodes a putative plastidic aldolase, an enzyme [Enzyme Commission number (EC): 220.127.116.11] that catalyzes the formation of d-glyceraldehyde-3-phosphate (GAP) and dihydroxyacetone phosphate (DHAP) from fructose-1,6-bisphosphate (FBP). Two plastidic aldolases from species N. paniculata were found in the leaves of this plant known for its tolerance in low-water conditions . S. elaeagnifolium gene shares a high homology (>90 %) with these genes both responding also to salt stress .
Third in abundance is a S. elaeagnifolium transcript (unigene21118) that presents 84 % homology to a tomato pathogenesis-related (PR) protein [iTAG v2.3: Solyc09g007010]. A similar PR protein is produced by another abundant transcript (cl9785) that is highly similar to a tomato gene [Solyc01g106620] annotated as PR1a gene. Both transcripts are significantly higher expressed in S. elaeagnifolium than their corresponding tomato and potato putative orthologs. The potato ortholog PR1 gene [GenBank: AJ250136.1] was isolated from P. infestans infected leaves and is induced significantly under pathogen and elicitor attack although it is expressed under normal conditions as well. The second S. elaeagnifolium transcript, cl9785, is highly similar to tomato PR1 precursor [NCBI: NP_001234358] that is not expressed at all in tomato flowers or leaves while the corresponding potato gene, a PR1-like gene [Potato genomics resource: PGSC0003DMT400013094] has low expression in potato flowers and leaves. Cl9785 deduced protein sequence shares 83 % identity with pepper PR1 precursor protein that was found to be induced under bacteria infection and possibly linked with the stimulation of ethylene synthesis .
Finally, one more highly expressed transcript, cl9787_2, shares significant similarity with a HT-B gene from S. peruvianum, a gene involved in the self-incompatibility of wild Solanum genera and is not expressed in self compatible species like S. lycopersicum . The strong expression of the gene in S. elaeagnifolium provides molecular evidence for the outcrossing of the species, common in wild Solanums. S. elaeagnifolium has another probable HT gene (cl9787_1) that is also expressed in flowers and leaves but lower than cl9787_2.
Identification of genes involved in terpene biosynthesis in S. elaeagnifolium
Plants use a number of secondary metabolites to cope with their abiotic and biotic environment and terpenes lie in the first line of plant defence against the risks posed. Not only terpenes are responsible for the biosynthesis of necessary hormones that facilitate plant responses, but oxidative and thermal stresses are also alleviated by terpene production . Furthermore, some monoterpenes have been implicated in allelopathic effects . Because of the importance of plant terpenes in a plethora of biological processes related to stress responses and since S. elaeagnifolium is a resiliant species that grows even on degraded soils, emphasis was laid on this group of secondary metabolites.
Employing BLAST suite of programs on S. elaeagnifolium unigenes, genes of the MVA and MEP pathways likely to participate in the biosynthesis of terpene precursors, as long as TPS genes were identified. The complete list of the putative genes involved in the MVA and MEP pathways is included in Table 3. Genes for key enzymes, such as 3-hydroxy-3-methylglutaryl-coenzyme A reductase (HMGR) [EC: 18.104.22.168] and DXS [EC: 22.214.171.124] have (as in tomato) multiple paralogues that are all expressed significantly in leaves and flowers. Putative S. elaeagnifolium acetoacetyl CoA thiolase (AACT) [Solyc07g045350], HMGR1 [Solyc02g082260] and 2-C-methyl-d-erythritol 4-phosphate cytidylyl-transferase (MCT) [Solyc01g102820] genes are present in the transcriptome as multiple alleles. Also genes involved in prenyl diphosphate synthesis, such as farnesyl pyrophosphate synthase (FPPS) and geranylgeranyl pyrophosphate synthase (GGPPS), also have many paralogues. Finally, several putative cis-prenyltransferase genes (CPT) believed to be involved in the biosynthesis of long-chain polyisoprenoids were also identified in S. elaeagnifolium. Two of them (cl6054.contig2 and cl6054.contig4) have homology to CPT5. For the complete list of the putative S. elaeagnifolium TPS genes identified in leaves and flowers, see table in Additional file 4: Table S1.
Three TPS genes (cl7653, cl1310 and cl9841), the putative HMGR1 gene (cl1634), and the DXS2 gene (unigene2314) were selected for further analysis. The specific TPS genes were selected for study because they are putatively involved in the production of all three major classes of terpenes, mono-, di- and sesqui- terpenes. HMGR and DXS code for critical enzymes of the two terpene biosynthesis pathways . According to BLAST results, HMGR1 has three alleles; three contigs that belong to the cluster cl1634. Cl1634 contigs 1, 2 and 4 have 92, 95 and 91 % similarity with tomato HMGR1 and all have significant FPKM values in the pooled mRNA from leaves and flowers (Table 3). On the contrary, unigene2314 is the only S. elaeagnifolium sequence that has high homology (92 %) with a tomato characterized DXS gene (Table 3).
For the putative TPS genes, transcript cl7653 is a cluster of eight sequences. Analysis of the sequences included in cl7653 indicates alternative splicing events taking place during the transcription of the corresponding gene. The different transcripts differ in three regions: in the first, four sequences have a 122 nt insertion, in the second, four sequences have a 94 nt insertion and in the last, four sequences have a 88 nt insertion. None of the inserted sequences has an open reading frame (ORF) indicative of functional proteins. Only one transcript/sequence of 2,143 nt contains a 1,653 nt putative CDS sequence that codes for a full 550 amino acid protein. The sequence, named hereafter cl7653, is the one with the highest FPKM value in flowers and leaves (see table in Additional file 4: Table S1) while the other seven transcripts/sequences have lowest FPKM values.
The alignment of cl7653 predicted protein sequence with closely related tomato proteins TPS9-sesquiterpene synthase 1 [NCBI: NP_001234481], TPS10 and TPS12 (also known as caryophyllene/α-humulene synthase - CAHS) [GenBank: AEP82783] shows a high conservation of amino acids throughout their length (Fig. 2a). TPS9 and TPS12 are known and characterized sesquiterpene synthases. The deduced cl7653 protein contains the DDxxD and NSE/DTE motifs (both boxed in Fig. 2a) that characterize TPS proteins.
The second putative TPS gene in study, cl1310, is a cluster of 25 sequences. However according to RSEM analysis only two of them are expressed above a FPKM threshold of 3. The two sequences differ only in a 131 nt insertion, indicating that one could correspond to an incompletely spliced transcript. The sequence of 2,801 nt that contains no intron sequence and has the highest expression in flowers and leaves, was analyzed and annotated hereafter as cl1310. Cl1310 possess a predicted CDS of 2,414 nt that codes for a 897 amino acids protein. The predicted protein shares 89 % similarity with the predicted ent-kaurene synthase (KS) protein from potato [NCBI: XP_006346019], 86 % similarity with tomato TPS24-KS protein [GenBank: AEP82778] [EC: 126.96.36.199] and 83 % similarity with N. attenuata KS protein [GenBank: AFA35954]. The alignment of tomato TPS24-KS protein with the predicted cl1310 amino acid sequence showed that the S. elaeagnifolium protein also contains the aspartate-rich DDxxD and NSE/DTE motifs both identical to tomato TPS24-KS corresponding motifs (Fig. 2b).
The third TPS gene identified, transcript cl9841 is a cluster of 9 sequences but only one is expressed in leaves and flowers; it contains a 1,824 nt putative CDS sequence that encodes a 607 amino acid full protein. The protein shares 78 % similarity with tomato TPS3 protein, a monoterpene camphene/tricyclene synthase [GenBank: AEM05853] and a putative camphene/tricyclene synthase from potato [NCBI: XP_006351730].
Functional characterization of S. elaeagnifolium putative TPS genes in yeast cells
The yeast strain AM94  was used to transform cl9841 putative monoterpene synthase together with the ERG20 (F96W-N127W) variant which shifts production towards GPP substrate . For the expression of cl1310, the gene was co-expressed in AM238 cells together with copalyl diphosphate synthase from Salvia pomifera and a variant of yeast ERG20 (F96C) producing GGPP. For the characterization of the putative sesquiterpene cl7653, the yeast strain AM109 was used . The cl7653 carrying plasmid was transformed either alone or together with a stabilised variant of HMG2(K6R) to increase substrate availability . As seen in Fig. 3a, cl9841 is an active monoterpene synthase enzyme producing a range of monoterpenes with the most prominent being camphene (52.55 %), β-myrcene (11.01 %) and limonene (10.44 %) and several minor additional compounds. The cl1310 expressing cells did not produce any compounds. The cl7653 enzyme was active and less promiscuous than cl9841, producing mainly caryophyllene (86.4 %) and lesser amounts of α-humulene (Fig. 3b). The caryophyllene peak was additionally validated with the mass spectrum of a standard compound.
Gas Chromatography/Mass Spectrometry (GC/MS) analysis of wounded leaves
GC/MS qualitative and semi-quantitative analysis was carried out for collected leaves, 4 hours (h) after their mechanical wounding. Unwounded leaves were also collected. The results are given in Tables 4 and 5. In particular, each leaf extract component is cited and accompanied by its retention time and a peak area percentage calculated by the GC/MS Solution software. Table 4 shows the common compounds detected both in unwounded and wounded leaves. Wounding can significantly affect the concentration of substances which are mainly aldehydes, ketones and alcohols.
The substances induced in wounded leaves are included in Table 5. What is interesting to point out is that the majority of the compounds with peak area over 0.2 % are aldehydes previously associated with wounding responses. (E)-caryophyllene is also induced by the wounding procedure as it was detected in the GC/MS chromatogram of the wounded leaves at 23.83 min. From Fig. 4, it is obvious that the characteristic peaks of (Z)-jasmone and (E)-caryophyllene occur only in the chromatogram of the wounded leaves. The presence of (E)-caryophyllene and geranyl linalool in wounded leaves was also validated by comparing both the peak retention times and mass spectra between the unknown samples and standards. The mass spectra of the later as acquired from unknown samples are illustrated in figures in Additional file 5: Figure S4 and Additional files 6: Figure S5 respectiverly, with typical mass fragments at m/z 133, 93, 69 for (E)-caryophyllene and 69, 81, 41 for geranyl linalool respectively.
Wounding and TPS expression
Since GC/MS analysis conducted in wounded leaves showed the rise in the synthesis of the sesquiterpene (E)-caryophyllene, the expression of cl7653 identified as caryophyllene synthase, was studied in real-time PCR experiments. Given that no monoterpene compounds were detected in the extractions of wounded leaves, the expression of cl9841 was not studied. What was studied was the expression of cl1310 - putative KS, of unigene2314 - putative DXS2 and of cl1634 - putative HMGR1 along with the allene oxide cyclase (AOC) gene, a gene involved in the formation of jasmonic acid (JA) and quickly induced by wounding in tomato leaves [34, 35]. Primers were designed to amplify the specific contigs of each of the clusters cl7653 and cl1310 (as analyzed above) while for cluster cl1634 primers were designed to amplify a common region of all three alleles.
As shown in Fig. 5, wounding of S. elaeagnifolium leaves induced the expression of the S. elaeagnifolium AOC homolog gene in all time points tested, providing evidence that plants undertake responses related to the wounding stress. The expression of sesquiterpene - caryophyllene synthase gene cl7653 was increased in all wounding time points compared to the control, the unwounded leaves (leaves from three independent controls-plants). The increase in the expression of cl7653 was quickly recorded at the time point 30 min after wounding. Yet the most pronounced increase in the expression of the caryophyllene synthase cl7653 was 2 h after wounding where the gene was expressed nearly 25 times significantly more than in the control. At the last time point, 4 h after wounding, the cl7653 expression was still significantly higher than the control but less than in the 1 and 2 h time points. On the other hand, the expression of unigene2314 - putative DXS2 gene is induced later than that of cl7653. However in its peak of expression, also at the 2 h after wounding time point, unigene2314 was expressed 50 times more significantly than in the control. Interestingly its expression fell sharply reaching the same expression as in the control unwounded leaves at 4 h after wounding. The expression of putative HMGR1 - cl1634 and KS - cl1310 remained unchanged (data not shown).
The S. elaeagnifolium transcriptome
S. elaeagnifolium mRNA from leaves and flowers was sequenced and reads were used to build a de novo S. elaeagnifolium transcriptome. The inclusion of the two tissues in the RNAseq libraries provides a representative sampling of the genes expressed in this wild and unexplored Solanum species. From the 75,618 unigenes assembled nearly 67 % was annotated by using the NR database. The percentage of annotated transcripts is similar to the N. benthamiana annotated sequences based on GenBank database (68.83 %) . However the proportions of S. elaeagnifolium unigenes that present matches with sequences in Swiss-Prot, KEGG, COG and GO databases were lower: 42 %, 39 %, 26 % and 48 % respectively. A percentage of 33 % of the unigenes had no NR hit, a number lower than the number of transcripts that remained without NR annotation in the de novo sequencing of sweet potato  but larger than those without NR annotation in chili pepper . The terms “binding and catalytic activity”, “cell and cell part”, “metabolic and cell process” were the most representative of the three main GO categories of cellular component, molecular function and biological process, assigned to the assembled S. elaeagnifolium unigenes. Similar results were obtained from annotating the transcripts of sweet potato . An interesting finding is that 20.4 % of the S. elaeagnifolium unigenes are classified as “response to stimulus” in the biological process GO category. Given the species tolerance to environmental stresses, genes involved are probably categorized in this percentage.
Transcript quantification estimated by RSEM software in S. elaeagnifolium leaves and flowers showed that most of the transcripts expressed amply are universally found to be strongly expressed in other Solanum databases, while some are unexpectedly abundant in S. elaeagnifolium leaves and flowers such as the PR transcripts. PR1 proteins are known defence-related proteins used by the plants in systemic acquired resistance. The high expression of these two putative PR genes in S. elaeagnifolium may imply that the plant has a priori constitutive defence mechanisms that make it resistant to pathogen attack. The constitutive expression of PR proteins is common in resistant cultivars  and has been suggested as a modern breeding goal.
Analysis of wounded S.elaeagnifolium leaves
Mechanical wounding resulted in the induction of a plethora of important chemical compounds in S. elaeagnifolium leaves. Among them, the sesquiterpene (E)-caryophyllene an attractant for natural enemies that parasitize herbivores. Recently it was found that caryophyllene has an anti-bacterial activity in flowers of Arabidopsis plants . Furthermore the volatile jasmone was the key compound detected in abundance in our wounded S. elaeagnifolium leaves indicative of the damage done. Jasmone, a product of jasmonic acid, is implicated in various aspects of plant defence . This finding agrees with the rise in the expression of the JA related, wounding-monitoring AOC gene, recorded in wounded leaves. Apart from jasmone, the majority of the rest of the compounds found were aldehydes and ketones. n-Nonanal and (E)-2-decanal are common volatile compounds that contribute to aroma in tomato and other fruits. Interestingly, nonanal and decanal were also detected in wounded tomato leaves but their concentrations did not vary significantly from unwounded controls . Nonanal was also found to be induced in damaged poplar leaves . (E)-2-decenal from Ailanthus altissima was found to have activity towards nematodes of the Meloidogyne genus . (E)-2-decenal oil from the plant Coriandrum sativum was found to have anti-fungal activity as vapor against Botrytis, Alternaria and Geotrichum . N-hexadecane, n-heptadecane and n-octadecane are also volatile compounds detected in many plants [46, 47].
Geranyl linalool is a diterpene alcohol produced by GGPP via the MEP pathway. Geranyl linalool further produces the volatile (E,E)-4,8,12-trimethyltrideca-1,3,7,11-tetraene (TMTT), an insect-induced terpene that is released from plants such as Arabidopsis and tomato under the attack of herbivores [48, 49]. It was shown that in tomato both geranyl linalool and TMTT are induced by JA treatment .
Terpene related genes and their expression after wounding
As a tentative to isolate genes related to terpene biosynthesis from S. elaeagnifolium we retrieved putative TPS genes using BLAST algorithms. Cl7653 was the one most expressed putative TPS. Its deduced amino acid sequence shares high homology (79 %) with sesquiterpene synthase Lycopersicum hirsutum2 (SSTLH2) protein from S. habrochaites that catalyzes the formation of germacrene D . Cl7653 is similar to tomato sesquiterpene synthases genes TPS9, TPS10, TPS12 and two SSTLH from S. habrochaites. TPS12 synthesizes β-caryophyllene and α-humulene . Cl7653 is wounding-responsive in S.elaeagnifolium leaves. Its induced expression that peaked 2 h after wounding suggests that probably this gene is involved in the defence plant system. In agreement with this increase in cl7653 transcriptomic activity, 2 h after wounding, CG/MS analysis has certified the increase in (E)-caryophyllene emission in wounded leaves 2 h after the cl7653 transcription peak, making highly probable that cl7653 is actually the gene responsible for the production of caryophyllene in S. elaeagnifolium. The particular finding is in accordance with the results in yeast cells showing that the expression of cl7653 produces (E)-caryophyllene. A (E)-caryophyllene synthase in maize was increased after attack in roots by Diabrotica virgifera larvae and in leaves by Spodoptera littoralis. The gene has a breeding value since it is low expressed in North American maize cultivars while it is higher in European ones . Cotton roots that have been treated with methyl-jasmonate also show an increase in a TPS that produces (E)-caryophyllene indicative of the involvement of this gene in herbivory attack defense systems . A similar wounding-responsive profile is also adopted by the S. elaeagnifolium putative DXS gene - unigene2314; its expression is even more pronounced than TPS cl7653 but it drops more drastically as the time after wounding proceeds. DXS is a gene involved in the MEP pathway, residing in the chloroplasts normally involved in monoterpenoid production (i.e. camphene) and diterpene production (i.e geranyl linalool). Normally the knockdown of DXS2 leads to the production of more sesquiterpenes than monoterpenes in tomato  but work in S. habrochaites has shown that sesquiterpenes may also be produced in the chloroplasts . There is also evidence that IPP and DMAPP may be transferred from the chloroplasts to the cytosol so that such DXS produced precursors are integrated to sesquiterpenes . In the present wounding experiment the non-induced putative HMGR1 combined with the high induced putative DXS2 and TPS12 (cl7653) showed that probably in S. elaeagnifolium the MEP pathway provides more terpenoid precursors for the production of sesquiterpenes than the MVA pathway.
S. elaeagnifolium is an important invasive species and a serious threat for crops in several areas around the world. Here, a leaves and flowers transcriptome was generated by next-generation sequencing, identifying 75,618 unigenes with mean length of 1,082 nt. Analysis of transcript abundance showed several genes associated with stress resistance. Some of them such as PR-like genes were uniquely abundant to S. elaeagnifolium. Leaf wounding experiments showed induction of numerous aldehydes, most of them known to participate in biotic stress resistance. Additionally, two terpenes, (E)-caryophyllene and geranyl linalool were detected in wounded tissues. Analysis of identified full length TPS genes identified a caryophyllene synthase and a camphene synthase. Real-time PCR confirmed the up-regulation of the caryophyllene synthase upon wounding and putative DXS2 which could relate to geranyl linalool and (E)-caryophyllene.
RNA sequencing and annotation of unigenes
For RNA-seq libraries total RNA was extracted from leaves and flowers of at least four S.elaeagnifolium open-field plants. mRNA was isolated using the FastTrack MAG mRNA isolation kit (Life technologies, Carlsbad, CA, USA). Mixed with the fragmentation buffer, mRNA was fragmented and the cDNA synthesized using the mRNA fragments as templates. Short fragments were purified and resolved in elution buffer, for end reparation and single nucleotide A addition. After that, the short fragments were connected with adapters. The suitable fragments were selected for the PCR amplification as templates. During the quality control steps, Agilent 2100 Bioanaylzer and ABI StepOnePlus Real-Time PCR System were used in quantification and qualification of the sample library. Finally, the library was sequenced on a Illumina HiSeq™ 2000 or other sequencer when necessary.
The raw reads produced by the sequencing were cleaned; reads with adaptors, with uknown nucleotides more than 5 %, and low quality reads were removed. Reads were de novo assembled into contigs using the Trinity suite . The resulting contigs, called unigenes, were clustered in families and unigenes were divided into two classes. One is clusters, with the prefix cl, containing several unigenes whith similarity between them more than 70 %. The other is singletons with the prefix unigene. In the final step, blastx alignment (e-value <0.00001) between unigenes and protein databases like NR, Swiss-Prot, KEGG and COG was performed, and the hits with the highest similarity were used to decide the sequence direction of unigenes. If results of different databases conflicted with each other, a priority order of NR, Swiss-Prot, KEGG and COG was followed. When a unigene could not be aligned to the above databases, ESTScan  was used to decide the sequence direction. A summary of the pipeline is presented in figure in Additional file 7: Figure S6.
Unigenes were classified in different classes and assigned GO and COG functional annotation. Blast2GO program  was used to get GO annotation of unigenes based on NR. After GO annotation, WEGO software  was used to do GO functional classification for all unigenes.
Transcript quantification was estimated from RNA-seq data using the RSEM software package. Unigenes were used as reference to estimate the abundance of expression based on the paired-end RNA-Seq data using the standard instructions and parameters as described in http://deweylab.biostat.wisc.edu/rsem/README.html.
Bioinformatics analysis for identifying S. elaeagnifolium terpene-related genes
A dataset of expressed terpenes-related genes from tomato and other Solanum species, was formed using sequences retrieved from the NCBI protein database. Terpene-related genes included the genes involved in the production of proteins of the MVA and MEP pathways and TPSs. The proteins of this dataset were used as queries in BLAST searches (tblastn algorithm, e-value 10−8) against our S. elaeagnifolium unigenes database. Several unigenes (both in clusters and singletons) were retrieved similar to Solanum genes. Emphasis was given in our study on five genes (unigenes), two encoding key proteins of the MVA and MEP pathways and three, important for the biosynthesis of terpenes, TPS proteins.
Wounding and expression by real-time PCR
S. elaeagnifolium seeds were collected from open-field plants fruits grown in the Aristotle university farm. The seeds were left to dry and then placed in water for 5 days in the dark. The emerging plantlets were then sown in small pots in the greenhouse until their transplantation in larger pots under stable temperature conditions. For the mechanical wounding experiment, leaves from plantlets with up to six to eight true leaves were cut with scissors and were collected 30 min (time point 1), 1 h (time point 2), 2 h (time point 3) and 4 h (time point 4) after wounding. Four plants were wounded and their leaves were collected in each time point while leaves were collected also from three control plants (unwounded, time point 0). All leaves, wounded and unwounded, were immediately frozen in liquid nitrogen and stored at -80 °C. Total RNA was extracted using the TRIzol Reagent according to the manufacturer’s protocol (Life technologies). The quantity and quality of the extracted total RNA was assessed by gel electrophoresis. First strand cDNA synthesis was carried out using as template 1 μg of each extracted total RNA, 0.5 mM dNTPs, 1× First-strand buffer, 10 mM DTT, 200 units (U) SuperScript II reverse transcriptase (Life technologies) and 250 ng random hexamers in 20 μl total volume, according to the manufacturer’s protocol.
Relative quantitative expression analysis was performed using primers (see table in Additional file 8: Table S2) specifically designed for real-time PCR amplification and -where possible- in two different exons based on information retrieved from the tomato gene orthologs. Real-time RT-PCR reactions were performed in a Rotor Gene 6000 (Qiagen) realtime PCR system. The reactions were performed in 1× KAPA SYBR® FAST Universal 2× qPCR master mix (Κapa Biosystems, Wilmington, MA, USA) containing 0.5 μM of each primer. The template was 1 μl of cDNA dilutions synthesized as described above. The cycling parameters were incubation at 95 °C for 2 min, followed by 30 or 35 cycles of 95 °C for 5 s, 60 °C for 20 s, 72 °C for 5 s, and a final extension step of 10 min at 72 °C. For the identification of the PCR products, a melting curve analysis was performed from 65 to 95 °C with each observation taken every 0.2 °C and a 5 s hold between observations. The AOC gene was used as a wounding monitoring control gene. The S. elaeagnifolium putative AOC ortholog (unigene23589) was identified using BLAST algorithms. The eukaryotic translation elongation factor-1a (EF1a) gene was used as reference; using BLAST algorithms the putative EF1a gene (cl630) was retrieved from S. elaeagnifolium unigenes bearing high similarity with tomato [NCBI: NM_001247106.1] and potato [GenBank: AB061263.1] EF1a genes (for AOC and EF1a primers see table in Additional file 8: Table S2). Two technical replications were performed for each biological replication i.e. each wounded plant. Relative quantitation and statistical analysis were performed using the REST software .
Samples from wounded and unwounded leaves (stored at -80 °C) were also used for GC/MS analysis. Leaves were collected 4 h after wounding. Leaves samples were pulverized in a mortar under liquid nitrogen. About 1 g of fine powder was extracted with 4 ml of a hexane:diethyl ether (90:10 v/v) mixture using vortex for 1 min. The mixture was then centrifuged for 2 min at 20,238 g. After the phase separation, the supernatant liquid was collected, dried with anhydrous sodium sulfate and filtered through a PTFE syringe filter (0.45 μm × 25 mm). The resultant extract was then concentrated to a final volume of 0.2 ml under nitrogen purge prior to GC/MS analysis. Leaf extracts were analyzed using a GC-2010 Plus Shimadzu gas chromatograph equipped with a GCMS-QP2010 Ultra gas chromatograph mass spectrometer, and a MEGA-5MS capillary column (30 m × 0.25 mm, 0.25 μm film thickness), in the splitless mode. The temperature of injector and detector was 250 °C and 300 °C respectively. The oven temperature was slowly increased with a rate of 3 °C/min from 60 °C up to 240 °C and maintained at this temperature for 5 min to equilibrate. Then the temperature was raised with 10 °C/min at 290 °C and kept isothermally for 10 min in order to elute compounds with higher boiling points. The carrier gas used for the analysis was helium at a flow rate of 1.3 ml/min. Mass spectra were acquired in a scan mode, while qualitative analysis was based on library search by using the following mass spectral libraries: FFNSC GC/MS Ver. 1.3 and Metabolite Component Database by Shimadzu, Wiley 7, NIST 11 and NIST 11 s.
Terpene production and analysis from yeast cells
Yeast strains grown on selective plates media were used to inoculate 5 ml liquid cultures incubated overnight at 30 °C. For sesquiterpene analysis, an overlay of 500 μl dodecane (1:10 v/v) was then added and the mixture was incubated for additional 2 days at 30 °C with shaking. Dodecane phase was isolated, centrifuged (20,238 g, 2 min) and about 100 μl were removed to be injected for GC analysis. Dodecane (≥99 %) and n-hexane (≥99 %) used for yeast extraction and standard preparation were both purchased from Sigma-Aldrich (St. Louis, MO, USA). Dodecane extracts from yeast cultures were analyzed using a GC-2010 Plus Shimadzu gas chromatograph-mass spectrometer as above. The temperature of injector and detector was 230 °C and 270 °C respectively. The oven temperature was initially held at 60 °C for 3 min and subsequently increased up to 190 °C with a rate of 10 °C/min. Then the temperature was slowly raised with 3 °C/min at 230 °C and kept isothermally for 20 min. The carrier gas used for the analysis was helium at a flow rate of 1.66 ml/min. For the qualitative and quantitative analysis, stock solution of caryophyllene in hexane was made and a calibration curve was drawn from the prepared working solutions. Monoterpene production from yeast cells was carried out as above, using an overlay of diisononyl phthalate (≥99 %) purchased from Sigma-Aldrich. The extracts were analysed by means of GC/MS with temperature of injector and detector at 230 °C and 300 °C correspondingly. The oven temperature was increased with 3 °C/min from 60 °C to 240 °C, maintained at this temperature for 5 min to equilibrate and subsequently elevated with a rate of 10 °C/min with a final isotherm at 290 °C for 5 min.
Availability of data
Illumina Hiseq 2000 raw transcriptome sequences are available at NCBI SRA database under the experiment accession number SRX1030234.
1-deoxy-D-xylulose-5-phosphate synthase 2
Potato virus Y
Tomato yellow leaf curl virus
Expressed sequence tags
Simple sequence repeat
Basic local alignment search tool
Kyoto encyclopedia of genes and genomes
Clusters of orthologous groups
Coding DNA sequence
Fragments per kilobase of exon per million fragments mapped
Enzyme commission number
3-hydroxy-3-methylglutaryl-coenzyme A reductase
Acetoacetyl CoA thiolase
2-C-methyl-d-erythritol 4-phosphate cytidylyl-transferase
Farnesyl pyrophosphate synthase
Geranylgeranyl pyrophosphate synthase
Tomato functional genomics database
Gas Chromatography/Mass Spectrometry
Allene oxide cyclase
Sesquiterpene synthase Lycopersicum hirsutum2
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This work was supported by the projects SysTerp (09SYN-23-879) and NUTRITOM (11SYN-3-480). Continuous support for the Institute of Applied Biosciences/CERTH from the General Secretariat of Research and Technology of Greece is also acknowledged.
The authors declare that they have no competing interests.
AT participated in the design of the study, carried out wounding experiment, gene expression and bioinformatics analyses and prepared the manuscript, AN, FT, CI, SK conducted experiments on terpene synthases, GC-MS analysis, and data analysis, AM participated in the design of the study, cloning and data analysis and AA is responsible for the overall supervision of the work. All authors read and approve the final manuscript.
The length distribution of assembled contigs and unigenes. On the x- axis the contigs and unigenes length in nucleotides (nt) and on y- axis the number of contigs and unigenes of each length.
GO category assignment for S. elaeagnifolium unigenes. Unigenes were categorized in the three categories of molecular function, cellular component and biological process. Most abundant GO-terms are cell in cellular component category, metabolic process in biological process category and binding in molecular function category.
Classification of S. elaeagnifolium unigenes into COG functional categories.
S. elaeagnifolium unigenes that bear similarity with annotated Solanaceae TPS genes. In some cases more than one unigenes have a hit on the same TPS in different sites. In the last column the FPKM values of unigenes are reported. The TPSs analyzed in the study are highlighted in bold.
Mass spectrum of (E)-caryophyllene detected in wounded leaves.
Mass spectrum of geranyl linalool detected in wounded leaves.
The pipeline used in the assembly process of S. elaeagnifolium mRNA reads. After the assembly of reads into contigs and the mapping of reads again into contigs, contigs were assembled in clusters of unigenes (prefix cl). All contigs not included in clusters remained as singletons (prefix unigene).
Primers used in the experiments and their sequences.
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Tsaballa, A., Nikolaidis, A., Trikka, F. et al. Use of the de novo transcriptome analysis of silver-leaf nightshade (Solanum elaeagnifolium) to identify gene expression changes associated with wounding and terpene biosynthesis. BMC Genomics 16, 504 (2015). https://doi.org/10.1186/s12864-015-1738-3
- Basic Local Alignment Search Tool
- Enzyme Commission
- Tomato Yellow Leaf Curl Virus