Background: Aloe vera is a perennial, succulent, drought-resistant plant that exhibits many pharmacological characteristics such as wound healing ability against skin burns, anti-ulcer, anti-inflammatory, anti-tumor, anti-viral, anti- hypercholesterolemic, anti-hyperglycemic, anti-asthmatic and much more. Despite great medicinal worth, little genomic information is available on Aloe vera. This study is an initiative to explore the full-scale functional genomics of Aloe vera by generating whole transcriptome sequence database, using Illumina HiSeq technology and its progressive annotation specifically with respect to the metabolic specificity of the plant. Results: Transcriptome sequencing of root and leaf tissue of Aloe vera was performed using Illumina paired-end sequencing technology. De novo assembly of high quality paired-end reads, resulted into 1,61,733 and 2,21,792 transcripts with mean length of 709 and 714 nucleotides for root and leaf respectively. The non-redundant transcripts were clustered using CD-HIT-EST, yielding a total of 1,13,063 and 1,41,310 unigenes for root and leaf respectively. A total of 6114 and 6527 CDS for root and leaf tissue were enriched into 24 different biological pathway categories using KEGG pathway database. DGE profile prepared by calculating FPKM values was analyzed for differential expression of specific gene encoding enzymes involved in secondary metabolite biosynthesis. Sixteen putative genes related to saponin, lignin, anthraquinone, and carotenoid biosynthesis were selected for quantitative expression by real-time PCR. DGE as well as qRT PCR expression analysis represented up-regulation of secondary metabolic genes in root as compared to leaf. Furthermore maximum number of genes was found to be up-regulated after the induction of methyl jasmonate, which stipulates the association of secondary metabolite synthesis with the plant’s defense mechanism during stress. Various transcription factors including bHLH, NAC, MYB were identified by searching predicted CDS against PlantTFdb. Conclusions: This is the first transcriptome database of Aloe vera and can be potentially utilized to characterize the genes involved in the biosynthesis of important secondary metabolites, metabolic regulation, signal transduction mechanism, understanding function of a particular gene in the biology and physiology of plant of this species as well as other species of Aloe genus. Keywords: Aloe vera, Next generation sequencing, Transcriptome, De novo assembly, Secondary metabolism, Differential gene expression * Correspondence: firstname.lastname@example.org Department of Bio and Nano Technology, Guru Jambheshwar University of Science and Technology, Hisar, Haryana 125001, India Full list of author information is available at the end of the article © The Author(s). 2018 Open Access This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated. Choudhri et al. BMC Genomics (2018) 19:427 Page 2 of 21 Background determined by the various complex interactions between The genus Aloe belongs to the family Xanthorrhoeaceae, the genome, gene products, and metabolites. Various subfamily Asphodeloideae consisting ofmany shrubby functional genomics approaches are now emerging as tropical/subtropical plant species with succulent and powerful tools to accelerate the comprehensive under- elongated leaves. The genus contains more than 360 standing of the molecular basis of biological functions. species, out of which only four have been reported to Genomics approaches have also proved to be significant exhibit medicinal properties: Aloe vera, Aloe arborescens, tools in identifying transcription factors, and candidate Aloe ferox, and Aloe perryi. Among all the species, Aloe genes involved in the plant’s secondary metabolism . vera Linne Synonym Aloe barbadensis Miller is considered Next-generation sequencing technology has revolution- to be medicinally most potent, therefore, it is most ized the genomics field by providing a rapid, cost- effect- popular [2, 3]. Aloe vera shows innumerable medicinal ive and efficient gene sequencing data, enabling the attributes such as skin burn healing , anti-inflammatory identification of genes related to metabolic pathways, es- , hepatoprotective , anti-tumor , anti-ulcer , pecially in non-model plants for which no reference gen- antihypercholesterolemic , anti-hyperglycemic , ome is available; for instance; American ginseng,  anti-asthmatic and antioxidant activities . Aloe Eucalyptus,  rubber tree  and many more. vera extracts have been demonstrated to be advanta- Transcriptome sequencing using Illumina mRNA-Seq geousinthe treatmentofevenAIDS. It has reads has proved to be an efficient approach in many similar anti-aging effects as exhibited by vitamin A plants for which transcriptome data is validated and derivatives . analyzed as well, including Eucalyptus,  blackberry, Aloe vera contains numerous active ingredients  Uncaria,  Lolium, orphan,  sesame,  including anthraquinones, polysaccharides, alkylben- alfalfa,  sweet potato,  Centella,  Ocimum zenes, dehydrabietic acid derivatives, salicylic acid, lectin, pear, rose-scented geranium,  Withania carotenoids, lignin, saponins etc. that attribute for its somnifera . The present study used NGS technology high therapeutic value . Many of the medicinal prop- for whole transcriptome sequencing of Aloe vera root and erties of Aloe vera are ascribed to secondary metabolites leaf tissues, performed using Illumina Hi-Seq technology. though they are relatively minor in their concentration It provides valuable sequence information from Aloe vera in the plant (< 1% dry weight) . Aloe vera exhibits root and leaf tissues with special emphasis on genes re- antibacterial property because of anthraquinones that lated to secondary metabolic pathways. Genes related to behave like tetracycline by blocking the ribosomal A site, secondary metabolic pathways were examined for differ- thus, interrupting bacterial protein synthesis . ential expression in root and leaf tissue by quantitative Saponins are another important group of secondary me- real-time PCR. Real-time PCR comprises a dynamic range, tabolites synthesized as defensive compounds against remarkable sensitivity, and sequence-specificity that en- pathogenic microbes and herbivores [18–20]. Saponins ables additional independent confirmation of NGS based present in Aloe vera also act as an effective data  Methyl jasmonate treatment was given to the ex- anti-microbial agent against various bacteria, viruses, perimental plant to check the relative expression of genes fungi, and yeasts . Aloe vera extract act as an anti- under stress conditions at different time intervals. The oxidant due to carotenoids present in it . Lignins transcriptome sequencing and analysis provides a strong present in Aloe vera penetrate deep into the skin and platform of genomic sequences, to serve biosynthetic help in introducing other medicinal ingredients to pene- pathway and metabolic engineering programs of basic as trate into the skin. Therapeutic effects of Aloe vera have well as applied research on Aloe vera and catalyze path of not been correlated well with individual metabolite and its change of use from extracts to molecules. it remains unknown whether the biological activities of the plant are due to a single component or the collab- Results orative efforts of many components . De novo transcriptome assembly and validation An increasing trend where consumers tend towards a Illumina Hi Seq platform sequencing results of cDNAs healthy lifestyle, coupled with the increased use of Aloe prepared from total RNA when processed by removing vera extracts as an ingredient in food, pharmaceutical the adapter sequences, ambiguous reads i.e. reads with and cosmetics products, increases its market growth unknown nucleotides “N” larger than 5%, and low-quality across the globe. International Aloe Science Council sequences i.e. reads with more than 10% quality threshold, (IASC) estimated that the global consumption of Aloe QV < 20 phred score, resulted in high-quality transcrip- vera will surpass 60,720.4 tonnes in 2016, accounting for tome data as 51,078,070 (2 × 150 bp; 14,868,243,650 revenues worth US$ 1.6 billion . Presently, a large nucleotides), 29,247,010 (2 × 150 bp; 5,907,896,020 nucle- industrial sector is attempting to exploit the great bio- otides) paired-end reads (QV > 20) for root and leaf, logical potential of Aloe vera. The biological potential is respectively. The reads obtained were further used for Choudhri et al. BMC Genomics (2018) 19:427 Page 3 of 21 de-novo assembly by Trinity RNA-Seq assembler  retrieve UniProt IDs making use of Protein information re- (Fig. 1: Flow chart: Bioinformatics Analysis Work flow). sources (PIR) like PSD, UniProt, SwissProt, TrEMBL, The analysis resulted into having, 1, 61,733 and 2, 21,792 RefSeq, GenPept and PDB databases. Accession IDs are assembled transcripts for root and leaf with a mean length searched directly in the dbxreftable of GO database. In root of 709 and 714 nucleotides for root and leaf respectively sample 18,459 CDS were found to be involved in biological (summary of obtained transcript, unigenes and CDS sta- processes (Fig. 4), 10,346 in cellular components (Fig. 5) tistics is given in Table 1). The non-redundant transcripts and 11,060 in molecular functions (Fig. 6) whereas in leaf were clustered together using CD-HIT-EST considering sample, 19,429 CDS were involved in biological processes 95% identity and query coverage to obtain unigenes. Over- (Fig. 7), 10,774 in cellular components (Fig. 8) and 11,830 all 1,13,063 unigenes for root and 1,41,310 unigenes for in molecular functions (Fig. 9). About 35% genes of root leaf have been identified with an average length of 743 bp and leaf were involved in biological processes, 39% having and 640 bp for root and leaf respectively, including 25,330 molecular functions and remaining 26% genes were identi- unigenes for root and 23,959 unigenes for leaf having se- fied to engage in cellular processes (Figs. 10 and 11). In case quence size > 1000 bp. Candidate coding regions within of biological processes of root and leaf, a maximum num- unigenes were identified using TransDecoder. A total of ber of genes (5890 genes in root and 6329 genes in leaf) 43,443 and 43,178 CDS were obtained for root and leaf were involved in metabolic processes followed by the genes with a mean length of 881 bp for root which is somewhat related to cellular processes (root 4766;leaf 5273) and larger than that of leaf (866 bp). single-organism process (root 3345;leaf 3398) of the plant. Some other genes were also identified including response Functional annotation to stimulus (root 753;leaf 744), localization (root 1231;leaf Identified CDS were searched against NCBI non-redundant 1201), biological regulation (root 940; leaf 989), multicellu- (Nr) protein database using Basic local alignment search lar organism process (root 177; leaf 173), biogenesis (root programme BlastX, considering E-value ≤1e-05.BLASTX 627; leaf 604), signaling (root 283;leaf 298), developmental resulted in the annotation of 37,194 and 37,720 CDS for process (root 210;leaf 197), reproductive process (root 115; root and leaf samples respectively. Out of above CDS, 6249 leaf 96), growth (root 22; leaf 26), immune system process from root and 5458 from leaf had no significant BLAST (root 19; leaf 18), rhythmic process (root 5; leaf 9), locomo- hit. The majority of hits were found to be against Elaeis tion (root 5; leaf 9), biological adhesion (root 6; leaf 2) and guineensis (34%) followed by Phoenix dactylifera (28%) cell killing activity (root 1; leaf 1). Cellular component GO (Figs. 2 and 3). GO mapping was carried out to assign the term distribution of function tells that mostly genes were functions for BLASTX annotated CDS, using Blast2GO involved in cell maintenance (root 3333; leaf 3506), mem- program. BLASTX result accession IDs were used to brane function (root 3263; leaf 3.317) and organelle Fig. 1 Flow chart: Bioinformatics Analysis Work flow. The figure summarizes the steps undertaken and tools used during Aloe vera transcriptome sequencing Choudhri et al. BMC Genomics (2018) 19:427 Page 4 of 21 Table 1 Summary of Transcript, Unigene and CDS Statistics Transcripts Root Leaf Unigene Root Leaf CDS Root Leaf Total no. 161,733 221,792 Total no. 113,063 141,310 Total no. 43,443 43,178 Length (bases) 114,692,240 158,472,568 Length (bases) 84,101,877 90,489,454 Length (bases) 38,282,214 37,413,222 Maximum length 15,043 16,503 Maximum length 15,043 16,503 Maximum length 11,679 12,837 Minimum length 201 201 Minimum length 201 201 Minimum length 297 297 Mean length 709 714 Mean length 743 640 Mean length 881 866 formation (root 2328; leaf 2464). GO distribution of the related to plant stress responses. A total no. of 706 hits genes related to molecular functions showed that max- were got against MYB related transcription factors in imum genes were referred to catalytic activity (root 5072; leaf sample, which are also involved in plant stress leaf 5366; leaf) and binding (root 4539; leaf 5085) followed responses as well as other biological processes like devel- by genes of the transporter (root 662; leaf 622) and struc- opment, differentiation, defense metabolism etc. Other tural molecular activity (root 374; leaf 344). A few other transcription factors enriched from the transcriptome genes related to molecular function, have been annotated data were C2H2 (root 554; leaf 487), WRKY(root 520; including molecular function regulator (root 90; leaf 101), leaf 596), FAR1 (root 503; leaf 516), B3 (root 455; leaf transcription factor to nucleic acid binding (root 104; leaf 486), C3H (root 436; leaf 461), ERF (root 409; leaf 374), 77), transcription factor to protein binding (root 22; leaf bZIP (root 395; leaf 357), G2-like (root 353; leaf 329), 37), electron carrier activity (root 51; leaf 47), nutrient res- ARF (root 228; leaf 319) and S1Fa-like (root 231; leaf ervoir (root 10; leaf 7) and metallochaperone activity (root 241). TFs, HD-ZIP (leaf 336) and HSF (root 221) were 4; leaf 4).(Additional file 1: Top 10 most represented GO found to be specific for leaf and root respectively terms of 3 major GO domains in Aloe vera root and leaf). (Tables 2 and 3). Transcription factor analysis KEGG pathway mapping of CDS Several transcription factors have been identified by The identified CDS were mapped to reference canonical searching the predicted CDS against plant transcription pathways in KEGG to review the potential involvement factor database PlantTFdb. Majority of hits were found of predicted genes in a particular biological pathway. In to be with basic helix loop helix (bHLH) transcription Aloe vera transcriptome KEGG analysis, 6114 CDS for factor, the number being 816 in root tissue and 806 in root and 6527 CDS for leaf were found enriched in 24 leaf tissue respectively. Although role of bHLH tran- different KEGG pathway categories. A total of 2902 scription factor is still unclear in plants. Second highest genes for root and 3139 genes for leaf were functionally hits were found to be with NAC (683) in root sample. assigned for metabolism comprising carbohydrate NAC is the largest family of plant transcription factors metabolism (root 527; leaf 560), energy metabolism Fig. 2 Top blast hit species distribution of root sample. The pie chart represents the number, name and distribution of significant blast hit species with respect to identified CDSs in root sample Choudhri et al. BMC Genomics (2018) 19:427 Page 5 of 21 Fig. 3 Top blast hit species distribution of leaf sample. The representation of number, name and distribution of significant blast hit species with respect to identified CDSs in leaf sample in the form of pie chart (root 315; leaf 376), lipid metabolism (root 289; leaf processing involving membrane transport (root 27; leaf 293), nucleotide metabolism (root 203; leaf 231), 27) and signal transduction (root 554; leaf 589). One amino acid metabolism (root 504; leaf 538), glycan gene was found specific for root working as a signal- biosynthesis and metabolism (root 126; leaf 130), ing molecule and interact to stimulate a signaling metabolism of cofactors and vitamins (root 244; leaf cascade. A total of 748 CDS in root and 758 CDS in 251), metabolism of terpenoids and polyketides (root leaf were found to be involved in cellular processes 131; leaf 134), biosynthesis of other secondary and 194 genes in root and 192 genes in leaf were metabolites (root 130; leaf 122) and xenobiotics found related to environmental adaptation by KEGG biodegradation and metabolism (root 66; leaf 69). analysis (Table 4). Genes related to genetic information processing has been assigned for their role in transcription (root 308; leaf 358), translation (root 659; leaf 708), folding, sort- Potential gene identification related to secondary ing and degradation (root 535; leaf 583), replication and metabolism from KEGG pathway mapping repair (root 186; leaf 180). In root and leaf tissue, 580 and In our research, several putative genes related to saponin, 616 CDS were involved in environmental information lignin, anthraquinone, carotenoid and phenylpropanoid Fig. 4 Biological Process GO term distribution of root sample. Figure representing the different biological processes and no. of genes involved in individual biological process and their distribution ratio in form of pie chart for root Choudhri et al. BMC Genomics (2018) 19:427 Page 6 of 21 Fig. 5 Cellular Component GO term distribution of root sample. The figure represents various cellular processes and distribution of identified genes in different cellular processes in the form of pie chart for root biosynthesis have been identified from Aloe vera root and mevalonate-5-diphosphate decarboxylase (MDD: root 1; leaf tissue by KEGG Pathway functional annotation. A leaf 1), isopentenyl-PP isomerase (IPP isomerase: root 2; total of 171 CDS from root encoding 80 enzymes and 165 leaf 1), farnesyl diphosphate synthase (FDS: root 1; leaf 1), CDS from leaf encoding 77 enzymes were identified which squalene synthase (SQS: root 1; leaf 1), squalene epoxidase are involved in different secondary metabolites biosyn- (SQE: root 4; leaf 1), cycloartenol synthase (CAS: root 6; thesis comprising saponin (root 12; leaf 15), anthraquin- leaf 6), 1-deoxy-D-xylulose-5-phosphate synthase (DOXP: one (root 31; leaf 43), lignin (root 25; leaf 23), carotenoid root 9; leaf 10) and 1-deoxy-D-xylulose-5-phosphate (root 31; leaf 32) and phenylpropanoid pathways (root 72; reductoisomerase (DOXPR: root 1; leaf 3). From leaf 52). transcriptome sequencing, 61 different transcripts from Sequencing of Aloe vera transcriptome reveals many root and 52 transcripts from leaf that encode UDP glyco- putative genes (number of different transcripts obtained syltransferase (UGT) have been obtained. Anthraquinones is given in bracket with each gene) related to saponin are another important secondary metabolites present in biosynthesis pathway including acetyl-CoA acetyltrans- Aloe vera. De novo sequencing of Aloe vera in this study ferase (ACT: root 3; leaf 9), HMG-CoA synthase has provided many unigenes encoding octaketide/polyke- (HMGS: root 1; leaf 2), HMG-CoA reductase (HMGR: tide synthase (8 from root and 12 from leaf), aldoketore- root 2; leaf 4), mevalonate kinase (MVK: root 9; leaf 14), ductase (25 from root and 22 from leaf) and phosphomevalonate kinase (PMVK: root 1; leaf 2), UDP-glycosyltransferase (61 from root and 52 from leaf) Fig. 6 Molecular Function GO term distribution of root sample. Representation of different molecular functions performed by annotated genes and their distribution ratio for root Choudhri et al. BMC Genomics (2018) 19:427 Page 7 of 21 Fig. 7 Biological Process GO term distribution of leaf sample. The figure represents different biological process and no. of genes involved in individual process and their distribution ration in pie chart form for leaf which play a key role in anthraquinone biosynthesis. En- lycopene epsilon-cyclase (root 1; leaf 1), zeaxanthin epoxi- zymes related to lignin biosynthesis viz. L-phenylalanine dase (root 18; leaf 15), violaxanthin de-epoxidase (root 7; leaf ammonia-lyase (PAL), caffeoyl CoA O-methyltransferase 9) and abscisic-aldehyde oxidase (root 1; leaf 1) (Table 5). (CCoAOMT), caffeic acid O-methyltransferase (COMT), 4-coumarate:coenzyme A(CoA) ligase (4CL), cinnamoyl-CoA Differential gene expression analysis and real-time reductase (CCR), hydroxycinnamoyl transferase (HCT), expression analysis of transcripts involved in secondary cinnamate-4-hydroxylase (C4H), 4-coumarate 3-hydroxylase metabolism (C3H), ferulate 5-hydroxylase (F5H), cinnamyl alcohol de- Differential expression of unigenes identified in root and hydrogenase (CAD) were identified from the Aloe vera data- leaf was assayed by calculating FPKM (Fragments per base by KEGG pathway mapping and the results were then kilobase of transcript per million mapped reads) values further validated by differential gene expression and real-time obtained from aligning the root and leaf high quality expression analysis. reads against a reference transcriptome formed by The transcriptomic analysis has provided various genes re- clustering both the samples unigenes. Transcripts were lated to carotenoid biosynthesis including phytoene synthase further classified as up and down regulated based on (root 10; leaf 4), 15-cis-phytoene desaturase (root 2; leaf 2), their log fold change (FC) value calculated by FC = Log2 zeta-carotene isomerase (root 1; leaf 2), prolycopene isomer- (Treated/Control) formula. FC value greater than zero ase (root 4; leaf 1), lycopene beta-cyclase (root 1; leaf 1), were considered up-regulated whereas less than zero Fig. 8 Cellular Component GO term distribution of leaf sample. The figure represents various cellular processes in pie chart form for leaf Choudhri et al. BMC Genomics (2018) 19:427 Page 8 of 21 Fig. 9 Molecular Function GO term distribution of leaf sample. Representation of different molecular functions performed by annotated genes and their distribution ratio in form of pie chart for leaf sample were down-regulated. Threshold P value was taken 0.05 normalized values of genes based on Pearson correl- to filter statistically significant results. A total of ation distances as well as based on complete linkage 59,188 CDS were found commonly expressed both in method. (Additional file 2: Heat map of differentially root and leaf tissue while 1427 genes were signifi- expressed genes Leaf vs Root). A separate heat map cantly up-regulated and 2208 genes were found was also generated for the identified unigenes that down-regulated in leaf tissue as compared to root ac- encode for different enzymes involved in secondary cording to differential gene expression values. A heat metabolites biosynthesis in root and leaf tissue (Fig. 12). mapwas constructedusing thelog-transformed and Genes encoding saponin biosynthesis like acetyl-CoA Fig. 10 GO Sequence Distribution of root sample. The figure represents the functional distribution of identified CDSs involved in cellular process, molecular function and biological process according to the percentage of genes participating in various functions for root Choudhri et al. BMC Genomics (2018) 19:427 Page 9 of 21 Fig. 11 GO Sequence Distribution of leaf sample. The functional distribution of identified CDSs involved in cellular process, molecular function and biological process according to the percentage of genes participating in various functions for leaf acetyltransferase (ACT), mevalonate kinase (MVK), phos- and octaketide synthase genes (OKS) were highly phomevalonate kinase (PMVK), mevalonate-5-diphosphate expressed in both root and leaf tissue. Quantitative decarboxylase (MDD) and cycloartenol synthase (CAS) real-time PCR assay, as Ct values, was performed for the were up-regulated in root tissue while DOXP synthase and 16 putative genes belonging to lignin, saponin and aloin DOXP reductoisomerase genes were found to be biosynthesis pathway. The unigenes related to saponin up-regulated in leaf tissue. UDP glycosyltransferase (UGT) pathway i.e. HMG-CoA reductase (root CDS_10956_ Table 2 List of Top 15 transcription factors enriched in Root Table 3 List of Top 15 transcription factors enriched in Leaf Sample Sample Transcription factors name # of Hits Name Of Transcription Factor # of Hits bHLH 816 bHLH 806 NAC 683 MYB_related 706 MYB_related 682 NAC 678 C2H2 554 WRKY 596 WRKY 520 MYB_related 533 FAR1 503 FAR1 516 B3 455 C2H2 487 C3H 436 B3 486 ERF 409 C3H 461 MYB 398 ERF 374 bZIP 395 bZIP 357 G2-like 353 HD-ZIP 336 S1Fa-like 231 G2-like 329 ARF 228 ARF 319 HSF 221 S1Fa-like 242 Choudhri et al. BMC Genomics (2018) 19:427 Page 10 of 21 Table 4 KEGG Pathway classification of Root and Leaf Sample Table 5 CDS present in specific pathways CDS Leaf Sample Metabolism Leaf Root Name Of Pathway Annotated CDS No. of Enzyme KO IDS Overview 435 367 Saponin Pathway 15 10 10 Carbohydrate metabolism 560 527 Anthraquinone Pathway 43 24 24 Energy metabolism 376 315 Lignin Pathway 23 10 10 Lipid metabolism 293 289 Carotenoid Pathway 32 18 18 Nucleotide metabolism 231 203 Phenylpropanoid Pathway 52 15 15 Amino acid metabolism 385 355 Root Sample Metabolism of other amino acids 153 149 Name Of Pathway Annotated CDS No. of Enzyme KO IDS Glycan biosynthesis and metabolism 130 126 Saponin Pathway 12 10 10 Metabolism of cofactors and vitamins 251 244 Anthraquinone Pathway 31 24 24 Metabolism of terpenoids and polyketides 134 131 Lignin Pathway 25 10 10 Biosynthesis of other secondary metabolites 122 130 Carotenoid Pathway 31 19 19 Xenobiotics biodegradation and metabolism 69 66 Phenylpropanoid Pathway 72 17 17 Genetic Information Processing Transcription 358 308 Translation 708 659 Folding, sorting and degradation 583 535 Replication and repair 180 186 Environmental Information Processing Membrane transport 27 27 Signal transduction 589 554 Signaling molecules and interaction 0 1 Cellular Processes Transport and catabolism 381 382 Cell motility 58 55 Cell growth and death 241 247 Cellular community 71 64 Organismal systems Environmental adaptation 192 194 Unigene_36039; leaf CDS_6769_Unigene_ 31,011), meva- lonate kinase (root CDS_20142_ Unigene_50309; leaf CDS_25786_Unigene_64544), mevalonate-5 diphosphate decarboxylase (root CDS_24864_Unigene_57650; leaf CDS_29708_Unigene_71225), isopentenyl-PP isomerase (root CDS_24864_Unigene_57650; leaf CDS_25506_ Uni- gene_64122) and cycloartenol synthase (root CDS_16290_ Unigene_44550; leaf CD_11153_ Unigene_41455) were expressed at higher level in root than in leaf tissue as given in DGE expression data. HMG-CoA synthase (root CDS_12664_Unigene_38987; leaf CDS _14177_ Unigene _46706) showed higher expression in root tissue than leaf. Enzymes related to aloin biosynthesis i.e. keto reductase Fig. 12 Heat Map of differentially expressed genes of leaf vs. root (root CDS_22866_ Unigene_54394; leaf CDS_15459_Uni- involved in lignin, saponin and anthraquinone biosynthesis pathway in Aloe vera. Green colour in the map represents low expression of gene_48740), octaketide synthase (root CDS_ 8049 _Uni- the unigenes whereas red colour in the map represents high gene_30214; leaf CDS_36399_ Unigene_84377), UDP- expression of the unigenes Glycosyltransferase (root CDS_5315_Unigene_22956; leaf Choudhri et al. BMC Genomics (2018) 19:427 Page 11 of 21 CDS_1908_Unigene_10,506), were highly expressed in of lignin pathway PAL (CDS_25139_Unigene_63439), both root and leaf tissue with somewhat higher expression COMT (CDS_32183_Unigene_76237), 4CL (CDS_30808_ in root than leaf. Genes encoding lignin biosynthesis Unigene_73318), CCR (CDS_30855_Unigene_73445), pathway were also expressed at higher level in Aloe vera HCT (CDS_18828_Unigene_54046), C3H (CDS_6947_U- root as compared to leaf tissue as presented in DGE data nigene_31430) and F5H (CDS_13705_Unigene_45900) (Fig. 13)(Tables 6, 7 and 8). were also analyzed for relative expression after methyl As the secondary metabolites are considered to be jasmonate induction and an increase in fold change was produced as a defense mechanism of plants under vari- noticed after 6 h of treatment while many of the genes ous biotic and abiotic stresses,  here stress condition were down-regulated after 12 and 24 h of MeJa treatment was provided to the plant by spraying a chemical elicitor, (Fig. 14). methyl jasmonate at time interval of 6, 12 and 24 h to stimulate the gene expression. Relative expression of Discussion genes using real-time quantitative PCR were calculated Aloe vera is one of the most popular medicinal plant with 2− ΔΔCT method as described by Livak and used worldwide nevertheless, hardly any work has been Schmittgen, 2001 [Here ΔΔCT = (CT -CT ) conducted on its functional genomics. Only a few target GAPDH time x -(CT - CT )time0]. nucleotide sequences encoding complete or partial gene target GAPDH Maximum gene expression was found after 12 h of sequences are available in public databases like NCBI. treatment in HMGR (CDS_6769_Unigene_ 31,011,~ No ESTs or genome survey sequences (GSS) from Aloe 5042.76 fold), MVK (CDS_25786_Unigene_64544, ~ vera have been deposited in the GenBank . There- 1910.85 fold), MDD (CDS_29708_Unigene_71225, ~ fore, results of this investigation on whole transcriptome 18,820.27 fold) and IPP isomerase (CDS_25506_Uni- sequencing of Aloe vera root as well as leaf tissues are gene_64122, ~ 44.33 fold) and decline in the expression important in the perspective of functional genomics of was noticed after 24 h of induction. Interestingly, HMGS the plant. (CDS _14177_ Unigene _46706, ~ 200 fold) and CAS (CD_11153_Unigene_41455, ~ 3 fold) were highly De novo transcriptome assembly and functional expressed after 24 h of treatment. Unigenes of aloin bio- annotation synthesis pathway were also upregulated and showed A number of high quality reads, fine transcripts and maximum expression after 24 h of methyl jasmonate in- CDS length obtained from Aloe vera next generation duction (KR, CDS_15459_Unigene_48740, ~ 16.8 fold; transcriptome sequencing indicates the functionality of OKS, CDS_36399_ Unigene_84377, ~ 1910.8 fold; UGT, Aloe vera sequencing at first sight. CDS were function- CDS_1908_Unigene_ 10,506, ~ 20.9 fold). Putative genes ally annotated and most of the identified CDS resulted Fig. 13 Real time expression bar diagram for root vs. shoot for the selected 16 unigenes involved in lignin, saponin and anthraquinone biosynthesis pathway in Aloe vera which represents the higher expression of these unigenes in root as compared to shoot Choudhri et al. BMC Genomics (2018) 19:427 Page 12 of 21 Table 6 Representing fold change in gene expression after 6,12and 24 h of methyl jasmonate treatment Pathway name Gene Name Fold Change after 6 h Fold Change after 12 h Fold Change after 24 h of methyl jasmonate methyl jasmonate methyl jasmonate treatment treatment treatment Saponin biosynthesis HMGS 5.74 4.86 222.86 Pathway HMGR 491.14 5042.76 16.56 MVK 250.73 1910.85 364.55 MDD 6653.97 18,820.27 7643.41 IPP 16.8 44.33 3.36 CAS 0.76 1.06 2.89 Anthraquinone KR 4.99 9.06 16.79 biosynthesis pathway OKS 2.75 1.02 1910.85 UGT 4.72 6.91 20.97 Lignin biosynthesis PAL 1.34 1.09 0.2 pathway COMT 344.89 7.67 14.03 4CL 22.16 124.49 70.52 CCR 8 3.2 1.67 HCT 0.71 1.66 0.57 into the significant blast hits for root and leaf samples the levels of secondary metabolites, to stimulate the pro- respectively, which represented a big coverage of Aloe duction of valuable secondary metabolites and to reduce vera genome. The majority of hits were found to be the level of an undesirable metabolite that have an ad- against Elaeis guineensis followed by Phoenix dactylifera verse effect on the quality of Aloe vera. for both the samples, showing closer relationship with Aloe vera genotypically. KEGG pathway mapping and potential gene identification GO mapping was carried out to assign the functions related to secondary metabolism of identified CDS and grouped into three main domains: KEGG is the most widely used biological database in the Biological processes, molecular function and cellular world for biological interpretation of genome sequences component. From functional GO distribution it was con- using server KASS [50, 51]. The identified CDS were cluded that in the biological processes maximum 5890 mapped to reference canonical pathways in KEGG and genes in root and 6329 genes in leaf were only limited to predicted genes were found potentially involved in 24 metabolism and even majority of top BLAST hits i.e. different KEGG pathway. Five different functional cat- 980 hits in root sample and 922 in leaf sample were egories were allotted to isolated CDS which encompass found to be involved in metabolic processes, proves high metabolism, genetic information processing, environ- metabolic activity of our research plant. mental information processing, cellular processes and organismal systems. It was found that 194 genes in root Transcription factor analysis and 192 genes in leaf were related to environmental The transcription factors (TFs) are sequence specific adaptation which proves well adapted feature of Aloe DNA binding proteins that interact with the promoter vera in diverse conditions. regions of target genes to modulate their expression. TFs The major secondary metabolite related constituents play a significant role in the regulation of plant develop- of Aloe vera include anthraquinones, saponin, lignin, ste- ment, reproduction, intercellular signaling, cell cycle, re- rols, polysaccharides, alkylbenzenes, dehydrabietic acid sponse to the environment as well as in modulation of derivatives, lactin and salicylic acid [52, 53] which attri- secondary metabolite biosynthesis. Transcription factors bute for its pharmacological activity. Biosynthetic path- like AP2/ERF, bHLH and MYB and NAC were found to way of secondary metabolites in Aloe vera remains be involved in regulating secondary metabolism [46, 47]. undiscovered till date. Several putative genes related to TFs family WRKYs have eminent role in regulating sec- saponin, lignin, anthraquinone, carotenoid and phenyl- ondary metabolism during stress conditions . Identi- propanoid biosynthesis have been identified from Aloe fied MYB and NAC transcriptional factors may function vera root and leaf tissue by KEGG Pathway functional as switches in lignin biosynthesis pathways as observed annotation. Saponins are the major secondary metabo- in other plants . Transcription factors identified in lites of Aloe vera, well known for pharmaceutical and Aloe vera database may play a crucial role in modifying cosmetic properties . Saponins are a complex and Choudhri et al. BMC Genomics (2018) 19:427 Page 13 of 21 Table 7 Candidate genes related to secondary metabolism identified in root by KEGG Pathway Mapping Pathway Enzyme Name EC Number Root Gene ID Sequence Length E value Lignin Pathway Phenylalanine ammonia lyase EC:18.104.22.168 CDS_26921_Unigene_60717 2142 0 Caffeoyl CoA O-methyltransferase EC:22.214.171.124 CDS_5516_Unigene_23585 720 2.69E-122 Caffeic acid O-methyltransferase EC:126.96.36.199 CDS_33315_Unigene_71353 1092 0 4-Coumarate:coenzyme A(CoA) ligase EC:188.8.131.52 CDS_14099_Unigene_41223 1830 4.56E-164 Cinnamoyl-CoA reductase EC:184.108.40.206 CDS_7112_Unigene_27968 1110 0 Hydroxycinnamoyl transferase EC:220.127.116.11 CDS_33828_Unigene_72226 1308 0E + 00 Cinnamate-4-hydroxylase EC:18.104.22.168 CDS_10076_Unigene_34389 1584 0 4-Coumarate 3-hydroxylase EC:22.214.171.124 CDS_7933_Unigene_29870 1668 0.00E + 00 Ferulate 5-hydroxylase EC: 1.14.-.- CDS_18772_Unigene_48194 1554 0 Cinnamyl alcohol dehydrogenase EC:126.96.36.199 CDS_10431_Unigene_35075 1065 0 Saponin Pathway acetyl-CoA C-acetyltransferase EC:188.8.131.52 CDS_18125_Unigene_47323 1248 0 HMG-CoA synthase EC:184.108.40.206 CDS_12664_Unigene_38987 1407 0 HMG-CoA reductase EC:220.127.116.11 CDS_10956_Unigene_36039 1728 0 Mevalonate kinase EC:18.104.22.168 CDS_20142_Unigene_50309 1167 0 Phosphomevalonate kinase EC:22.214.171.124 CDS_24841_Unigene_57598 1551 0 Mevalonate-5-diphosphate decarboxylase EC:126.96.36.199 CDS_26736_Unigene_60412 1266 0 Isopentenyl-PP isomerase EC:188.8.131.52 CDS_24864_Unigene_57650 1071 0 Farnesyl diphosphate synthase EC:184.108.40.206 220.127.116.11 CDS_4879_Unigene_21816 1119 0 Squalene synthase EC:18.104.22.168 CDS_3000_Unigene_14589 1230 0 Squalene epoxidase EC:22.214.171.124 CDS_7723_Unigene_29373 1329 0 Cycloartenol synthase EC:126.96.36.199 CDS_16290_Unigene_44550 2463 0 DOX Phosphate synthase EC:188.8.131.52 CDS_29944_Unigene_65832 2163 0 DOXP Reductoisomerase EC:184.108.40.2067 CDS_3999_Unigene_18493 1413 0 Aloin Pathway keto reductase EC:220.127.116.11 CDS_22866_Unigene_54394 1164 0 Octaketide synthase EC:2.3.1.- CDS_8049_Unigene_30214 1212 5.63E-76 UDP glycosyltransferase EC:2.4.1.- CDS_5315_Unigene_22956 2112 1.14E-62 Carotenoid Pathway phytoene synthase EC:18.104.22.168 CDS_17552_Unigene_46473 1251 0 15-cis-phytoene desaturase EC:22.214.171.124 CDS_15090_Unigene_42743 918 0 zeta-carotene isomerase EC:126.96.36.199 CDS_23145_Unigene_54818 1140 0 prolycopene isomerase EC:188.8.131.52 CDS_13175_Unigene_39706 1070 0 lycopene beta-cyclase EC:184.108.40.206 CDS_12118_Unigene_38053 1533 0 lycopene epsilon-cyclase EC:220.127.116.11 CDS_14946_Unigene_42534 1707 0 zeaxanthin epoxidase EC:18.104.22.168 CDS_28676_Unigene_63548 1992 0 violaxanthin de-epoxidase EC:22.214.171.124 CDS_37413_Unigene_78465 1404 0 abscisic-aldehyde oxidase EC:126.96.36.199 CDS_12581_Unigene_38831 4152 0 chemically varied group of compounds consisting of tri- steroid are preferentially formed via MVA pathway, terpenoid or steroidal aglycones linked to oligosacchar- whereas, monoterpenes, diterpenes, and carotenoid are ide moieties. Steroidal saponins are hypothesized to formed predominantly via the MEP pathway  There share a common route with triterpene saponin from C5 is no information as of today that which of the pathways isoprenoids, isopentenyl diphosphate (IPP) to the forma- (MVA or MEP) or both are involved in the biosynthesis tion of the C30 unit squalene and 2, 3 oxidosqualene. of saponins precursors and subsequently the number of The cytosolic MVA pathway was accepted as the only genes that are involved in the final biosynthesis of sapo- biosynthetic route to IPP until the plastid bound MEP nins in planta / Aloe vera. Squalene synthase (SQS) pathway was elucidated in bacteria and plants. Now, it is catalyzes the condensation of two farnesyl pyrophos- generally suggested that sesquiterpenes, triterpenes and phate (C15 unit) to 30 carbons compound squalene, the Choudhri et al. BMC Genomics (2018) 19:427 Page 14 of 21 Table 8 Candidate genes related to secondary metabolism identified in leaf by KEGG Pathway Mapping Pathway Enzyme Name EC Number Leaf Gene ID E value Sequence length Lignin pathway PAL:Phenylalanine ammonia-lyase EC:188.8.131.52 CDS_25139_Unigene_63439 0 2142 CCoAOMT: Caffeoyl CoA O-methyltransferase EC:184.108.40.206 CDS_8759_Unigene_36297 1.02E- 807 COMT: Caffeic acid O-methyltransferase EC:220.127.116.11 CDS_32183_Unigene_76237 0 1092 4CL: 4-Coumarate:coenzyme A(CoA) ligase EC:18.104.22.168 CDS_30808_Unigene_73318 0 1662 CCR: Cinnamoyl-CoA reductase EC:22.214.171.124 CDS_30855_Unigene_73445 7.34E- 1017 HCT: Hydroxycinnamoyl transferase EC:126.96.36.199 CDS_18828_Unigene_54046 6.33E- 777 C4H: Cinnamate-4-hydroxylase EC:188.8.131.52 CDS_13347_Unigene_45300 0 1653 C3H: 4-Coumarate 3-hydroxylase EC:184.108.40.206 CDS_6947_Unigene_31430 0 1593 F5H: Ferulate 5-hydroxylase EC:1.14.-.- CDS_13705_Unigene_45900 2.09E- 1083 CAD: Cinnamyl alcohol dehydrogenase EC:220.127.116.11 CDS_12114_Unigene_43205 0 1062 Saponin pathway Acetyl-CoA acetyltransferase EC:18.104.22.168 CDS_15891_Unigene_49443 0 1248 HMG-CoA synthase EC:22.214.171.124 CDS_14177_Unigene_46706 0 1407 HMG-CoA reductase EC:126.96.36.199 CDS_6769_Unigene_31,011 0 1749 Mevalonate kinase EC:188.8.131.52 CDS_25786_Unigene_64544 0 1167 Phosphomevalonate kinase EC:184.108.40.206 CDS_25395_Unigene_63890 0 1551 Mevalonate-5-diphosphate decarboxylase EC:220.127.116.11 CDS_29708_Unigene_71225 0 1266 Isopentenyl-PP isomerase EC:18.104.22.168 CDS_25506_Unigene_64122 2.72E- 1161 Farnesyl diphosphate synthase EC:22.214.171.124 CDS_11635_Unigene_42360 0 1221 126.96.36.199 Squalene synthase EC:188.8.131.52 CDS_463_Unigene_2687 0 1230 Squalene epoxidase EC:184.108.40.206 CDS_5257_Unigene_26107 0 1575 Cycloartenol synthase EC:220.127.116.11 CDS_11153_Unigene_41455 0 2457 DOXP(1-deoxy-D-xylulose-5-phosphate)synthase EC:18.104.22.168 CDS_22770_Unigene_59944 0 2223 DOXP(1-deoxy-D-xylulose-5-phosphate) EC:22.214.171.1247 CDS_20571_Unigene_56673 0 1413 reductoisomerase Anthroquinone Keto reductase EC:126.96.36.199 CDS_15459_Unigene_48740 0 1299 Pathway Oktaketide synthase EC:2.3.1.- CDS_36399_Unigene_84377 1.23E- 1212 UDP Glycosyltransferase EC:2.4.1.- CDS_1908_Unigene_10,506 1.95E-35 2112 Carotenoid pathway phytoene synthase EC:188.8.131.52 CDS_7115_Unigene_31975 0 1197 15-cis-phytoene desaturase EC:184.108.40.206 CDS_13567_Unigene_45668 0 1710 zeta-carotene isomerase EC:220.127.116.11 CDS_30973_Unigene_73723 0 1083 prolycopene isomerase EC:18.104.22.168 CDS_11458_Unigene_41985 0 1776 lycopene beta-cyclase EC:22.214.171.124 CDS_7694_Unigene_33583 0 1104 lycopene epsilon-cyclase EC:126.96.36.199 CDS_22879_Unigene_60075 0 1620 zeaxanthin epoxidase EC:188.8.131.52 CDS_25413_Unigene_63924 0 1992 violaxanthin de-epoxidase EC:184.108.40.206 CDS_22464_Unigene_59446 0 1401 abscisic-aldehyde oxidase EC:220.127.116.11 CDS_21911_Unigene_58585 4152 Choudhri et al. BMC Genomics (2018) 19:427 Page 15 of 21 Fig. 14 Methyl Jasmonate induced expression in leaf after 6, 12 and 24 h. Different colours representing the unigenes of different pathways: orange coloured are the unigenes of lignin pathway green coloured are the unigenes of saponin pathway and blue coloured are the unigenes of anthraquinone pathway. Vertical axis representing fold change of the unigenes with time first committed intermediate in sterol and triterpene biosynthesis, regulating the biological activities of saponin biosynthesis pathway . Squalene synthase is saponins, catalyzed by glycosyltransferases . Several well characterized in various plants like Chlorophytum unigenes encoding acetyl-CoA acetyltransferase, HMG-CoA borivilianum,  Dioscorea zingiberensis, and Sir- synthase, HMG-CoA reductase, mevalonate kinase, phos- aitia grosvenorii . Squalene epoxidase (SQE) with phomevalonate kinase, mevalonate-5-diphosphate decarb- the cofactors O and NADPH catalyzes the conversion oxylase, isopentenyl-PP isomerase, farnesyl diphosphate of squalene to 2,3-oxidosqualene that acts as a sub- synthase, squalene synthase, squalene epoxidase, cycloarte- strate for various oxidosqualene cyclases . Oxidos- nol synthase, 1-deoxy-D-xylulose-5-phosphate synthase, qualene cyclases (OSC) catalyze the cyclization of 2, 1-deoxy-D-xylulose-5-phosphate reductoisomerase and 3-oxidosqualene which is a branching point for the UDP glycosyltransferases which may be potentially involved sterol and triterpenoids saponin synthesis . Differ- in saponin biosynthesis pathway, have been identified from ent OSCs have been characterized in the past few years transcriptome sequencing. From Aloe vera transcriptome and named after their respective products like lanos- sequencing data no unigene encoding β-amyrin synthase terol synthases, cycloartenol synthases, lupeol was found, it denotes the lack of triterpenoid saponin in synthases and β-amyrin synthases (BASs) [64, 65]. our research plant. However downward steps towards sap- Glycosylation is the final step in steroidal saponin onin biosynthesis are still unknown for Aloe vera. Choudhri et al. BMC Genomics (2018) 19:427 Page 16 of 21 Anthraquinones, another important group of second- geranylgeranyl diphosphate (GGPP) which acts as a pre- ary metabolites in Aloe vera are tricyclic aromatic qui- cursor for carotenoids is synthesized by recruiting MEP nines having strong antibacterial, antiviral, antifungal pathway of isoprenogenesis. Further, condensation of activity. Aloin, an anthraquinone glycoside is one of the two GGPP molecules is catalyzed by phytoene synthase most active metabolite of this group present in Aloe vera (PSY). Subsequent desaturation by phytoene desaturase . The conjugation of a metabolite with a sugar moi- produces lycopene while the next tier of modifications is ety eases its entry into the target cells leading to the en- catalyzed by cyclases, hydroxylases, and ketolases, result- hancement of the pharmacological activity [68, 69]. To ing in the production of different carotenoids . date, very little is known about the biosynthetic steps Various genes belonging to carotenoid biosynthesis in- leading to the formation of aloin/anthraquinones in Aloe cluding phytoene synthase, 15-cis-phytoene desaturase, vera. Abe et al.  have identified from Aloe arbores- zeta-carotene isomerase, prolycopene isomerase, lycopene cens a plant-specific polyketide synthase of type-III beta-cyclase, lycopene epsilon-cyclase, zeaxanthin epoxi- called octaketide synthase (OKS), that shares 50% amino dase, violaxanthin de-epoxidaseand abscisic-aldehyde oxi- acid sequence identity with other plant enzymes dase have been isolated from sequencing, may pave the belonging to chalcone synthase superfamily. OKS cata- way of carotenoid biosynthesis in Aloe vera. In short, the lyzes the iterative condensation of eight molecules of unigenes related to different secondary metabolites bio- malonyl-CoA, might be involved in the biosynthesis of synthesis, identified from transcriptome sequencing may the octaketide anthrone aloin in Aloe vera. However, unravel the secondary metabolism which is most respon- recombinant OKS expressed in E. coli has been reported sible for potent applications of Aloe vera and still to produce unnatural octaketide SEK4 / SEK4b as undiscovered. derailed shunt products either due to misfolding or gly- cosylation of heterologously expressed recombinant pro- Differential gene expression analysis and real-time tein or the absence of interactions with an unidentified expression analysis of transcripts involved in secondary tailoring enzyme possibly ketoreductases. The physio- metabolism logical role of OKS in planta is yet to be identified. Earl- Differential Gene Expression (DGE) enables quick and ier Grun and Franz  studied the in vitro biosynthesis thorough analysis of the gene expression under various of aloin from aloe-emodin anthrone and reported that conditions for a variety of tissues as a comparative land- the enzyme responsible for the C- glycosylation of scape . Based on FPKM values, it was revealed that aloe-emodin anthrone is specific for UDP-Glc. The most of the genes related to secondary metabolism were transfer of activated sugar like UDP-glucose to aglycone highly expressed in root as compared to leaf tissue. Most acceptor molecule is catalyzed by the enzyme UDP- of the root specific transcripts for saponin biosynthesis glycosyltransferase. Various genes like octaketide/polyke- pathway were found up regulated in DGE data, same tide synthase, aldoketoreductase, and UDP-glycosyltransferase was also reported in Asparagus racemosus for steroidal have been identified from transcriptome sequencing which saponin biosynthesis . can be useful for unravelling the aloin biosynthesis in Several putative genes involved in saponin biosynthesis Aloe vera. like acetyl-CoA acetyltransferase (ACT), mevalonate Enzymes related to lignin biosynthesis viz. L-phenylalanine kinase (MVK), phosphomevalonate kinase (PMVK), ammonia-lyase (PAL), caffeoyl CoA O-methyltransferase mevalonate-5-diphosphate decarboxylase (MDD) and (CCoAOMT), caffeic acid O-methyltransferase (COMT), cycloartenol synthase (CAS) were up-regulated in root 4-coumarate:coenzyme A(CoA) ligase (4CL), cinnamoyl-CoA tissue while DOXP synthase and DOXP reductoisome- reductase (CCR), hydroxycinnamoyl transferase (HCT), rase genes were found to be up-regulated in leaf tissue cinnamate-4-hydroxylase (C4H), 4-coumarate 3-hydroxylase indicating that plastid bound MEP pathway for saponin (C3H), ferulate 5-hydroxylase (F5H), cinnamyl alcohol de- biosynthesis is dominant in leaf tissue. UDP glycosyl- hydrogenase (CAD), meticulously investigated for their roles transferase (UGT) and octaketide synthase genes (OKS) in plant development, have been identified from the Aloe were highly expressed in both root and leaf tissue stipu- vera sequencing database which may be helpful to reveal the late that aloin is synthesized in both root and leaf tissue steps toward the lignin biosynthesis in Aloe vera. in Aloe vera. Aloe vera has been reported to have anti-aging effect The results obtained from quantitative real-time PCR similar to vitamin A derivatives. Carotenoids in Aloe assay of selected genes of saponin biosynthesis including vera, serve as precursors of vitamin A in human diet, HMG-CoA synthase, HMG-CoA reductase, mevalonate and are of interest as potential anti-cancer agents . kinase, mevalonate-5 diphosphate decarboxylase, isopentenyl- In the past few years, genes encoding enzymes involved PP isomerase and cycloartenol synthase reveal that mostly in carotenoid biosynthesis in plants have been identified geneswerefound more expressed inrootthaninleaf tissue and characterized at the molecular level. Briefly, as given in DGE expression data. Exceptionally, HMG-CoA Choudhri et al. BMC Genomics (2018) 19:427 Page 17 of 21 synthase showed higher expression in root tissue which was and characterization of gene related to the specialized revert to DGE expression value. From quantitative real time metabolism in the plant as well as understanding the expression results it was UDP-glycosyltransferase, found function of gene set(s) in the biology and physiology of highly expressed in both root and leaf tissue with somewhat plant, metabolic pathways and their regulations, signal more expression in root indicating biosynthesis of anthraqui- transduction mechanism, and marker-assisted breeding nonesinleafaswellas root. Putative genesencoding lignin particularly for chemotype development in this species biosynthesis pathway were also substantially better expressed as well as other species of genus Aloe. in Aloe vera root as compared to leaf tissue as presented in DGE data indicating its reliability. Conclusions The secondary metabolites are considered to be pro- Aloe vera is well known plant used worldwide for its duced as a defense mechanism of plants against various medicinal and cosmetic properties due to its specialized undesirable environmental encounters including biotic metabolic competence. However, despite significant and abiotic stresses . Several studies have demon- knowledge on chemical composition and healthful prop- strated that chemical elicitors like methyl jasmonate me- erties, any significant information about its genomics is diate such metabolic responses to environment through completely lacking. Therefore, in the present study, tran- an extensive transcriptional reprogramming of the plant scriptome sequence data for Aloe vera root and shoot metabolism. In this study it was observed that most of was generated using NGS technology. The transcriptome the genes of saponin pathway were up-regulated on ex- sequences have been assembled, annotated and analyzed posure of leaf tissue to methyl jasmonate, similar to that with special emphasis on secondary metabolism. The reported in Asparagus racemosus, a saponin rich medi- assembly and genes have been validated by gene expres- cinal plant . Expression of HMG-CoA reductase, sion analysis. The potential genes isolated can be mevalonate kinase, mevalonate-5 diphosphate decarb- exploited for characterization of metabolic understand- oxylase and isopentenyl-PP isomerase genes was max- ing and modulation of saponin, aloin, carotenoid and imum after 12 h of treatment and declined after 24 h of lignin biosynthesis in Aloe vera. Identified transcription treatment while HMG-CoA synthase and cycloartenol factors may be recruited to understand their relative synthase showed maximum expression after 24 h of regulatory significance across different metabolic pro- treatment. The aglycone moiety of saponins is a triter- cesses in the plant and undertake metabolic engineering pene derivative. Triterpenes are usually synthesized pre- studies. To our knowledge, this would be the first tran- dominantly via mevalonate pathway of isoprenogenesis scriptome sequencing study of Aloe vera until now. wherein HMGS catalyzes a step that not only holds the second degree of regulatory position but also produces a Methods precursor for the primary regulatory step, the HMGR Sample preparation and Total RNA isolation catalyzed reaction. The observed high expression of CAS Aloe vera was grown in the herbal nursery at Guru is in alignment with the elevation in saponin biosynthesis Jambheshwar University of Science and Technology, through improved production of triterpene alcohols in Hisar, India. Young leaves and roots were collected from preference to triterpene hydrocarbon like β-amyrin the healthy plant, snap freezed in liquid nitrogen and through carbon flux control at this branch point in favour stored at − 80 °C for further use. Total RNA was isolated of sterols. Failure to have a detectable level of expression from each tissue using RNeasy Plant Mini Kit (Qiagen) of β-amyrin synthase is an avowal of this postulation. according to manufacturer’s instructions. The quality of Aloin biosynthesis pathway related genes were also upreg- the isolated RNA was checked on 1% denaturing agarose ulated and showed maximum expression after 24 h of me- gel for the presence of 28S and 18S bands. Further, the thyl jasmonate induction, indicating the correlation of RNA quality and quantity was analysed by using Qubit both aloin and saponin with defense mechanism of Aloe fluorometer. vera. There was a little fold change in expression was no- ticed for the putative genes encoding lignin biosynthesis, Library preparation showing no significant role of lignin in plant defense Total RNA isolated from the plant samples was used for mechanism during stress conditions. the preparation of RNA-Seq paired end sequencing li- De novo assembly of transcriptome data in conjugation braries with the help of TrueSeq® Stranded mRNA sam- with DGE analysis served as a powerful approach for the ple preparation kit (Illumina). Enrichment of mRNA identification of genes involved in the biosynthesis of from the total RNA was done with the help of poly-T at- important secondary metabolites pertaining to different tached magnetic beads which was followed by enzymatic chemical classes in Aloe vera - a non-model plant. The fragmentation and 1st strand cDNA conversion. The transcriptome database generated by this study will pro- second strand was then synthesised form the 1st strand vide an important resource that may aid in identification using second strand mix and Act-D mix to facilitate Choudhri et al. BMC Genomics (2018) 19:427 Page 18 of 21 RNA dependent synthesis. Then the double stranded then used to predict coding sequences within them using cDNA samples were purified using AMPure XP beads TransDecoder. (Agencourt Biosciences). These beads selectively binds larger double stranded cDNA samples and excess of Gene ontology analysis primers, nucleotides, salts and enzymes were removed For the annotation, the predicted CDS were searched making the products free from any kind of contami- against NCBI non redundant(Nr) protein database nants. It was then followed by adapter ligation, A-tailing (http://www.ncbi.nlm.nih.gov) using Basic local align- and enrichment by limited number of PCR cycles. The ment search tool (BLASTx) with a common significance PCR amplified library was analyzed in Tape Station 4200 threshold cut-off of E-value ≤1e-05. Gene ontology (GO) (Agilent Technologies) using High Sensitivity (HS) annotations of the CDS were carried out with the help D5000 Screen Tape assay kit as per manufacturer of Blast2GO program . The BLASTx result accession instructions. IDs were searched directly in the gene product table (dbxref) of GO database. The GO mapping differenti- ated the predicted CDS into three major domains repre- Sequencing and quality control senting gene product properties namely: Biological The cDNA library was then used for paired end sequen- process, Molecular function and Cellular component. cing using Illumina Hi-Seq platform (2 × 150 bp chemis- Each predicted CDS may have more than one GO term try) to generate the raw data for both the samples. In assigned either in the same domain or in different paired end sequencing the template fragment is se- domains i.e. biological process, molecular function and quenced in both forward and reverse directions. The cellular component . samples were allowed to bind with complementary adapter oligos on paired-end flow cell with the help of kit reagents. The adapters were designed in order to Functional annotation of KEGG pathway allow selective cleavage of the forward strands after For the identification of possible involvement of the pre- re-synthesis of the reverse strand during sequencing. dicted CDS in various biological pathways, the CDS were The opposite end of the fragment was then sequenced mapped to the reference canonical pathways in Kyoto from the copied reverse strand. Prior to the assembly Encylopedia of Genes and Genomes (KEGG) database the raw data obtained was processed to obtain high . Five major divisions under which the CDS were quality reads. Trimmomatic v0.35 was used to remove distributed included metabolism, genetic information adapter sequences, ambiguous reads (reads with un- processing, environmental information processing, cellu- known nucleotides “N” larger than 5%), and low-quality lar processes and organismal systems. The information sequences (reads with more than 10% quality threshold obtained upon KEGG analysis included KEGG Orthol- (QV) < 20 phred score). A minimum length of 100 nt ogy (KO) assignments, their corresponding enzyme (nucleotide) after trimming was applied. After removing commission (EC) number and prediction of metabolic the adapter and low quality sequences from the raw data pathway using KEGG automated annotation server high quality reads were retained for root and leaf sample KASS . respectively. This high quality (QV > 20), paired-end reads were used for de-novo assembly. Abundance estimation and differential gene expression De-novo transcriptome assembly, validation and CDS analysis (DGE) prediction FPKM (Fragments Per Kilobase of transcript per million The high quality reads for both the samples were then mapped reads) values were calculated to measure the assembled into transcripts using RNA-Seq assembler expression level of each assembled transcript sequence. Trinity . While assembling the transcripts there is For FPKM measurement a reference transcriptome was a chance that large amounts of misassembled tran- first generated by clustering both the samples unigenes scripts, erroneous and poorly supported transcripts i.e. leaf and root. The high-quality cleaned reads from may arise, therefore, all high quality reads were as- each sample were aligned separately on reference sembled with their respective assembled transcripts transcriptome (clustered unigene of both the samples) using Burrows-Wheeler Aligner . The non-redundant using burrows wheeler aligner (bwa). The read count transcripts were further clustered together using CD- profile from the output file (.sam) of bwa alignment was HIT-EST-454  at 95% identity and query coverage. generated by using SAMtools . Differential gene After the assembly and clustering of transcripts, sequences expression (DGE) analysis was performed employing were obtained that could not be extended further, these a negative binomial distribution model (DESeqv1.8.1 sequences were termed as unigenes. The unigenes were package http://www-huber.embl.de/users/anders/DESeq/) Choudhri et al. BMC Genomics (2018) 19:427 Page 19 of 21 . Dispersion values were calculated using following Additional files parameters: method = blind, sharing mode = fit-only and Additional file 1: Table S1 and S2.: Top 10 most represented GO terms fit type = local. On the basis of log fold change (FC) the of 3 major GO domain in root and leaf. (DOCX 15 kb) transcripts were further classified as up and down regu- Additional file 2: Heat map of differentially expressed genes Leaf vs lated. The log fold change value was calculated by using Root. (PNG 507 kb) the formula: FC = Log2 (Treated/Control). Transcripts Additional file 3: List of primers used for real time PCR. (DOCX 12 kb) having FC value greater than zero were considered up-regulated whereas less than zero, were Acknowledgements down-regulated. To obtain statistically significant results P The author’s acknowledge Eurofins Genomics India Pvt. Ltd., Bengaluru, India for illumina sequencing and bioinformatics analysis. MR acknowledge the value threshold of 0.05 was used. With the help of Mul- support of Haryana State Council of Science and Technology, Panchkula in tiple Experiment Viewer (MEV v4.9.0), a complete linkage the form of Junior Research Fellowship. hierarchical cluster analysis was performed on top 100 dif- Funding ferentially expressed genes. A heat map (cluster) depicts This work was supported by University Grants Commission, New Delhi, in the the level of transcript abundance. Levels of expression are form of Major Research Project vide Grant No. F: 41–586/2012(SR). represented as log2 ratio of transcript abundance between Availability of data and materials leaf and root samples. A heat map was constructed The dataset generated and /or analysed during the current study are employing the log-transformed and the normalized value available in the NCBI short sequence read archive (Accession number: of genes based on Pearson correlation distance as well as SRR5167034 and SRR5161731) and Bioproject number: PRJNA359629. based on complete linkage method. Authors’ contributions VC conceived the research plan and designed the project. RK and AK helped to sample plant material and contributed in RNA extraction. PC and MR performed research and drafted manuscript. PC, MR, VC and RS participated Transcription factor analysis in data analysis. VC and RS drew inferences from data, and critically The predicted CDS were searched against Plant tran- improved and edited the manuscript. PC and MR contributed equally as first scription factor database (PlantTFdb)  to obtain the author to this manuscript. All authors have read and approved the final manuscript. transcription factors from both root and leaf CDS. Competing interest The authors declare that they have no competing interests. Gene validation with qRT-PCR Ethics approval and consent to participate The transcripts obtained by sequencing were further val- Aloe vera was grown in the herbal nursery at Guru Jambheshwar University idated by qRT-PCR. Sixteen unigenes involved in anthra- of Science and Technology, Hisar, India under natural conditions according to institutional and national guidelines. quinone, saponin and lignin biosynthesis were selected for quantitative real-time expression. RNA was isolated with the help of CIA-PCIA method from the root and Publisher’sNote Springer Nature remains neutral with regard to jurisdictional claims in leaf samples as well as from the plant which was treated published maps and institutional affiliations. externally with methyl jasmonate (250 μM) at time inter- val of 6, 12 and 24 h. Isolated RNA was further reverse Author details Department of Bio and Nano Technology, Guru Jambheshwar University of transcribed with the help of Revert Aid First Strand Science and Technology, Hisar, Haryana 125001, India. Centre of Innovative cDNA Synthesis Kit (Thermo Scientific) using oligo and Applied Bioprocessing (CIAB), (A National Institute under Department of dT(18) primers. Specific primers were designed for six- Biotechnology, Govt. of India), Sector-81 (Knowledge City), Manauli P.O., S.A.S. Nagar, Mohali, Punjab 140306, India. teen unigenes and two housekeeping genes (GAPDH and beta tubulin) with the help of Primer Express soft- Received: 18 May 2017 Accepted: 22 May 2018 ware v3.0.1 (List of primers is given in Additional file 3). The qRT-PCR was carried out in triplicates using SYBR® References Green Jump Start™ Taq Ready Mix™ (Sigma) on Applied 1. Fox LT, Gerber M, Preez JL, Plessis JD, Hamman JH. Skin permeation Biosystems’ Step One™ Real Time PCR System. The enhancement effects of the gel and whole-leaf materials of Aloe vera, Aloe marlothii and Aloe ferox. J Pharm Pharmacol. 2015;67(1):96–106. reaction mixture used included 10 μl of SYBR green 2. Pugh N, Ross SA, ElSohly MA, Pasco DS. Characterization of Aloeride, a new master mix, 20 pmol/μl forward and reverse primers and high-molecular-weight polysaccharide from Aloe vera with potent 2 μl of cDNA for a reaction volume of 20 μl. The immunostimulatory activity. J Agric Food Chem. 2001;49(2):1030–4. 3. 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Published: Jun 1, 2018