Abstract
BackgroundAloe 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.ResultsTranscriptome 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.ConclusionsThis 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.
Highlights
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, antihypercholesterolemic, anti-hyperglycemic, anti-asthmatic and much more
De novo transcriptome assembly and validation Illumina Hi Seq platform sequencing results of cDNAs prepared from total RNA when processed by removing the adapter sequences, ambiguous reads i.e. reads with unknown nucleotides “N” larger than 5%, and low-quality sequences i.e. reads with more than 10% quality threshold, QV < 20 phred score, resulted in high-quality transcriptome data as 51,078,070 (2 × 150 bp; 14,868,243,650 nucleotides), 29,247,010 (2 × 150 bp; 5,907,896,020 nucleotides) paired-end reads (QV > 20) for root and leaf, respectively
Overall 1,13,063 unigenes for root and 1,41,310 unigenes for leaf have been identified with an average length of 743 bp and 640 bp for root and leaf respectively, including 25,330 unigenes for root and 23,959 unigenes for leaf having sequence size > 1000 bp
Summary
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, antihypercholesterolemic, anti-hyperglycemic, anti-asthmatic and much more. Aloe vera shows innumerable medicinal attributes such as skin burn healing [4], anti-inflammatory [5], hepatoprotective [6], anti-tumor [7], anti-ulcer [8], antihypercholesterolemic [9], anti-hyperglycemic [10], anti-asthmatic[11] and antioxidant activities [12]. Aloe vera extracts have been demonstrated to be advantageous in the treatment of even AIDS [13]. It has similar anti-aging effects as exhibited by vitamin A derivatives [14]
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